Studies of Amyloid Nanostructure

Sumner Makin

Clare College

University of Cambridge
















This dissertation is submitted for the degree of Doctor of Philosophy.


2
Preface







This dissertation is the result of my own work and includes nothing which is the
outcome of work done in collaboration except where specifically indicated in the text.


3
Acknowledgements
Thanks to my supervisor Louise Serpell for her active encouragement, guidance and
assistance throughout the project. Thusnelda Stromer for extensive discussions, her
patience in testing Clearer and helpful feedback.
I am very grateful for the assistance provided by our collaborators. Professor Atkins
for detailed discussions and access to facilities. Pawel Sikorski for his outstanding
help with data collection, discussions and substantive suggestions for Clearer. Gayatri
Chavali for her help with data collection, particularly the supply of a cryo-loop for
alignment. Jan Johansson for the supply of the KFFEAAAKKFFE peptide. James
Elliot for help with data analysis and Sam MacDonald for assistance with early data
collection.
Professor David Lomas and his group were invaluable; Didier Belorgey, Robin
Carrell, Damian Crowther, Mark Davies, Kerri Kinghorn, Meera Mallya, Elena
Miranda, Richard Page, Russell Phillips, Lynda Sharp and Alison Warrington for the
meetings, support and discussions.
Professor Randy Read and his group for providing a friendly environment, which was
conducive to work.
Brenda Sumner and Nick, Seth, Tristan and Gully Makin, for their love, support and
wonderfully critical reading.


4
Abstract
Amyloid fibril self-assembly, from a disparate group of soluble precursor peptides, is
central to the pathology of many diseases. Knowledge of the structure and formation
of these fibrils is critical to the understanding required for the rational design of drugs
capable of inhibiting fibrillogenesis and promoting disaggregation. Amyloidogenic
potential is thought to be an almost universal property of protein. It is therefore
desirable that the three-dimensional structure and architecture of amyloid be
understood. The insolubility and texture of the amyloid fibrils frustrate the usual
techniques of X-ray crystallography and solution nuclear magnetic resonance.
We have investigated the structure of amyloid fibrils formed from various peptides,
including islet amyloid polypeptide (type II diabetes) and designed peptides.
Computer programs have been written which enable structural analysis using data
from X-ray fibre diffraction, electron microscopy and electron diffraction. Our
twelve-residue, sequence-designed peptide forms fibrous nano-crystallites, which
diffract to high resolution (> 0.1 nm). Our analyses favour a hydrogen-bonded -sheet
as the fundamental crystalline entity within these fibrils and show how the fibril is
held together. Fine structural details have been revealed, including salt-bridges and -
bonding between adjacent phenylalanine residues. Consequently, the data from
many different fibrils contributes to the understanding of the formation and structure
of the generic amyloid fibril.


5
Abbreviations
Å Angstroms
AA Amyloid A
AAAK Peptide with sequence KFFEAAAKKFFE
A Amyloid beta peptide
AFM Atomic force microscopy
APP Amyloid precursor protein
apoSAA Apolipoprotein serum amyloid A
BSE Bovine spongiform encephalopathy
CD Circular dichroism
CJD Creutzfeldt-Jakob disease
CR Congo red
Cryo-EM Cryo electron microscopy
DQCSA Double quantum chemical shift anisotropy
DRAMA Dipolar decoupling at the magic angle
DRAWS Dipolar coupling in a windowless sequence
ED Electron diffraction


6
EM Electron microscopy
EPR Electron paramagnetic resonance
fpRFDR-CT Finite-pulse radio-frequency driven recoupling constant time
FT Fourier transform
FTIR Fourier transform infrared spectroscopy
H1 First predicted -helical region, residues (109-122) of cellular prion
hCT Human calcitonin
HDX Hydrogen-deuterium exchange
HypF-N N-terminal domain of the bacterial hydrogenase maturation factor
HypF
IAPP Islet amyloid polypeptide (amylin)
IgLC Immunoglobulin light chain
JAI Java advanced imaging library
MAS Magic angle spinning
MS Mass spectrometry
MQNMR Multiple quantum nuclear magnetic resonance
NMR Nuclear magnetic resonance
PDB Protein data bank


7
PrP Prion protein
PrP
C
Prion protein, cellular form
PrP
Sc
Prion protein, scrapie form
REDOR Rotational echo double resonance
RR Rotational resonance
SANS Small angle neutron scattering
SAXS Small angle X-ray scattering
SDSL Site directed spin labelling
SH3 Src-homology 3 domain
SSNMR Solid state nuclear magnetic resonance
STEM Scanning transmission electron microscopy
TEM Transmission electron microscopy
TTR Transthyretin
XD X-ray diffraction





8
Contents
Preface ...................................................................................................................... 2
Acknowledgements ................................................................................................... 3
Abstract..................................................................................................................... 4
Abbreviations............................................................................................................ 5
Contents.................................................................................................................... 8
Table of Figures ...................................................................................................... 16
1 Introduction..................................................................................................... 20
1.1 Biological Background............................................................................. 20
1.1.1 Definition of Amyloid...................................................................... 20
1.1.2 Amyloid in Disease .......................................................................... 21
1.1.3 Alzheimer’s Disease Amyloid.......................................................... 26
1.1.4 Amyloid and Oligomer Toxicity....................................................... 27
1.1.5 Protein Folding and Misfolding........................................................ 29
1.1.6 Natural Amyloid-Like Products........................................................ 30
1.1.7 Bionanotechnology Applications...................................................... 30
1.2 Current Understanding of Amyloid Structure ........................................... 31
1.2.1 Introduction...................................................................................... 31


9
1.2.2 Problems Associated with Studying Amyloid Structure.................... 33
1.3 Techniques Used to Examine Amyloid Structure ..................................... 33
1.3.1 The Use of Synthetic Peptides for Studies of Amyloid Structure ...... 33
1.3.2 X-ray Diffraction.............................................................................. 34
1.3.3 Electron Microscopy ........................................................................ 36
1.3.4 Electron Diffraction.......................................................................... 39
1.4 Other Techniques Used to Examine Amyloid Structure............................ 41
1.4.1 Fourier Transform Infra Red Spectroscopy....................................... 41
1.4.2 Atomic Force Microscopy................................................................ 42
1.4.3 Neutron Scattering ........................................................................... 44
1.4.4 Hydrogen-Deuterium Exchange ....................................................... 45
1.4.5 Solid State Nuclear Magnetic Resonance.......................................... 46
1.4.6 Other Methods ................................................................................. 49
1.5 Electron Microscopy Theory.................................................................... 50
1.5.1 Beam Specimen Interaction.............................................................. 50
1.5.2 Imaging............................................................................................ 52
1.6 Diffraction Theory ................................................................................... 53
1.6.1 Introduction...................................................................................... 53


10
1.6.2 Fourier Transform............................................................................ 53
1.6.3 Convolution Theorem....................................................................... 53
1.6.4 Sample Texture ................................................................................ 55
1.6.5 Ewald Sphere ................................................................................... 55
1.6.6 Problems .......................................................................................... 59
1.7 Experimental Methods for X-ray Fibre Diffraction................................... 60
1.7.1 Introduction...................................................................................... 60
1.7.2 Glass Capillary and Stretch Frame.................................................... 60
1.7.3 Magnetic Field ................................................................................. 61
1.7.4 Mat .................................................................................................. 62
2 Application for the Structural Analysis of Amyloid ......................................... 64
2.1 Abstract ................................................................................................... 64
2.2 Introduction ............................................................................................. 64
2.3 Preparation............................................................................................... 66
2.3.1 Format Conversion........................................................................... 66
2.3.2 Centring........................................................................................... 66
2.3.3 Background Removal ....................................................................... 67
2.3.4 Contrast Enhancement...................................................................... 71


11
2.4 Peak Measurement ................................................................................... 72
2.4.1 Automated........................................................................................ 72
2.4.2 Manual ............................................................................................. 73
2.5 Unit Cell Determination........................................................................... 74
2.5.1 Search.............................................................................................. 74
2.5.2 Spot Position Predictor..................................................................... 76
2.6 Simulation of Amyloid Fibre Diffraction Patterns .................................... 77
2.6.1 Sampling of Intensities in Reciprocal Space ..................................... 77
2.6.2 Reflection Shape .............................................................................. 80
2.6.3 Structure Factors .............................................................................. 81
2.6.4 Other Factors.................................................................................... 82
2.6.5 Optimisation..................................................................................... 83
2.6.6 Automation ...................................................................................... 84
2.6.7 Testing............................................................................................. 84
2.7 Other Features.......................................................................................... 86
2.7.1 Introduction...................................................................................... 86
2.7.2 Fourier Space Operations ................................................................. 86
2.7.3 Determining the Repeat Distance from Micrographs ........................ 86


12
2.7.4 General Features .............................................................................. 88
2.7.5 PDB Display and Manipulation........................................................ 89
2.7.6 Image Mathematics .......................................................................... 90
2.8 Discussion ............................................................................................... 90
2.8.1 Comparison of Clearer with Other Programs .................................... 90
2.8.2 Application Use ............................................................................... 91
2.8.3 General Improvements ..................................................................... 92
2.8.4 Specific Improvements..................................................................... 93
2.9 Conclusion............................................................................................... 94
3 Characterisation of Islet Amyloid Polypeptide Fibrils ...................................... 95
3.1 Abstract ................................................................................................... 95
3.2 Introduction ............................................................................................. 95
3.3 Methods................................................................................................... 98
3.3.1 Peptide and Incubation..................................................................... 98
3.3.2 Electron Microscopy ........................................................................ 98
3.3.3 Cryo Electron Microscopy................................................................ 98
3.3.4 Electron Diffraction.......................................................................... 99
3.3.5 X-ray Diffraction.............................................................................. 99


13
3.4 Results....................................................................................................100
3.4.1 Negative Stain Electron Microscopy................................................100
3.4.2 Platinum/Carbon Shadowed Electron Microscopy...........................100
3.4.3 Cryo Electron Microscopy...............................................................101
3.4.4 Electron Diffraction.........................................................................103
3.4.5 X-ray Diffraction.............................................................................105
3.4.6 Structural Interpretation...................................................................108
3.5 Discussion ..............................................................................................109
3.5.1 General Fibril Morphology..............................................................109
3.5.2 Understanding of Structure Derived from Diffraction Data..............110
3.5.3 Hypothetical Modelling...................................................................111
3.5.4 Conclusion......................................................................................112
4 Molecular Basis for Fibril Formation and Stability .........................................114
4.1 Abstract ..................................................................................................114
4.2 Introduction ............................................................................................114
4.3 Methods..................................................................................................116
4.3.1 Peptide and Incubation....................................................................116
4.3.2 Electron Microscopy .......................................................................116


14
4.3.3 Electron Diffraction.........................................................................116
4.3.4 X-ray Diffraction.............................................................................117
4.3.5 Structural Determination .................................................................117
4.4 Results....................................................................................................118
4.4.1 Electron Microscopy .......................................................................118
4.4.2 X-ray Fibre Diffraction ...................................................................118
4.4.3 Electron Diffraction.........................................................................119
4.4.4 Indexing..........................................................................................120
4.4.5 Modelling........................................................................................122
4.5 Discussion ..............................................................................................129
4.5.1 The Role of Side-chains in Amyloid Formation and Structure .........129
4.5.2 Conclusion......................................................................................131
5 Discussion......................................................................................................133
5.1 Models of Amyloid Structure..................................................................133
5.1.1 Introduction.....................................................................................133
5.1.2 Largely Native Structures................................................................133
5.1.3 Water-Filled Nanotube....................................................................136
5.1.4 General -Helices............................................................................138


15
5.1.5 Cross- Tubule................................................................................140
5.1.6 Conventional Cross- Structure.......................................................141
5.2 Conclusion..............................................................................................155
6 Bibliography...................................................................................................157



16
Table of Figures
Figure 1.1 The characteristic cross- pattern 21
Figure 1.2 Schematic showing cleavage of A from APP 27
Figure 1.3 Structural hierarchy in amyloid fibrils 32
Figure 1.4 Structure of transthyretin amyloid 35
Figure 1.5 Fibre diffraction patterns of A (11-25) 36
Figure 1.6
Electron microscope images of A (11-25) and A (1-40)
fibrils
39
Figure 1.7 Electron diffraction pattern from IAPP amyloid fibrils 41
Figure 1.8 Atomic force micrograph of Sup35 fibrils 44
Figure 1.9 Summary of NMR distance information for A (10-35) 48
Figure 1.10 Diffraction geometry 56
Figure 1.11
Side view of the diffraction geometry showing circle traced
out by a reflection
57
Figure 1.12
Side view of the diffraction geometry; the circle centred at the
fibre axis does not intersect with the Ewald sphere
58
Figure 1.13
Side view of the diffraction geometry; the case in which no
diffraction occurs
58
Figure 1.14
Unaligned A (1-40) fibrils and stretch frame aligned A (11-
25) fibrils
60
Figure 1.15 Stretch frame used to align fibrils 61


17
Figure 1.16 Orientation of fibres after alignment 63
Figure 2.1 Procedure for processing general fibre diffractograms 66
Figure 2.2 Centring of the diffraction pattern 67
Figure 2.3 Image histogram and cumulative frequency distribution 70
Figure 2.4 Circularly symmetric background reduction 70
Figure 2.5
Comparison of electron diffraction pattern with contrast-
enhanced version
72
Figure 2.6 Screenshot of the automated peak finder 73
Figure 2.7 Manually measuring the resolution of a peak 74
Figure 2.8 Indexing of reflections and determination of the unit cell 76
Figure 2.9 Diffraction simulation window for MacOS X 77
Figure 2.10 Process by which simulated diffractograms are calculated 79
Figure 2.11 Reflection shapes for a true fibre and the general case 81
Figure 2.12
Simulated and empirical diffraction patterns for A (11-25)
fibrils
85
Figure 2.13
Simulated and empirical diffraction patterns for cellulose
triacetate I
85
Figure 2.14 Graph relating visibility to length of box 85
Figure 2.15 Superposition of images 89


18
Figure 3.1 Negative stain electron micrograph of IAPP amyloid fibrils 100
Figure 3.2
Platinum/carbon shadowed electron micrograph of mature
IAPP amyloid fibrils
101
Figure 3.3
Cryo-electron micrographs of IAPP fibrils and Fourier
transform
103
Figure 3.4 Electron diffraction patterns before and after dehydration 105
Figure 3.5 X-ray fibre diffraction patterns from IAPP fibrils 107
Figure 4.1 Negative stain electron micrographs of AAAK amyloid 118
Figure 4.2 X-ray fibre diffraction pattern from amyloid nanocrystals 119
Figure 4.3 Electron diffraction pattern from the fibrous nanocrystals 120
Figure 4.4
Comparison between simulated and observed diffraction
patterns for incorrect model
125
Figure 4.5
Comparison between simulated and observed diffraction
patterns for proposed model
126
Figure 4.6 Orientations of aromatic rings 127
Figure 4.7 Structure of amyloid nanocrystals 128
Figure 5.1 Pair of transthyretin molecules 135
Figure 5.2 Transthyretin amyloid fibrils 136
Figure 5.3 Perutz’s model of amyloid 138
Figure 5.4 Antiparallel -helix 140


19
Figure 5.5 Possible structure of A (1-40) 141
Figure 5.6 Models of insulin fibrils 144

Chapter 1. Introduction

20
1 Introduction
1.1 Biological Background
1.1.1 Definition of Amyloid
Rokitansky is generally credited with the first description of amyloid in 1842 as a
firm, greyish, “lardaceous-gelatinous” substance infiltrating the livers of patients with
syphilis and tuberculosis (Rokitansky 1846). In 1854, Rudolph Virchow gave amyloid
its name after noticing that it stained pale blue with iodine and sulphuric acid, similar
to corpora amylacea in brain tissue. He believed that it was similar to cellulose and
consequently amyloid means starch (amylase) like (Virchow 1854; Sipe and Cohen
2000). It is now known that this is due to associated proteoglycans and
glycosaminoglycans and that the core of amyloid is protein (Snow et al. 1987;
Kisilevsky and Snow 1988).
Amyloid fibrils are formed by the polymerisation of a normally soluble, non-toxic
protein into extracellular, insoluble aggregates with a large molecular weight.
Amyloid is defined by a series of empirical observations. Specific chemical staining
forms part of the definition. After staining with Congo red (CR), plaques composed of
the fibrils appear orange in tissue sections. An apple green birefringence pattern is
seen when the stained sample is viewed between crossed polarisers, (Puchtler et al.
1961; Puchtler and Sweat 1965). The birefringence is due to an ordered structure in
which dye binding sites are symmetry related (Carter and Chou 1998). Amyloid can
be extracted using a water purification method (Pras et al. 1968). Binding to the
histological benzothiazole dye thioflavine T results in a shift in fluorescence (LeVine
1993). Neither dye is completely specific but each empirical observation forms part of
the definition. The aggregates are rich in -structure, with resistance to proteolysis
and even strong chemical denaturants. Circular dichroism (CD) and Fourier transform
infrared spectroscopy (FTIR) both show a high percentage of -structure (Hilbich et
al. 1991). X-ray diffraction reveals a characteristic pattern, similar to that observed in
silk fibroin and described as cross-. The cross- pattern is comprised of two
Chapter 1. Introduction

21
reflections, a sharp one at 4.7 Å parallel to the direction of the fibre and a more
diffuse spot between 10 and 11 Å perpendicular to the fibre direction (Figure 1.1)
(Eanes and Glenner 1968). Electron microscopy (EM) reveals fibrils that are
unbranching, 70 to 120 Å in diameter and of indeterminate length (Cohen et al. 1982).

Figure 1.1. The X-ray fibre diffractogram of amyloid has a characteristic cross- pattern, with
the 4.7 Å reflection along the same direction as the fibrils.
1.1.2 Amyloid in Disease
The diseases collectively known as the amyloidoses are characterised by the
deposition of extracellular amyloid fibrils. These are generally divided into five
subdivisions; systemic, hereditary, central nervous system, ocular and other localized
amyloidoses (Sipe and Cohen 2000). A substantial number of human and animal
amyloidoses have been described to date (Table 1.1 and Table 1.2, respectively).
Further examples continue to be found; amyloid deposits have been discovered in the
cell-free fraction of bronchoalveolar lavage fluid in patients with pulmonary alveolar
proteinosis (Gustafsson et al. 1999). Whilst amyloid is defined to be extracellular,
there are intracellular deposits thought to be otherwise of the same structural class.
X-ray beam
Bundle of fibres
E
q
u
a
t
o
r
i
a
l

d
i
r
e
c
t
i
o
n

4.7 Å
10-11 Å
Chapter 1. Introduction

22
These include paired-helical filaments formed from tau in Alzheimer’s disease
(Grundke-Iqbal et al. 1986), Lewy bodies formed from -synuclein in Parkinson’s
disease (Spillantini et al. 1998) and polyglutamine huntingtin deposits in
Huntington’s disease (Chen et al. 2002). Perhaps the correct nomenclature for such
material is amyloid-like. Nevertheless, the literature does not generally use such a
term (Perutz et al. 2002) and the distinction becomes impractical in the case of
amyloid formed from synthetic peptide fragments or proteins not normally associated
with disease.
Chapter 1. Introduction

23
Table 1.1. Classification and nomenclature of the human amyloidoses, assembled from (Husby et al. 1994; Kelly 1996; Sunde et al. 1997; Xing and Higuchi
2002; Blumenthal 2004).
Amyloidogenic protein Precursor to Amyloidogenic Protein Syndrome
Immunoglobulin light chain
(IgLC) or fragments of V
L

domain
Monoclonal immunoglobulin light
chain (i.e. or )
AL amyloidosis: primary isolated or associated with multiple
myeloma
AH Immunoglobulin heavy chain () AH amyloidosis: isolated
76-residue N-terminal
fragment of amyloid A (AA)
Apolipoprotein serum amyloid A
(apoSAA)
Secondary systemic amyloidosis: resulting from infections,
chronic inflammation, tumours, familial Mediterranean fever,
tumour necrosis factor receptor associated periodic syndrome,
Muckle-Wells syndrome
Mutant transthyretin Mutant transthyretin Familial amyloid polyneuropathy I and II
Transthyretin (TTR) or its
fragments
Native transthyretin Senile systemic amyloidosis

2
-microglobulin
2
-microglobulin
Haemodialysis related amyloidosis: associated with chronic
endstage renal failure
Approximately 90-residue
apolipoprotein A-I N-terminal
fragments
Apolipoprotein A-I variants Familial amyloid polyneuropathy III
Apolipoprotein A-II Apolipoprotein A-II Familial amyloidosis
Chapter 1. Introduction

24
Amyloidogenic protein Precursor to Amyloidogenic Protein Syndrome
71-residue gelsolin fragment Gelsolin Familial amyloid polyneuropathy IV
Lysozyme or its fragments Lysozyme variants (not native)
Hereditary non-neuropathic systemic amyloidosis (Ostertag-
type)
110-residue cystatin C
fragment
Cystatin C Hereditary cerebral haemorrhage
Amyloid peptide (A) (39 to
43 residues)
Amyloid precursor protein (APP),
native and variants
Alzheimer's disease, Down syndrome, hereditary or sporadic
cerebral amyloidosis
Prion protein, scrapie form
(PrP
Sc
) (not cellular form,
PrP
C
)
Prion precursors, native and variants
Transmissible spongiform encephalopathies, including kuru,
Creutzfeldt-Jakob Disease (CJD) and variant Creutzfeldt-Jakob
Disease
Calcitonin or its fragments Procalcitonin Medullary thyroid carcinoma associated amyloidosis
Atrial natriuretic factor Atrial natriuretic factor Isolated atrial amyloidosis
Islet amyloid polypeptide
(IAPP)
Pro-islet amyloid polypeptide Type 2 diabetes, insulinoma
Insulin Insulin Injection localised amyloidosis, insulinoma
Prolactin Prolactin Aging pituitary prolactinoma
ABri BRI-L Familial British dementia
Chapter 1. Introduction

25
Amyloidogenic protein Precursor to Amyloidogenic Protein Syndrome
Keratoepithelin Keratoepithelin Keratoepithelin amyloidosis: lattice dystrophies of the cornea
Lactoferrin Lactoferrin Familial cornea amyloidosis
Lactadherin Lactadherin Aortic medial amyloidosis
Keratin Keratin Primary localised cutaneous amyloidosis
Fibrinogen -chain variant
fragments
Fibrinogen -chain variants Hereditary renal amyloidosis
Chapter 1. Introduction

26
Table 1.2. Classification and nomenclature of animal amyloidoses (Xing and Higuchi 2002).
Amyloid protein Precursor Syndrome
PrP
Sc
Prion precursors
Transmissible spongiform
encephalopathies,
including scrapie (sheep
and goat) and similar
bovine (BSE), feline, mink,
elk and mule deer diseases.
AA Apolipoprotein serum amyloid A
Reactive AA amyloidosis
(mouse)
Apolipoprotein A-II Apolipoprotein A-II Mouse senile amyloidosis

The amyloidoses are often cited as examples of post evolutionary disease (Csermely
2001; Dobson 2002). Modern medical practices are one cause of such disease.
2
-
microglobulin accumulates during blood dialysis, which after several years, results in
skeletal deposition of amyloid (Gejyo et al. 1985; Gejyo et al. 1986). Cannibalism in
members of the Fore tribe in Papua New Guinea caused kuru. Bovine spongiform
encephalopathy appeared as a result of feeding cows with animal material,
demonstrating an infectious route for amyloidosis (Gajdusek 1988). Many
amyloidoses are diseases of old age and the incidence of such disease has grown as
life spans have increased over the last century. In addition to humans, a relationship
between aging and amyloidosis has been examined in mice, hamsters, cats, dogs,
cattle, ducks and horses (Blumenthal 2004).
1.1.3 Alzheimer’s Disease Amyloid
Alzheimer’s disease is the best-known amyloidosis. It is estimated to cost the US
economy some $100 billion annually (Ernst and Hay 1994). Alois Alzheimer, a
Bavarian neuropsychiatrist, first noted the disease. In November 1901, a patient
referred to as Auguste D. presented with an unknown brain disorder; the 1906 post-
mortem revealed lesions in the brain (Alzheimer 1907; Graeber and Mehraein 1999;
Gorman and Chakrabartty 2001). Some twenty years ago, the principal component of
these plaques was found to be amyloid formed from A (Glenner and Wong 1984;
Chapter 1. Introduction

27
Masters et al. 1985). A is a 4-kDa peptide cleaved from amyloid precursor protein
(APP) (Kang et al. 1987) by -secretase (beta-site APP cleaving enzyme) followed by
-secretase as shown in Figure 1.2. Most APP is degraded in the secretory pathway
before reaching the cell surface by -secretase. A is always present in healthy
subjects (Seubert et al. 1992) and is a result of normal proteolytic processing (Shoji et
al. 1992). The predominant A species in vivo has forty residues, whilst A (1-42) is
the major component of senile plaques and may nucleate amyloidogenesis (Jarrett et
al. 1993; Iwatsubo et al. 1994). All species of in vivo A are able to cofibrilise
(Hasegawa et al. 1999). Alzheimer’s disease’s prominence among the amyloidoses
has resulted in substantial effort being expended in examining fibrils formed from A
(Serpell 2000).
12345678901234567890123456789012345678901234567890
1 10 20 30 40
NH2 COOH
Extracellular Space Membrane Cytosol
VKMDAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVVIATVIVITLVMLKK
NL GQ VI X
G
F
NH2 COOH
40 42 43
-Secretase
-Secretase
-Secretase
Swedish double
mutation
Flemish
mutation
Dutch
mutation
Florida
mutation
London
mutations
Australia
mutation
671 714
A
APP

Figure 1.2. Schematic showing cleavage of A from APP; the A sequence is in bold type (Storey
and Cappai 1999; Burkoth et al. 2000). A dashed box indicates the transmembrane domain.
Vertical lines show the sites of secretase cleavage. Hydrophobic regions of A are in blue.
1.1.4 Amyloid and Oligomer Toxicity
The amyloid hypothesis suggests that the formation and accumulation of amyloid is
central to disease pathology. Amyloid toxicity has been demonstrated on many
occasions (Kelly 1996; 1998b). Alzheimer's amyloid interacts with endothelial cells to
produce superoxide free radicals (Thomas et al. 1996; Hardy and Selkoe 2002) and is
responsible for the destruction of neurons (Lansbury 1999). Prion aggregates are
responsible for disease transmission in the transmissible spongiform encephalopathies
Chapter 1. Introduction

28
(Prusiner 1998). In other cases, it is the sheer quantity of amyloid; kilograms of this
material disrupt organs such as the liver or spleen (Tan and Pepys 1994; Pepys 1996).
The oligomer hypothesis takes the view that it is the oligomeric precursors to amyloid
which are primarily responsible for toxicity (Kirkitadze et al. 2002; Stefani and
Dobson 2003). Fibrils are clearly immobile which raises the question of how they can
effect change in nearby cells. One piece of evidence, apparently contrary to the
amyloid hypothesis, is that the degree of cognitive impairment shows poor correlation
with the quantity of amyloid deposited in the brain in Alzheimer’s disease (Morris et
al. 1996). Furthermore, studies using amyloid fibrils not associated with the
amyloidoses show that they can have a similar effect on cells as those made of
proteins linked to disease (Stefani and Dobson 2003). These include aggregates
formed from the src-homology 3 (SH3) domain of the phosphatidyl inositol-3-kinase
(Frederikse 2000) and the N-terminal domain of the bacterial hydrogenase maturation
factor HypF (HypF-N) (Chiti et al. 1999). The studies observed a series of well-
defined, pre-fibrillar species, which substantially impaired cultured cell viability.
Mature amyloid was not found to have any substantial effect on the cultures. This
implies that cytotoxicity is due to the supramolecular structure of pre-fibrillar
aggregates and not the amino acid sequence (Bucciantini et al. 2002). Alzheimer’s A
oligomers have been studied in detail (Lambert et al. 1998; Hartley et al. 1999; Lin et
al. 1999; Walsh et al. 1999; Bhatia et al. 2000; Monji et al. 2000; Nilsberth et al.
2001; Walsh et al. 2002). Similar studies concerning familial amyloidotic
polyneuropathy (Sousa et al. 2001) and Parkinson’s disease (Conway et al. 2000b;
Goldberg and Lansbury 2000) have been conducted. These studies suggest that
oligomers may interact with cell membranes, leading to oxidative stress and increases
in free Ca
2+
causing apoptosis or necrotic cell death.
It should not be concluded from the above studies that amyloid is unimportant. The
amyloid cascade hypothesis takes account of both oligomers and amyloid (Hardy and
Selkoe 2002). Neither should it be neglected that amyloid fibrils are large inactive
reservoirs of toxic species (Walsh et al. 2002). Contrarily, mature fibrils are a
potential sink for toxic agent. Any doubt as to harm caused by amyloid is removed in
Chapter 1. Introduction

29
those diseases in which amyloid forms the greater part of the diseased organ (Pepys
1996).
Once a link between amyloid and amyloidosis pathology has been established, the
fibril structure is more than intellectual curiosity. Understanding of the structure of
amyloid is necessary for the rational design of drugs to prevent aggregation and
promote disaggregation. One way in which such an agent can be devised is by using
peptide mimetics (Lashuel et al. 2000). Examples of agents have been conceived in
many cases (Kolstoe and Wood 2004), including IAPP (Kapurniotu et al. 2002;
Rijkers et al. 2002; Scrocchi et al. 2002) and A (Tjernberg et al. 1996; Talaga 2001).
1.1.5 Protein Folding and Misfolding
Knowledge of amyloid structure also contributes to the understanding of protein
folding and misfolding. Amyloidogenic potential may be an almost universal property
of protein (Stefani and Dobson 2003). This important alternative protein-folding state
addresses fundamental aspects of biophysics. Indeed, a change in our understanding
of protein folding, previously established for soluble globular proteins, may be
required. Amyloid precursor proteins appear to be extremely diverse. There is
considerable variation in size and sequence (Fandrich and Dobson 2002) with
molecular masses varying from less than a single kilodalton to tens of kilodaltons.
Precursors do not share a common tertiary structure; they may even be unstructured or
-helical. In spite of this, amyloid fibrils have a similar external morphology and
internal structure. The molecular basis of amyloid toxicity also seems to display
common features (Stefani and Dobson 2003).
Proteins not associated with disease have been shown to form fibrils in vitro. These
include SH3 (Guijarro et al. 1998), acylphosphatase (Chiti et al. 1999), cold shock
protein A (Alexandrescu and Rathgeb-Szabo 1999) and cold shock protein B (Gross
et al. 1999). Conditions for amyloid fibril formation include a low pH, lack of specific
ligands, high temperature and moderate concentrations of salts or co-solvents.
Although amyloid is very stable, there might be a significant activation energy barrier
to amyloidogenesis (Kusumoto et al. 1998). Mutations associated with hereditary
Chapter 1. Introduction

30
amyloidoses often destabilise the native state of the protein, thus reducing this barrier
(Kelly 1998a; Dobson 1999; Radford and Dobson 1999). Natural proteins in their
native states deploy several strategies to avoid intermolecular association of -strands
(Richardson and Richardson 2002). Strategies include covering with helical or non-
repetitive structure, having no edges (-barrel), a sharp bulge in the -sheet or
prolines and charged residues. Statistical analysis of globular protein sequences shows
that nature disfavours both sequences of alternating polar and non-polar residues
(Broome and Hecht 2000) and clusters of several consecutive hydrophobic residues
(Schwartz et al. 2001). Most aggregation disease proteins are either secreted or
membrane bound, or a fragment of such a protein. Although the aggregated form may
have the lowest Gibbs energy (Gazit 2002a), the removal of the source of
unaggregated protein results in disaggregation (Pepys et al. 2002). It is therefore
important to know how these proteins adopt highly organised multi-molecular
structures that are not specifically encoded for in the sequence (Uversky 2002). This
is important in protein handling and production, where general protein aggregation is
a serious problem (Clark 1998).
1.1.6 Natural Amyloid-Like Products
Amyloid-like material is also a natural product (Kelly and Balch 2003), the earliest
example being the silk of the egg-stalk of the lacewing Chrysopa (Parker and Rudall
1957; Geddes et al. 1968). The cross- structure is also found in mammalian ocular
lenses (Frederikse 2000) and it is hypothesised that fibrillar deposits of serum amyloid
A induce lysis of bacterial cells, thus protecting the host in chronic amyloid diseases
(Hirakura et al. 2002). Curli are highly aggregated amyloid-like fibres produced by
Escherichia coli and Salmonella (Chapman et al. 2002) and cross- spider silk fibres
also have the characteristic features of amyloid (Li et al. 2001).
1.1.7 Bionanotechnology Applications
Finally, the emerging field of bionanotechnology offers industrial application for
amyloid (Zhang 2003; Waterhouse and Gerrard 2004). This requires a fundamental
understanding of the macromolecules, which are the elemental components from
which nanostructures are constructed. Nano-structural components require the
Chapter 1. Introduction

31
properties of structural compatibility and chemical complementarity. Amyloid
precursors satisfy this requirement, so investigation is needed to understand the
structure, assembly and dynamic behaviour of amyloid fibres (Mihara and Takahashi
2001; Zhang et al. 2002). By way of demonstration, a conducting nanowire was
constructed by using Sup35 amyloid as a natural scaffold to align gold particles
(Scheibel et al. 2003). Similarly, silver nanowires were also assembled; ionic silver
was reduced inside amyloid nanotubes formed from diphenylalanine (Reches and
Gazit 2003). A great many potential applications have been envisaged including using
fibrils in catalysis and electronics, as a plastic, a support for the growth of cells or a
therapy for treating humans and animals (Dobson and MacPhee 2004).
1.2 Current Understanding of Amyloid Structure
1.2.1 Introduction
The characteristic cross- diffraction pattern gives insight into the basic structure of
amyloid. Peptides are in a -strand conformation, with a distance of 6.9 Å between
adjacent pairs of residues along the direction of the chains (Figure 1.3). -strands,
perpendicular to the direction of the fibre, are spaced 4.7 Å apart and laterally
associated to form a -sheet ribbon. These -sheets run along the direction of the fibre
and are stacked approximately 10 to 11 Å apart. The laminated -sheets comprise the
protofilaments, which form the fibril (Figure 1.3). The ribbons may be twisted and the
protofilaments themselves intertwined (Lashuel et al. 2000). Protofilaments should be
distinguished from the pre-fibrillar intermediates known as protofibrils (Harper et al.
1997b; 1999; Walsh et al. 1999). Substantive evidence for protofilaments is provided
by electron microscopy. Helical reconstruction showed twisted structure for SH3 and
insulin fibrils (Jimenez et al. 1999; Jimenez et al. 2002). Similarly, intracellular
paired-helical filaments (Crowther 1991) have been shown to have a protofilament
substructure. Cross-sections of fibres analysed using single particle methods allowed
the number of protofilaments to be determined (Serpell et al. 2000b). In the case of
IAPP, the splitting of fibrils can be explained using protofilaments (Goldsbury et al.
1997), an electrolucent core may also be detected (Cohen et al. 1982; Serpell et al.
2000b).
Chapter 1. Introduction

32
70-120 Å
Single
-strand

-sheets

Protofilament

Fibril

Two to six
protofilaments

25-30 Å
4.7 Å

10-11 Å

6.9 Å



Figure 1.3. The structural hierarchy in amyloid. Fibrils are composed of protofilaments.
Protofilaments are built from laminated -sheet ribbons.
Amyloid fibrils formed from the same precursor peptide may have different structures
at all levels of detail. Under the same experimental conditions, differing numbers and
organisations of protofilaments are observed, whilst the structure within the
protofilament appears to remain the same (Fraser et al. 1991b; Bauer et al. 1995;
Goldsbury et al. 1997; Jimenez et al. 1999; Bouchard et al. 2000; Jimenez et al.
2002). Several varieties of fibril may be present in a single electron micrograph. This
polymorphism was demonstrated in many types of in vitro amyloid, including A,
calcitonin, IAPP, SH3 and insulin fibrils. Cryo-electron microscopy of insulin fibrils
combining helical reconstruction with single particle analysis revealed diverse low-
resolution three-dimensional fibrils containing two, four and six protofilaments.
Atomic force microscopy also revealed similar diversity in amyloid derived from A
(Goldsbury et al. 2001) and
2
-microglobulin (Kad et al. 2001; Kad et al. 2003).
Cryo-electron microscopy of ex vivo material from patients with hereditary non-
neuropathic, systemic amyloidosis demonstrated that spontaneous polymorphism is
also present in disease fibrils (Jimenez et al. 2001).
In the case that experimental conditions are changed, then both the arrangement of
protofilaments and their internal structure may differ. Polymorphism may be
Chapter 1. Introduction

33
attributed to staining conditions (Cohen et al. 1982), since ion concentration has been
shown to affect fibril conformation (Fraser et al. 1991b). Solid-state nuclear magnetic
resonance of fibrils formed from A (11-25) and human calcitonin at various pHs
both showed structural diversity at the atomic level, whilst maintaining a cross-
structure (Naito et al. 2004; Petkova et al. 2004).
1.2.2 Problems Associated with Studying Amyloid Structure
Structural studies of amyloid fibrils are impeded by a series of problems relating to
the characteristics of amyloid fibrils. They are neither three-dimensionally crystalline
nor soluble (Lansbury 1992; Kelly 1997), which prevents the use of conventional
techniques such as single-crystal X-ray crystallography and solution nuclear magnetic
resonance. Although amyloidogenesis resembles crystallisation (Jarrett and Lansbury
1993), single crystal formation has proved as difficult as for insoluble fibrous silk
proteins (Lotz et al. 1982). Disorder within the sample is a serious issue since it
reduces the amount of available information. Polymorphic structures also present
problems when attempting to compare data from X-ray diffraction and electron
microscopy (Diaz-Avalos et al. 2003a).
1.3 Techniques Used to Examine Amyloid Structure
1.3.1 The Use of Synthetic Peptides for Studies of Amyloid Structure
Structural examination requires as much order within the sample as possible. Ex vivo
material is rarely used, since synthetic samples can be grown in the conditions to
maximise orientational order. Additionally, synthetic peptides are more readily
available and purification is not required. Full-length peptides form amyloid that
appears to be less ordered than truncated versions. A (11-25) amyloid fibrils have a
similar morphology and pH dependence as full-length A (Fraser et al. 1991b) and
may form the core of fibrils formed from full-length A. Similar results have been
shown for other A fragments including A (11-28), A (13-28), A (15-28) and A
(29-42) (Castano et al. 1986; Gorevic et al. 1987; Halverson et al. 1990; Barrow and
Zagorski 1991; Fraser et al. 1991a; Barrow et al. 1992; Burdick et al. 1992; Fraser et
al. 1992b).
Chapter 1. Introduction

34
Other peptides, including human non-disease related peptides, such as SH3 and those
that are sequence designed are employed as amyloid precursors. These can be used to
investigate the generic nature of amyloidogenesis and the importance of side chain
interactions. Amyloid formed from proteins with four to six residues has all the
characteristics of fibrils formed from 100-residue peptides (de la Paz et al. 2002;
Reches et al. 2002; Tjernberg et al. 2002). The advantages of such an approach are a
far higher quality of experimental data, the fibrils being more amenable to alignment
and that it also allows the removal of disordered regions.
1.3.2 X-ray Diffraction
Much of the published information on protein structure is based on X-ray diffraction
data (XD). Detailed information at high resolution (approximately 1 to 3 Å) can be
obtained from the analysis of X-ray scattering patterns. Although single-crystal X-ray
crystallography is not possible, X-ray fibre diffraction has proved to be a very
powerful technique. The primary evidence for amyloid fibrils having a common core
structure composed of laminated, continuous -sheets running along the fibre arises
from X-ray fibre diffraction (Eanes and Glenner 1968; Blake and Serpell 1996; Sunde
et al. 1997).
The cross- pattern’s characteristic features were first described in diffraction from
the egg stalk of the lacewing Chrysopa (Geddes et al. 1968). The proposed structure
was formed from extended -strands folded back on themselves, forming a -sheet
25 Å wide. The -ribbons described were flat and stacked face-to-face (Pauling and
Corey 1951). The same pattern was observed for amyloid formed from the Bence
Jones protein (Eanes and Glenner 1968).
Indexing of meridional diffraction signals suggested the presence of helical repeats.
Transthyretin amyloid was found to have a helical pitch of 115.5 Å, corresponding to
24 -strands and a twist of 15 degrees per strand (Figure 1.4). A twisted -pleated
sheet has been shown to have a lower free energy than an untwisted sheet (Chothia
1973). On this basis, a model of the core structure of the generic amyloid fibril was
built (Blake and Serpell 1996; Sunde et al. 1997).
Chapter 1. Introduction

35

Figure 1.4. The structure of transthyretin amyloid, based on X-ray diffraction data (Serpell et al.
1997).
Examination of peaks on the equator of X-ray diffraction patterns allows the number
and arrangement of protofilaments to be interpreted. A (1-40) fibrils were modelled
using three to five tubular protofilaments, each built from a pair of -sheets
(Malinchik et al. 1998). Small angle X-ray scattering (SAXS) studies on fibrils
formed from a wide variety of A fragments arrived at similar models involving
hollow cylinders (Lu et al. 2003) or bundles thereof (Inouye et al. 1993). In one case
it was not possible to distinguish between an 86 Å diameter tubule or walls of cross-
sheets 71 Å apart (Kirschner et al. 1987). Difficulties may also arise in the event of
polymorphism being present in the sample.
Much of the early work on amyloid used fibrils formed from A fragments and
mutants thereof (Kirschner et al. 1987; Halverson et al. 1990; Fraser et al. 1992b;
Inouye et al. 1993; Fraser et al. 1994; Inouye and Kirschner 1996). A detailed
structure of A (11-25) fibrils was built based on X-ray fibre diffraction data
(Sikorski et al. 2003). Diffraction patterns were recorded from the magnetically
aligned specimen using three mutually orthogonal beam directions, one of which was
parallel to the magnetic field. All three patterns were different, suggesting that the
fibrils are composed of crystallites with a preferred orientation. The A (11-25)
peptide was in an extended -strand conformation; these -strands were then stacked
to form an antiparallel -sheet. The pseudo-unit cell was monoclinic ( = 122°) with
dimensions a = 9.42 Å, b = 25 Å and c = 6.9 Å. There was therefore a slip along the
chain direction of 6.9 Å, which is twice the length of an amino acid unit in an
extended conformation.
Other studies have postulated similar cross- structures from X-ray data in the cases
of amyloid fibrils formed from short prion protein (PrP) fragments (Nguyen et al.
Chapter 1. Introduction

36
1995); the first predicted -helical region, residues (109-122) of PrP
C
(H1) (Inouye
and Kirschner 1996); eleven-residue N-termini of the apoSAA family (Kirschner et
al. 1998) and IAPP (Makin and Serpell 2004b).
a
b
c
a
b
c

Figure 1.5. Fibre diffraction patterns from A (11-25) fibrils (Sikorski et al. 2003). Images a and
b are perpendicular to the direction of preferred orientation, while image c is parallel to the fibre
axis.
1.3.3 Electron Microscopy
Transmission electron microscopy (TEM) is a form of microscopy in which the
properties of the specimen are measured in terms of the specimen’s interaction with a
beam of electrons. This beam is passed though lenses composed of electric and
magnetic fields allowing very high-resolution data to be obtained in a manner
analogous to the operation of a light microscope. Electron microscopy does not
require a crystalline sample and the result need not be implicitly averaged as with
neutron and X-ray diffraction experiments. Unfortunately, the contrast of micrographs
of many biological samples is poor and increasing the flux of the electron beam to
compensate results in damage to the specimen. Cryo electron microscopy (cryo-EM)
reduces the radiation damage by cooling the specimen using liquid nitrogen or
helium. Alternatively, the specimen may be stained with a material such as uranyl
Chapter 1. Introduction

37
acetate; however the image will be of the stain rather than the specimen itself; hence
little information about the interior of the fibril is revealed. Shadow electron
microscopy involves imaging heavy metal atoms that had previously been deposited
at an angle, delivering improved definition of vertical features. EM is a visual
technique, which allows the examination of a sample to confirm the presence of
ordered fibrils (Figure 1.6).
Much of the information about the number of protofilaments involved in the fibril
substructure is derived from EM (Kirschner et al. 1987; Fraser et al. 1991a; Fraser et
al. 1991b; Serpell et al. 1995; Goldsbury et al. 1997; Jimenez et al. 1999; Serpell et
al. 2000b; Jimenez et al. 2001; Jimenez et al. 2002). Groups of filamentous structures
wound around a common axis are sometimes observed, whilst cross-sections show
between three and six units composing the fibril. Single particle analysis combined
with helical reconstruction of micrographs has revealed low-resolution three-
dimensional structures of insulin fibrils with two, four or six protofilaments (Jimenez
et al. 2002). As discussed earlier, polymorphism may arise spontaneously or as a
result of the differing conditions for fibril formation.
Three-dimensional reconstruction of cryo-electron microscope images resulted in
low-resolution (≈25 Å) structures of protofilaments for amyloid formed from SH3
(Jimenez et al. 1999) and insulin (Jimenez et al. 2002). Ex vivo Asp67His lysozyme
and Leu60Arg apolipoprotein were also studied but structural variability and disorder
prevented reconstruction (Jimenez et al. 2001). A great diversity of helical fibrils was
observed. Single particle averaging and analysis was combined with helical
reconstruction, which dealt with the problem of variable pitch (Boettcher et al. 1996;
Jimenez 2000). The resulting structures showed how the protofilaments were arranged
around an electrolucent core. These structures implied possible arrangements of
strands within the protofilaments. The model suggested that protofilaments had the
same overall twist as the fibril itself. SH3 fibrils were composed of four
protofilaments with cross-section dimensions of 20 by 40 Å and a crossover repeat of
~600 Å. Insulin fibrils had a larger cross-section of 30 by 40 Å with crossover repeats
of between 355 and 900 Å depending on the number of protofilaments in the fibril.
Chapter 1. Introduction

38
Models of lysozyme fibrils, with a periodicity of ~3000 Å, were also constructed; a
six-protofilament model most closely matched the experimental results.
Images of fibrils composed of A (11-25) compared to A (1-42) showed that fibrils
formed from the shorter peptide were more consistently homogenous, straight and
uniform with higher contrast and better-defined edges (Serpell and Smith 2000).
Tjernberg found that making substitutions and deletions in the A (14-23) peptide had
a significant effect on the morphology of the amyloid formed, however all A
peptides longer than eleven residues formed fibrils of similar morphology (Tjernberg
et al. 1999). Structural elucidation of the protofilament has then proceeded by either
three-dimensional reconstruction (Jimenez et al. 1999) or direct visualisation (Serpell
and Smith 2000). Fourier transforms of regions of electron micrographs showed a
similar cross- pattern to X-ray diffractograms and in the case of A (11-25) fibrils,
striations 4.7 Å apart were visible. These striations perpendicular to the fibre axis
were clear after the application of translational averaging. They have been interpreted
as being stacks of -strands. It was not known whether the fibril was twisted so the
fibre was cut into boxes containing a specified number of striations and boxes with
the same number of striations averaged along the fibre. Boxes containing six or
twelve striations gave qualitatively better results than those with four, eight or ten.
The core of the fibril also appeared to be electrolucent, which was consistent with
images of the cross-sections of cores that have been processed using single-particle
averaging techniques (Kirschner et al. 1987; Fraser et al. 1991a; Fraser et al. 1991b;
Serpell et al. 1995; Serpell et al. 2000b). Electron micrographs of A (10-35) fibrils
showed a 1200 Å helical twist, allowing a model to be built (Lakdawala et al. 2002).
Scanning transmission electron microscopy (STEM) uses a smaller probe than TEM,
which scans across the image. It allows the mass per unit length of fibrils to be
determined by comparison with a standard, such as the tobacco mosaic virus. This
information can be combined with data from other techniques, especially nuclear
magnetic resonance, to build a model. A protofilament composed of a pair of -sheets
was proposed for A (1-40) fibrils (Antzutkin et al. 2000; Antzutkin 2004; Petkova et
al. 2004) and similar structures postulated for A (10-35) and A (1-42) fibrils
Chapter 1. Introduction

39
(Antzutkin et al. 2002). STEM complemented protease digestion, cryo-EM and mass
spectroscopy in the analysis of Ure2p, to build a model based on a cross- core (Baxa
et al. 2003). In the study of a designed seventeen-residue peptide, STEM formed part
of a battery of techniques in conjunction with X-ray diffraction, TEM and nuclear
magnetic resonance (Kammerer et al. 2004). It can also be used simply as another
form of microscopy (Goldsbury et al. 2000a; Goldsbury et al. 2000b).

Figure 1.6. Electron microscope images showing the morphology of A (11-25) and A (1-40)
fibrils (Sikorski et al. 2003).
1.3.4 Electron Diffraction
Electron diffraction (ED) patterns are theoretically very similar to X-ray
diffractograms (Dyson 2004). A sample is illuminated with a beam of electrons and
the resulting diffraction pattern recorded using film or another detector. A sharp,
strong 4.7 Å reflection is normally very clear but little else can generally be seen.
Most examples of this type of pattern are from amyloid-like fibrils formed from -
synuclein (Serpell et al. 2000a), paired-helical filaments (Berriman et al. 2003) and
polyglutamine fibrils (Perutz et al. 1994). In general fibre diffraction, high-resolution
reflections are spread over a greater volume in reciprocal space than those at lower
resolution, resulting in a lower relative intensity. If an electron beam is used, then the
relative intensity of high resolution reflections are further reduced owing to changes
in the structure factors. The structure factors for an electron beam are calculated from
the X-ray structure factors using the Mott formula, which involves division by the
distance from the origin in reciprocal space squared. Thus, the reflection intensity is
Chapter 1. Introduction

40
divided by a total factor proportional to the radius to the fourth power and hence some
reflections are much stronger than others. The incident electron beam also obscures
low angle data; it is very strong compared with the intensity of the reflections and
saturates the film, thereby preventing their recovery.
Electrons are charged and have a far stronger interaction with matter in comparison to
X-rays. Electron diffraction can therefore take advantage of a much lower beam width
than X-ray diffraction; hence a far smaller sample can be examined. This enabled
individual amyloid nanocrystals from a seven-residue peptide to be selected and the
diffraction patterns from single crystals recorded (Diaz-Avalos et al. 2003a; b). The
image area being diffracted from can be viewed in real space. Consequently, the
relative orientations of fibres and their diffraction patterns can be determined. Another
result of the strength of interaction is radiation damage; the microscope operator may
observe the diffraction pattern fading as the irradiated region is permanently damaged.
Long exposures increase the signal to noise ratio and reveal weak signals, whereas
short exposures ensure that the specimen remains intact.
Quantitative analysis of intensities is further impeded by the requirement for
calibration of the exposed film to establish the relationship between film transparency
and incident flux density. Other electron diffraction studies have used amyloid fibrils
formed from IAPP (Chapter 3) (Makin and Serpell 2004b), a twelve-residue sequence
designed peptide with sequence KFFEAAAKKFFE (see Chapter 4), scrapie prion
(Wille et al. 2002), Sup35 (King and Diaz-Avalos 2004) and the WW domain FBP28
(Ferguson et al. 2003).
Chapter 1. Introduction

41
4.7 Å


Figure 1.7. Electron diffraction pattern from IAPP amyloid fibrils (Chapter 3).
1.4 Other Techniques Used to Examine Amyloid Structure
1.4.1 Fourier Transform Infra Red Spectroscopy
A Michelson interferometer, with a movable mirror, has an interference pattern,
which is the Fourier transform of the spectrum of the source. In Fourier Transform
Infrared Spectroscopy (FTIR), this interference pattern is Fourier inverted to allow the
measurement of the absorbance spectrum of a sample (Jackson and Mantsch 1995).
Normal mode analysis of simple molecules allows the theoretical spectrum to be
calculated in these cases. The reverse of this process is not possible and different
structures may have indistinguishable absorption spectra.
Especially in conjunction with isotopic labelling (Anderson et al. 1996), FTIR is able
to distinguish between parallel and antiparallel arrangements and obtain detailed
information about the orientation of amide carbonyls. The amide I band, which is the
carbonyl stretching vibration of the amide group (1700 to 1600 cm
-1
), is sensitive to
-structure. Evidence for antiparallel sheets involves splitting of the amide band into
low and high frequency bands due to strong inter-strand dipole coupling. Studies of
amyloid of various types observed a strong amide I band near 1630 cm
-1
and a weaker
band near 1690 cm
-1
(Hilbich et al. 1991; Fraser et al. 1992b; Conway et al. 2000a).
This spectrum was close to that simulated for Pauling’s cross- structure (Krimm and
Bandekar 1986). Percentages of secondary structure were calculated by curve fitting
Chapter 1. Introduction

42
to the experimental spectrum. Unfortunately, another study showed that that the
position of bands should not be over-interpreted (Wilder et al. 1992), particularly
since amyloid might be regarded as being a separate class of structures. Therefore, the
presence of a low frequency amide band is a necessary but not sufficient condition for
the assignment of antiparallel -structure (Lansbury 1992). Measurements on parallel
-sheet protein showed that these amide I bands were not unique to antiparallel
structures (Khurana and Fink 2000). Booth used FTIR to show that there was some
residual helical and disordered fold in lysozyme fibrils (Booth et al. 1997); this more
flexible structure may surround the rigid core. FTIR provides the only support for the
-sheets in full-length A fibrils being in an antiparallel conformation (Halverson et
al. 1990; Hilbich et al. 1991). This was contradicted by solid-state nuclear magnetic
resonance studies, which were claimed to be more reliable, since the nuclear magnetic
resonance data was not based on purely empirical models (Yamada et al. 1998) or
normal mode calculations (Bandekar and Krimm 1988) that were based on
substantially simplified model systems (Antzutkin et al. 2000).
1.4.2 Atomic Force Microscopy
Atomic force microscopy (AFM) offers direct, high-resolution visualisation without
the requirement for averaging (Stine et al. 1996). The height of a solid probe over a
specimen surface is measured, with individual molecules examined in air or solution.
Physiological conditions are possible without the requirement for fixing or staining.
Time dependent aspects of the molecular interactions can be observed including the
molecular conformation and aggregation state.
In vitro assembly of amyloid, including fibrils and protofibrils, can be studied using
time lapse AFM. Thus, information about the directionality, growth rate and
morphology of individual protofibrils is obtained (Goldsbury et al. 1999). Atomic
resolution is not possible with biological samples, due to the end radii of available
tips, limiting this resolution to flat periodic structures, such as graphite. Fibrils imaged
using AFM appear larger than those in electron micrographs. Additionally, the tip-
sample interaction may also distort or destroy many soft biological samples. Tapping
Chapter 1. Introduction

43
rather than dragging the tip over the sample reduces but does not eliminate this effect
(Chamberlain et al. 2000).
Fibrils may be pre-assembled in a test tube, then absorbed on to a mica surface or
assembled on the surface. Different distributions of fibrils are formed in each case.
The cause is probably fibril immobilisation due to the constraining effect of the mica.
It is not known which better represents physiological conditions, since in vivo, there
are many surfaces, including cell membranes. Substantial work has been done on A
(Harper et al. 1997a; Harper et al. 1997b; 1999) and amyloid formed from other
peptides, including IgLC (Ionescu-Zanetti et al. 1999), IAPP (Goldsbury et al. 1997)
and
2
-microglobulin (Kad et al. 2001; Kad et al. 2003). The images showed that
growth was normally bi-directional (Blackley et al. 1999; Blackley et al. 2000) but
often blocked at one end. Protofibrils themselves were observed to be growing from
one end of a fibril (Goldsbury et al. 1999). Structural diversity and twisting
protofilament substructure were often observed (Kad et al. 2001).
Chapter 1. Introduction

44
1 m

Figure 1.8. Atomic force micrograph of Sup35 fibrils (Stromer and Serpell, unpublished).
1.4.3 Neutron Scattering
Neutron diffraction (Bacon 1975) is similar to both electron diffraction and X-ray
diffraction. A beam of neutrons is fired at the sample and the scattering pattern
observed. Unlike electrons, neutrons have no charge and therefore do not interact with
the charges on the nuclei or electron clouds. Instead, neutrons have a nuclear
magnetic moment, resulting in an interaction with the nuclei of atoms making up the
specimen. This interaction makes it easier to detect light atoms, such as hydrogen, in
the presence of heavier ones, which would normally be expected to dominate the
interaction. Additionally, atoms with similar atomic numbers such as deuterium and
hydrogen, can be distinguished, allowing isotopic substitution for labelling purposes.
Radiation damage is largely eliminated, owing to the weak nature of the interaction.
Unfortunately, the technique is limited by the available neutron sources, which are
nuclear reactors and high-energy spallation sources.
Chapter 1. Introduction

45
Studies of micelle-like oligomers, involved in A fibril formation, used curve fitting
of small angle neutron scattering (SANS) data to study a solution cooled to slow
fibrillogenesis (Yong et al. 2002). Spherocylindrical structures were modelled with
sizes consistent with the diffractogram. Likewise, A (10-21) fibril formation was
monitored in the presence of zinc ions (Morgan et al. 2002a). X-ray and neutron
scattering studies showed that a crystallised human serum amyloid P component was
a pentameric species (Wood et al. 1988). Nuclear magnetic resonance and electron
microscopy studies of mature A (10-35) fibrils were complemented by small angle
neutron scattering data (Burkoth et al. 2000).
1.4.4 Hydrogen-Deuterium Exchange
Hydrogens in a protein structure normally undergo rapid exchange with those in the
solvent. If the solvent contains deuterium, then this is exchanged into the protein, thus
increasing the protein’s mass. Determination of the quantity of incorporated
deuterium is normally accomplished using two-dimensional nuclear magnetic
resonance, mass spectrometry (MS) or FITR. The rate of exchange is dependent on
the protein structure and solvent accessibility. Therefore, by measuring protein
exchange, inferences about the protein dynamics can be made. Hydrogens bonded to
carbons do not, for the purposes of these experiments, exchange and those bonded to
heteroatoms on the side-chains generally exchange too rapidly to be detected.
Backbone amide hydrogen exchange rates can be measured, so information can be
gathered along the length of the backbone. All amino acids, except prolines, have
amide hydrogens. Proton exchange is much slower if the hydrogen is involved in a
hydrogen bond, as is the case in a -sheet or -helix. In contrast, solvent accessible
hydrogens will exchange very rapidly. Therefore, hydrogen-deuterium exchange
(HDX) does not provide a high-resolution three-dimensional structure but probes
structure at the resolution of a single residue (Li and Woodward 1999; Englander
2000). A problem is the loss of exchange information via back exchange during fibril
solubilisation.
Exchange protection in mature
2
-microglobulin fibrils has been observed in a variety
of conditions, over large regions of the chain, including those in the native loops
Chapter 1. Introduction

46
(McParland et al. 2000; Hoshino et al. 2002; Yamaguchi et al. 2004). This suggested
a wide -sheet or an ideal -helix. This was also the case for cold shock protein A
fibrils, in which all amide protons were found to be protected from exchange
(Alexandrescu 2001). A study using A (1-40) amyloid fibrils found that at least 50 %
of residues did not exchange even after a thousand hours of exposure (Kheterpal et al.
2000). These exchange times are not generally observed in globular proteins. Whilst
much of the protein exists in a highly protected, rigid core, a substantial proportion is
not involved in the protective -sheet structure. In the case of A (25-35) fibrils,
residues 28-35 formed this core (Ippel et al. 2002). Later studies on A (1-40) fibrils
showed the N-terminus to be substantially better protected (> 50 %) than the C-
terminal segment (35 %) (Wang et al. 2003). Similarly, fibrils formed from lysozyme
had some residual helical and disordered fold present (Booth et al. 1997). Such
structures contradict the view that strong hydrogen bonding is present along the whole
length of the peptide.
1.4.5 Solid State Nuclear Magnetic Resonance
Nuclear magnetic resonance (NMR) is a well-established technique used to describe
the high-resolution structure of molecules. Nuclear spins are aligned by a large
magnetic field of the order of one Tesla. These spins are then perturbed by sequences
of radio frequency waves and the resulting electromagnetic output detected by means
of induction coils. Solution NMR is not possible due to amyloid being extremely
insoluble. Solid state NMR (SSNMR) refers to the use of NMR on condensed matter
that is neither liquid nor in solution (reviewed (McDowell and Schaefer 1996)).
Unfortunately, the spectral resolution of solid state NMR is orders of magnitude lower
than solution NMR. This line broadening, of the order of 10 kHz, is due to the
angularly dependent anisotropic interactions and dipole-dipole interactions between
nuclei in the solid. In liquids, these interactions are averaged out since the molecules
rotate rapidly and randomly. Chemical shift data can be obtained using magic angle
spinning (MAS). This can substantially reduce the line-width by spinning the solid
sample about an axis at 54.5˚ (the magic angle) to the external magnetic field
(Stejskal and Memory 1994). Relaxation measurements can be made by selectively
reintroducing weak dipolar recoupling.
Chapter 1. Introduction

47
If the angular speed is matched to a multiple of the chemical shift difference between
appropriate spins, then rotational resonance (RR) leads to recoupling. RR therefore
requires a substantial isotropic chemical shift difference in the homonuclear spin pair.
Techniques such as rotational echo double resonance (REDOR) (Gullion and Schaefer
1989) and dipolar decoupling at the magic angle (DRAMA) (Tycko and Dabbagh
1990) involve dephasing pairs of nuclei of the same isotope with no isotropic shift
difference. Dipolar recoupling in a windowless sequence (DRAWS) allows detection
of weak, dipolar-coupling interactions between spin ½ nuclei with substantial
chemical-shift anisotropies (Mehta et al. 1996; Gregory et al. 1997; Gregory et al.
1998). Constant-time finite-pulse radiofrequency-driven recoupling (fpRFDR-CT) is
also an example of a dipolar recoupling technique; it minimises distortions in the
experimental data due to pulse sequence imperfections (Ishii et al. 2001a).
In the case of amyloid,
13
C labels are usually employed. Pulse sequences use the
direct dipolar interactions to allow the determination of distances between
strategically placed spin pairs (Figure 1.9). The dipolar interaction is inversely
proportional to the cube of the distance between the nuclei in the spin pair. It also
depends on the magnetic moments of the nuclei and the cosine of the angle between
the internuclear vector and the external magnetic field. More recently, multiple
quantum NMR (MQNMR) (Yen and Pines 1983) has been employed. Signals from
groups of coupled nuclear spins are detected; showing that labelled residues occur in
groups of a particular size. Measurement of internuclear distances using these
techniques is possible at up to 6 Å in favourable cases, with a standard error of
between 0.1 Å and 0.2 Å (Tycko 2000). Additionally, torsion angles and absolute
orientations of bonds and functional groups with respect to the external magnetic field
can be determined. Double quantum chemical shift anisotropy (DQCSA) and 2D
MAS exchange techniques both measure the relative orientations of a pair of
13
C
tensors. These tensors depend on the orientations of the carbonyl groups and therefore
the torsion angles. Line widths indicate the degree of structural order.
Chapter 1. Introduction

48
5.7 4.9 5.1 5.7 4.9
5.6 5.1
11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35
5.1 5.1
5.2
5.5 5.8

Figure 1.9. Summary of NMR distance information for A (10-35); this fits the model for a -
strands being parallel and in register. No evidence for a -turn is observed. (Data taken from
(Burkoth et al. 2000; Lynn and Meredith 2000).)
Most papers concerning SSNMR have reported on amyloid composed of truncated or
full-length A. The exceptions were two early papers on two amyloidogenic
fragments, IAPP (20-29) (Griffiths et al. 1995) and hamster prion H1 (109-122)
(Heller et al. 1996). Both used rotational resonance to conclude that the structure was
composed of -strands. Many studies concentrated on short truncated A peptides and
found antiparallel -strands in A (34-42), A (26-40), A (26-43) and A (16-22)
(Jarrett et al. 1994; Lansbury et al. 1995; Balbach et al. 2000). A cis linkage between
residues 37 and 38 was proposed (Spencer et al. 1991) but later concluded to be a
trans linkage (Costa et al. 1997). Parallel and in-register -strands were found in a
series of DRAWS experiments on A (10-35) (Benzinger et al. 1998; Gregory et al.
1998; Benzinger et al. 2000; Burkoth et al. 2000). Similarly, experiments using a
wide variety of NMR techniques on full-length A revealed in-register parallel -
sheets (Antzutkin et al. 2000; Balbach et al. 2002; Petkova et al. 2002; Antzutkin et
al. 2003). Line widths suggested a degree of structural disorder at the N-terminus.
Some non- structure was found at residues 25, 26 and 29 (Antzutkin et al. 2003).
This may be necessary, since a fully extended -strand is too wide to fit into the
diameter of fibres observed in micrographs and therefore there must be a turn
somewhere. The authors postulated the existence of a turn between -sheets, though
this is not common in general protein structure.
Limitations on the distances measurable using SSNMR mean that it is often combined
with other techniques. Using the constraints established by SSNMR data, some
Chapter 1. Introduction

49
members of the ensemble of possible structures can be eliminated. STEM has been
used to obtain mass per unit length data so that a model may be constructed
(Antzutkin et al. 2000; Petkova et al. 2002). They did not however completely refute
the possibility of a -helical structure. Whilst FTIR measurements generally indicated
antiparallel organisations of -strands (Jarrett et al. 1994; Lansbury et al. 1995), they
were not consistent with later, more reliable NMR studies (see FTIR section). The
SSNMR investigation into A (11-25) gave a pair of pH dependent structures,
different to that expected from X-ray studies under different conditions (Sikorski et
al. 2003; Petkova et al. 2004). This suggested that the -strand packing is
environmentally dependent and the result may be explained by slippage along the
chain axis (Makin and Serpell 2004a).
1.4.6 Other Methods
Site directed spin labelling (SDSL) involves the use of electron paramagnetic
resonance (EPR) to determine structure at the level of the backbone fold in native-like
conditions. EPR uses the same principle as NMR but applied to unpaired electrons
rather than nuclei. Most stable molecules have closed shells without unpaired spins.
Unpaired spins are introduced by means of site specific labelling of engineered
cysteine residues with a sulphydryl-specific paramagnetic nitroxide compound. The
EPR spectrum depends on the structural microenvironment of the spin label including
its secondary structure, proximity to other spin labels and solvent accessibility. A
study of full-length A fibrils found parallel in-register -strands (Torok et al. 2002),
whilst a mostly native structure in a head-to-head, tail-to-tail arrangement was
proposed for amyloid formed from transthyretin (Serag et al. 2002).
Protease digestion leaves the cross- core of the fibril. The technique was employed
to assign the -turn position to be between residues 26 and 29 in A (10-43) fibrils
(Hilbich et al. 1991). In the case of Ure2p it is disputed as to whether the fibrils are
amyloid at all. Although they have the characteristic birefringence pattern and
micrograph appearance, which in conjunction with mass spectrometry and protease
digestion suggest a cross- structure (Baxa et al. 2003), other studies have used these
Chapter 1. Introduction

50
techniques to propose a structure is that largely native and therefore predominantly -
helical (Bousset et al. 2004).
Selective mutation experiments have proved effective, including demonstrating the
effect of charge-charge interactions to stabilise -sheet conformation (Fraser et al.
1994). Other studies have used amyloid formed from Sup35 mutated with cysteine
residues (Scheibel et al. 2001), rat IAPP with point mutations from human IAPP
(Green et al. 2003), A (Serpell 2000),
2
-microglobulin (Smith et al. 2003) and IgLC
(Hurle et al. 1994; Stevens et al. 1995). Finally, circular dichroism spectroscopy has
been applied to A (10-43) and -synuclein fibrils (Hilbich et al. 1991; Conway et al.
2000a) to describe the fibrils’ -sheet content.
1.5 Electron Microscopy Theory
1.5.1 Beam Specimen Interaction
If electron microscopy is used to describe the structure of amyloid, it is necessary to
understand how the structure influences the image on the micrograph. As imaging
takes place using an electron beam, the interaction between the electron beam and the
specimen should be considered. The electrons in the column travel at speeds
comparable to the speed of light, hence relativistic quantum mechanics is required.
The requisite mathematical machinery requires the use of the Dirac equation.
Fortunately, the effect of spin can be neglected, as it represents only about 1 % of the
total interaction (Fujiwara 1961); meaning that a suitable first order approximation is
the Schrödinger equation, with relativistic corrections to the wavelength and electron
mass,
ψ ψ ψ E V
m
h
p
f
= + ∇ −
2
2
2

2
c
eV
m m
p
e f
+ =
Chapter 1. Introduction

51
e p
A
m eV
c
eV
h
2
2
+ |
.
|

\
|
= λ
where m
e
is the rest mass of the electron, o is the electron wave function, E is the total
energy of the electron, e is the charge on the electron, h is Planck’s constant, V
A
is the
accelerating voltage and V
p
is the potential. Passing through a specimen changes the
potential in the Schrödinger equation and thus the wavelength of the electrons,
introducing a phase shift φ(x,y).
( )
( )
í
|
|
.
|

\
|
− = dz
z y x
y x
, ,
1 1
2 ,
specimen vacuum
λ λ
π φ
( ) ( )
( ) ( )
í
|
|
.
|

\
|
+ + |
.
|

\
| +
− + |
.
|

\
|
= dz m z y x V V e
c
z y x V V e
m eV
c
eV
h
e s A
s A
e A
A
, , 2
, ,
2
2
2 2
π
φ
Approximating this shows that passing through the specimen advances the phase by
( ) ( )
í |
|
.
|

\
|
+ = dz z y x V
c m
eV
h
em
y x
s
e
A e
, , 1
2
,
2
π
φ
where V
s
(x, y, z) is the potential at a point (x, y, z) in the specimen, and the line
integral is parallel to the electron beam (Saxton 1980). This equation shows that by
finding the phase of the electron beam leaving the specimen, the projection of the
potential can be found. Once the projection is known, the potential at any point can be
calculated using the methods of three-dimensional reconstruction. The potential is
related to the charge density o
s
and permittivity of free space c
0
by the Poisson
equation.
0
2
ε
ρ
s
s
V − = ∇
Chapter 1. Introduction

52
This is in contrast to X-ray diffraction, in which the scattering factors depend almost
entirely on the electron charge density; whereas electron scattering amplitudes are
also dependent on the nuclear charge.
1.5.2 Imaging
Let
o
ψ be the object wave function, which is the wave function of the electrons
leaving the specimen and
i
ψ the image wave function, that is, the wave function of
the electrons in the image plane.
The Fourier transforms of the image and object wave functions are related by the
wave function transfer function

( ) k W (Teague 1983).
( ) ( ) ( ) k k k
o i
W Ψ = Ψ

( ) ( )
4
3
2
2
exp k k k
S
C i D i W λ πλ
π
+ =

where λ is the electron wavelength, D is the defocus and
S
C is the spherical
aberration. Here 0 > D is over focus. (There are also a number of envelope functions,
which are not shown here.) If the specimen is such that the phase of the object wave
function is small and the amplitude unity, then the weak phase object approximation
(Frank 1996) can be employed. This gives the result that the measured intensity is
twice the convolution of the phase of the object wave function with the inverse
Fourier transform of the imaginary part of the wave function transfer function,
[ ] ( ) [ ] ( )
4
3
2
2 2
sin arg FT 2 FT k k
S o i
C D λ πλ ψ ψ
π
+ = .
Within this approximation, the phase of the object wave function can be found simply
by dividing by
( )
4
3
2
2
sin 2 k k
S
C D λ πλ
π
+ ,
known as the contrast transfer function, in Fourier space.
Chapter 1. Introduction

53
1.6 Diffraction Theory
1.6.1 Introduction
Much of what is known about the three-dimensional structure of protein is from
diffraction studies. X-ray diffraction theory and fibre diffraction in particular are
covered in detail in many excellent books (Vainshtein 1966; Blundell and Johnson
1976; Fraser et al. 1976; Holmes and Blow 1980; Vibert and Squire 1987). This brief
summary illustrates how this theory relates to the included work.
The problem is the scattering of a beam of electrons from a sample. Formally, the
Huygens-Kirchhoff Integral should be solved. In the far field approximation, the
phase varies linearly across the aperture and Fraunhofer diffraction occurs. The three-
dimensional diffraction pattern is the three-dimensional Fourier transform of the
sample structure. The space in which the three-dimensional diffraction pattern exists
is known as reciprocal space.
1.6.2 Fourier Transform
Fourier transforms are written as capitals, hence the Fourier transform (FT) of a
function f(x) is written
( ) [ ] ( ) ( )
í í í

∞ −

∞ −

∞ −

= = x x k x
x k 3 . 2
FT d e f F f
i π

Discrete Fourier transforms are used for computations in practice.
1.6.3 Convolution Theorem
The Fourier transform of the sample structure can be worked out by repeated
application of the convolution theorem. This theorem states that multiplication in real
space is equivalent to convolution in reciprocal space.
( ) [ ] ( ) [ ] ( ) ( ) [ ] x x x x g f g f * FT FT FT =
Chapter 1. Introduction

54
The sample is composed of a series of crystallites at varying angles. These crystallites
can be thought of a being a small part of an infinitely large crystal. This crystal is
constructed from a lattice of parallelepiped shaped building blocks (unit cells). Points
on the lattice r
lmn
are defined by linear combinations of integer multiples of three
lattice vectors { } c b a , , .
c b a r n m l
lmn
+ + =
These unit cells are themselves composed of identical symmetry related objects
known as the crystallographic asymmetric units. The space group defines the number
and orientation of asymmetric units. Mirror and inversion symmetries are not allowed
since proteins are chiral and only one type of enantiomer is allowed.
A real space sample can be represented by a series of multiplications and
convolutions. The Fourier transform of the unit cell is the molecular transform. The
Fourier transform of the lattice is another lattice. This reciprocal lattice has reciprocal
lattice vectors { }
* * *
, , c b a calculated using
( ) c b a
c b
a
×
×
=
.
*
,
( ) c b a
a c
b
×
×
=
.
*
,
( ) c b a
b a
c
×
×
=
.
*

Points on the reciprocal lattice
*
r , with Miller indices [ ] l k h are defined thus
* * * *
c b a r l k h
hkl
+ + =
Structure factors F
hkl
are the values of the molecular transform at r
hkl
*
.
The crystallites have a finite size, which is equivalent to multiplying an infinite crystal
by a cut-off function, such as a top hat function. Hence, by applying the convolution
theorem, the infinitely narrow spots are convolved with the Fourier transform of the
cut-off function. So the result is a lattice of spots of finite size. Next, the orientational
disorder is applied by convolving the lattice of spots with an angular function,
representing the distribution of crystallites. In the case of a true fibre, the crystallites
Chapter 1. Introduction

55
are randomly distributed about the fibre axis. As a result, the spots are convolved with
circles centred on the fibre axis and in planes perpendicular to this axis; the diffraction
produced is equivalent to a rotation photograph. Hence fibre diffraction patterns have
layers of reflections perpendicular to the fibre axis, known as layer lines.
1.6.4 Sample Texture
Texture is a description of the distribution of fibril orientations (Kocks et al. 1998). It
determines the shape of the reflection in reciprocal space and hence affects both the
shape and intensity of the signals on the diffractogram. In general, the texture can be
complicated (Detavernier et al. 2003), however amyloid fibrils are relatively simple.
In the case of a true fibre, there is a rotational degree of freedom about the fibre axis;
this results in a diffraction pattern with infinite cyclic symmetry about that axis. The
diffraction pattern’s symmetry is like that of a rotating single crystal experiment;
however there is also disorder in the orientations of individual fibrils about the mean.
Sample texture depends on the method of alignment, the precursor peptide and the
experimental conditions.
1.6.5 Ewald Sphere
The diffractograms observed by the detector are two-dimensional. Only points lying
on the surface of a sphere in reciprocal space satisfy the geometrical requirements for
diffraction to occur. Given the position of a lattice point, the corresponding position
of the reflection on the detector can be calculated (Figure 1.10).
Chapter 1. Introduction

56

Figure 1.10. The diffraction geometry, a sample lattice point (x
lattice
, y
lattice
, z
lattice
) in red and its
circle are shown, diffraction occurs where this circle intersects with the sphere. The resulting
signal on the detector plate has the coordinates (x
imageplate
, y
imageplate
).
To achieve this, the position of the reflection on the Ewald sphere must first be
determined. The constraint provided by the Ewald sphere is
( )
2 2
sphere
2
sphere
2
sphere
1 1 λ λ = + + + z y x

In the case that the fibre axis is parallel to the y-axis then there are three possibilities.
If the circle intercepts with the Ewald sphere (Figure 1.11), then the condition is
2
lattice
2
lattice
2
sphere
2
sphere
z x z x + = + and
lattice sphere
y y =
X-rays
Ewald sphere
Detector
x
z
y
Chapter 1. Introduction

57
These three equations can be solved to give:
( )
2
lattice
2
lattice
2
lattice 2
1
sphere
z y x z + + − = λ

( )
2
2
lattice
2
lattice
2
lattice
2
4
1
2
lattice
2
lattice sphere
z y x z x x + + − + ± = λ


Figure 1.11. Side view of the diffraction geometry shows the circle traced out by the reflection
(red) intersecting with the Ewald sphere at (x
sphere
, y
sphere
, z
sphere
) (green).
Alternatively, the circle may not intercept with the Ewald sphere, in which case the
angular disorder perpendicular to this circle is important in giving the circle a finite
thickness on the surface of a sphere (shown in red, Figure 1.12) and the equations are
as follows:
2
lattice
2
lattice
2
lattice
2
sphere
2
sphere
z y x z y + + = + and 0
sphere
= x
( )
2
lattice
2
lattice
2
lattice 2
1
sphere
z y x z + + − = λ

( ) ( )
2
2
lattice
2
lattice
2
lattice
2
4
1
2
lattice
2
lattice
2
lattice sphere
z y x z y x y + + − + + = λ

2
lattice
2
lattice
z x +
y
z
x
( )
lattice lattice lattice
, , z y x
( )
imageplate imageplate
, y x
( )
sphere sphere sphere
, , z y x
lattice
y
Chapter 1. Introduction

58
Figure 1.12. The circle centred at the fibre axis (y-axis) does not intersect with the Ewald sphere.
Nevertheless diffraction may still occur since the diffraction circle has a finite thickness and is
represented by a two-dimensional circular surface on the surface of a sphere (red).
There is no intercept if
2 2
lattice
2
lattice
2
lattice
4 λ > + + z y x (Figure 1.13).

Figure 1.13. The case in which no diffraction occurs. The radius of the sphere containing the
lattice point is greater than the diameter of the Ewald sphere.

y
z
x
( )
lattice lattice lattice
, , z y x
( )
imageplate imageplate
, y x
( )
sphere sphere sphere
, , z y x
2
lattice
2
lattice
2
lattice
z y x + +
y
z
x
( )
lattice lattice lattice
, , z y x
2
lattice
2
lattice
2
lattice
z y x + +
λ
2
Chapter 1. Introduction

59
Once the position on the Ewald sphere is known, the position of the spot on the image
plate can be calculated
1
sphere
sphere
imageplate
+
=
λ
λ
z
D x
x ,
1
sphere
sphere
imageplate
+
=
λ
λ
z
D y
y
1.6.6 Problems
Diffraction detectors only measure the intensity of the wave function, not its phase. In
single crystal X-ray diffraction, the integrated intensity of reflections is measured and
after the application of intensity correction factors, the amplitude of the structure
factors can be calculated.
In order to calculate the structure of the sample from its structure factors, both the
amplitude and phase of the structure factors are required. The absence of the phase
information is known as the phase problem. Crystallographers are able to solve this
problem using a variety of methods including molecular replacement, multiple
isomorphous replacement and anomalous dispersion. Neither is there a problem in
electron microscopy, in which phases can be experimentally determined under the
weak phase object approximation. Fibre diffraction structures are generally
determined by modelling a structure and then comparing the simulated diffractogram
with the observed pattern. The most prominent exceptions are the use of isomorphous
replacement to determine the structure of the tobacco mosaic virus TMV (Stubbs and
Diamond 1975) and molecular replacement in the case of the ribgrass mosaic virus
(Wang et al. 1997).
Overlapping reflections can also be a problem, further reducing the amount of
information available. Reflections may overlap due to angular disorder or the diffuse
nature of the signals. The choice of the Lorentz intensity correction factor also
depends substantially on the sample texture (Vainshtein 1966). These make
calculation of the intensity of individual reflections difficult or impossible.
Chapter 1. Introduction

60
1.7 Experimental Methods for X-ray Fibre Diffraction
1.7.1 Introduction
The quantity and quality of diffraction information is very dependent on the amount
of order in the sample (Lorenz and Holmes 1993). The general problem was first
considered in the case of tobacco mosaic virus fibrils (Bernal and Fankuchen 1941).
In the absence of alignment, the pattern is a series of concentric rings; if there is some
alignment, the reflections form arcs (Sunde et al. 1997) (Figure 1.14). Investigators
therefore wish to align fibrils with respect to one another, which may achieve a high
degree of orientation and a diffraction pattern with far more information (Sikorski et
al. 2003). The correct technique and maximum degree of orientation depends strongly
on the type of fibre.

Figure 1.14. Comparison of unaligned A (1-40) amyloid fibrils (left) and stretch frame aligned
A (11-25) fibrils (right). Arrows indicate the location of the 4.7 Å reflections.
1.7.2 Glass Capillary and Stretch Frame
Long fibres are likely to be very viscous and thus a stretch frame will yield the best
results. The frame can be used to mount a pair of glass capillaries. These capillaries
are sealed flat using melted wax and a droplet rests between the two (Figure 1.15).
The fibrils orient parallel to the capillaries as the drop dries over several hours
(Damas et al. 1995; Sunde et al. 1997) (Figure 1.16). A threaded arrangement allows
Chapter 1. Introduction

61
the capillaries to be separated gradually during drying, leading to some stretching of
the fibre sample, although the sample may break even without stretching.
Laterally aggregated samples can also be encouraged to align by drying them down to
form a disk. This can be obtained by drawing 2 to 3 cm of solution into a siliconized
capillary of 0.7 mm diameter and then allowing the solution to dry.

Figure 1.15. A stretch frame can be used to align fibrils. Inset shows sample suspended between
the waxed ends of two glass capillaries. The capillaries are attached to the stretch frame by
means of Plasticine.
1.7.3 Magnetic Field
Most filamentous macromolecular assemblies are oriented by magnetic fields
(Glucksman et al. 1986). Magnetic alignment is more appropriate for samples
composed of small crystallites, which are grown in a magnetic field. Alignment of
these samples can be achieved using a 2.4 Tesla permanent magnet (Hummingbird
Sample
Capillary Wax
Stretch frame
Plasticine
Chapter 1. Introduction

62
Instruments, Arlington, MA). The fibrils are oriented parallel to the direction of the
magnetic flux density vector (Figure 1.16). Bond resonance in certain side-chains
causes anisotropy in the diamagnetic susceptibility, resulting in a force on the fibrils
and thus a preferred orientation (Worcester 1978; Pauling 1979; Glucksman et al.
1986). The sample is prepared in the same manner as for a disk, with the sample
placed between the poles of the magnet and dried over several weeks. Kirschner first
used this to study A and its fragments (Inouye et al. 1993). Magnetic alignment has
also proved very effective for the alignment of other amyloid fibrils (Inouye and
Kirschner 1997; Malinchik et al. 1998; Sikorski et al. 2003).
1.7.4 Mat
Alternatively, a thin flat film can be formed with the fibres aligned parallel to the
plane of the film (Figure 1.16). A larger volume of solution is required and the film
must be mounted such that the X-ray beam can be passed both in the plane of film and
perpendicular to that plane.
The mat can be produced by depositing solution on a glass slide, drying and detaching
the residue from the substrate. Whilst this method has been successfully applied in the
case of poly-amino acids (Fandrich and Dobson 2002), removing the mat from the
surface can be difficult if the mat is brittle, perhaps owing to short fibres. Parafilm
and Teflon can also be used as a substrate and the mat has been used for aligning
polymers, AA (Turnell et al. 1986) and polyglutamine fibrils (Perutz et al. 2002). To
avoid problems with lifting off the mat, a cryo-loop (Hampton) normally used to
freeze single crystals can be employed. The loop is immersed in the fibril solution and
then lifted out to dry, resulting in a film across the plane of the loop (Makin and
Serpell 2005).
Chapter 1. Introduction

63

Figure 1.16. Illustration of the orientation of fibres after alignment by stretch frame, cryo-loop
and magnetic field (from top to bottom). Block arrows indicate the X-ray beam directions.
Magnetic Field
Chapter 2. Application for the Structural Analysis of Amyloid

64
2 Application for the Structural Analysis of Amyloid
2.1 Abstract
Amyloid has a characteristic cross- structure. Structural studies of amyloid
necessarily reflect its characteristics. The examination of amyloid structure is
impeded by problems peculiar to amyloid. Existing applications, which are not
specific to amyloid diffraction, have difficulty with these issues and are unable to
exploit amyloidal features. We have therefore developed a suite of programs
specifically for the study of amyloid fibre diffraction patterns. It is also suitable for
many general fibre diffraction problems.
Our Java based application (Clearer), employs a series of libraries to process
experimental data, particularly X-ray and electron diffractograms. Components within
the suite aid and automate crucial elements in the sequence of analysis. Background
subtraction and contrast enhancement allow weak signals to be observed and then
peak profiling gives their resolutions. The indexing process is semi-automated, so the
user can obtain the unit cell. Finally, simulation of diffraction patterns ensures that
structures modelled using an external program can be tested and compared with the
experimental diffractogram. This allows the structure of amyloid to be examined in
detail.
2.2 Introduction
The purpose of the application was to facilitate the process of examining amyloid
structure. Both portability and usability were intrinsic to the design; these made Java
(Sun Microsystems) the obvious choice of language. Rapid application development
and the Java Advanced Imaging library (JAI) enabled better use of development
resources. The aim was to be as user friendly as possible. Accordingly, the system
was built with a modern graphical user interface and without batch files, lists of
parameters or idiosyncratic user-interface metaphors. Sensible defaults and clear
language were also essential to help new users and enable rapid working.
Chapter 2. Application for the Structural Analysis of Amyloid

65
Each component was developed in response to a specific practical requirement.
Development proceeded as a response to issues arising from the analysis of the
peptides described in Chapter 3 and Chapter 4. Feedback from users was crucial, both
in terms of demand for features and human-computer interaction issues.
We have benefited greatly from the availability of ancillary software. The underlying
image processing engine relies on the Java Advanced Imaging library, in which many
of its methods are available as C routines for speed. One-dimensional graphs are
displayed by JFreeChart. The molecular visualisation component allows protein data
bank (PDB) files to be viewed; this was based on an existing application (Jmol),
implemented with the assistance of Jmol developers.
The sequence of analysis for fibre diffraction patterns generally involves several
stages (Figure 2.1). First, the image is prepared for processing, including removing
the background. Secondly, the required data is extracted from the image. Finally, this
data is processed to reveal information about the structure of the sample.
Amyloid samples suffer from low crystallinity, small crystal size and lack of good
packing. A carefully chosen processing strategy is required to make best use of the
available data. Each stage is analysed in turn.
Chapter 2. Application for the Structural Analysis of Amyloid

66

Figure 2.1. Flowchart showing the procedure for processing general fibre diffractograms. Based
on (Stubbs 1999).
2.3 Preparation
2.3.1 Format Conversion
A very wide variety of image formats are output by detectors and used by diffraction
processing programs. The range of formats in general use is even greater. Writing
input filters is time consuming and does not result in new structures. The CCP13
website lists some 22 types, before accounting for byte order and other nuances. We
therefore chose to limit the input to those available from the underlying library
including RAW, BMP, GIF, JPEG, PNG, PNM and TIFF. Marcvt (Marresearch,
Norderstedt), Fit2D (A. Hammersley, ESRF), Denzo (Otwinowski and Minor 1997)
and XCONV (CCP13) all offer the ability to convert the output of detectors into TIFF
files, which are compatible with most image processing applications.
2.3.2 Centring
The centre of the pixel array collected from the detector rarely matches the centre of
the beam. It is therefore necessary to realign the image so that systematic error does
not affect the following analysis. Figure 2.2 shows the component used for this
Structure Modelling
Image Analysis
Indexing
Image Processing
Format Conversion
Chapter 2. Application for the Structural Analysis of Amyloid

67
purpose. On the right, traces along the x and y axes in the positive and negative
directions will line up once the image is properly centred. Pressing the calculate
button crudely calculates the optimum x and y shifts by comparing peak positions on
each of the traces. Alternatively, blue concentric rings are overlaid so the process can
be completed by eye.

Figure 2.2. The user can centre the diffraction pattern to prevent the introduction of systematic
error into the analysis.
2.3.3 Background Removal
The background is unwanted low frequency data, which is added to the diffraction
pattern. Reasons for its existence include detector-specific noise (fog) and white
radiation – the incident beam not being completely monochromatic. Additionally X-
ray scattering from air, the sample holder, amorphous material in the specimen such
as solvent and disordered polymer and components of the camera all contribute. The
background may show a high level of variation across the field and is a source of error
Chapter 2. Application for the Structural Analysis of Amyloid

68
in intensity measurements. In the case of electron diffraction, the background is
particularly strong and weak spots may be obscured.
There are three types of methods to determine the background, experimental
measurement, simulation and estimation from the diffractogram. The diffraction
experiment can be repeated without the sample; this method does not account for
amorphous scattering from the sample and is time consuming, as it must be repeated
many times. Computational simulation is unreliable since a great many parameters
must be estimated to be input into the model, which may not correctly simulate the
amorphous scattering. Finally, the background can be estimated from the spaces
between reflections in the diffractogram. This estimation is difficult if layer lines
overlap, which is often a problem at larger radii. We implemented several methods of
estimation.
The simplest form of background estimation is to calculate the local mean, using a
box filter. Each pixel is replaced by the average of the pixels in a box centred on its
position. Since the background is low resolution, a large box is used and the
calculation may require a large number of calculations. It may be better to do the
calculation in Fourier space. A box filter is a convolution operation, so it is equivalent
to multiplication by a sinc function in reciprocal space. Alternatively, the box may be
replaced by a Gaussian, so the effects of the sharp box edges are avoided. This
method can also be used for background removal in electron micrographs.
In single crystal X-ray crystallography, the individual reflections are small; hence an
inclined plane is a suitable function for the local background (Rossmann 1979). Early
attempts employed a similar strategy, using a series of inclined planes or splines.
Unfortunately, amyloid’s angular disorder results in large reflections, many of which
may overlap. Therefore, a single, global function, interpolated from the gaps between
signals, may be more appropriate. One approximation is that the background varies
linearly with the polar angle, with the parameters determined using a set of
experimental and computationally derived values (Fraser et al. 1976). Alternatively,
Chapter 2. Application for the Structural Analysis of Amyloid

69
the lower orders of two-dimensional cylinder function expansion can be calculated
using selected points between layer lines (Millane and Arnott 1985).
If the background is circular, other methods are appropriate. A polynomial fit to the
circularly averaged image is surprisingly effective. The beam stop must be excluded
and non-quadratic polynomials are prone to over fitting. We have developed a
statistical approach in which the image is divided into concentric circular annuli, each
one pixel thick. If an annulus contains a signal, its histogram (intensity frequency
distribution) will be the sum of two approximately normal distributions (Figure 2.3).
These are a tall, narrow Gaussian at low intensities from the background and a low,
wide distribution at higher intensities due to the reflection. The aim of the program is
to determine the mean of the background distribution. If the background distribution
has a roughly constant standard deviation, then it is only necessary to determine the
mean plus a constant offset. The algorithm finds the background intensity by
considering the cumulative frequency distribution and using a user supplied value for
the minimum percentage of the image that is background. A value of 50 % was found
to work well in most cases (Figure 2.4). Care should be taken not to introduce
artefacts by underestimating the percentage of any annulus occupied by the signal,
since this will result in overestimation of the background intensity at some
resolutions.
Chapter 2. Application for the Structural Analysis of Amyloid

70
C
u
m
u
l
a
t
i
v
e

F
r
e
q
u
e
n
c
y

Intensity
F
r
e
q
u
e
n
c
y

Intensity

Figure 2.3. Illustrations of the image histogram (left) and cumulative frequency distribution
(right). By analysing the cumulative frequency distribution, the background intensity can be
determined.
For the case that the background is not circularly symmetric, an iterative approach can
be used (Ivanova and Makowski 1998). Experimentation is required to determine the
correct number of iterations; too many can result in an estimation with many of the
foreground’s features present as artefacts.

Figure 2.4. Circularly symmetric background reduction on an electron diffraction pattern,
before (left) and after (right).
Chapter 2. Application for the Structural Analysis of Amyloid

71
2.3.4 Contrast Enhancement
Weak spots appear to be obscured when displayed, both by the background and also
the range of intensities in the image. Changing the display’s minimum and maximum
intensity values, corresponding to black and white, can reveal these signals. Values
that reveal some signals will obscure others. We therefore seek a method of changing
the intensities such that the whole image can be surveyed (Figure 2.5). Electron
diffraction images are particularly affected, as discussed in Chapter 1.
The image is first divided into single pixel wide, concentric annuli; then, an
appropriate contrast stretch is performed on each annulus and the image reassembled.
The contrast stretch requires the selection of intensity values corresponding to black
and white. Three different methods were developed. The first simply used the
minimum and maximum values from the annulus. Secondly, the stretch used
minimum and maximum values from the corresponding annulus in the locally
averaged image. Finally, the image histogram of each annulus was analysed and the
distribution of intensities normalised such that all the annuli in the output had the
same means and standard deviations.
The best method depends on the noise level in the diffractogram and level of
enhancement required. The first gives the most aggressive enhancement of signals but
also increases the noise. This is particularly visible if there are no reflections at a
particular radius. Using a locally averaged image reduces the effect of high-frequency
noise by making the stretch aware of the annulus’ surroundings. The final method is
also less sensitive, since it largely eliminates the effects of outliers on the choice of
minimum and maximum values. More aggressive methods are also prone to
introducing artefacts such as the white bands visible in Figure 2.5. Random noise can
be reduced by locally averaging the image beforehand, although this also softens bona
fide reflections.
Chapter 2. Application for the Structural Analysis of Amyloid

72

Figure 2.5. Comparison of original electron diffraction pattern (left) with contrast-enhanced
version (right). Spots barely visible in the original are clear in the enhanced image.
2.4 Peak Measurement
2.4.1 Automated
After viewing peaks, their d-spacings must be determined. Peak finding greatly
speeds up this process and delivers more accurate results, since measurements are
based on a large proportion of the reflection rather than simply the maximum point.
The user supplies the angular range to be studied, the expected peak width in pixels
and the diffraction settings and the process is as follows.
The diffractogram is divided into user-specified circular sectors (wedges) and one-
dimensional radial averages calculated for each. A local mean of the radial average
based on the expected peak width ensures that high frequency noise is not counted as
a peak. Approximate maxima are found by double differentiation, whilst checking for
clipping. Finally, the actual maximum is determined by fitting an inverted parabola to
the peak using the raw values centred on the approximate maximum. This generates a
list of peak radii from which their spacings and relative intensities are calculated
(Figure 2.6).
Chapter 2. Application for the Structural Analysis of Amyloid

73

Figure 2.6. Screenshot of the automated peak finder. The radially averaged diffractogram, in this
case averaged over the full 360°, is shown on the left.
2.4.2 Manual
Following the peak finding measurements, it is wise to check the results visually
(Figure 2.7). The peak finder may be confused by salt or dust, or give incorrect results
if the user supplied expected peak width is very wrong. If the reflections are diffuse,
then a small signal may appear as a shoulder in a much larger peak. Interactive
resolution calculation and a zoom function allow rapid verification of the calculated
values and the peaks can be sorted into categories prior to finding the unit cell. Peak
measurements were tested by comparing results from other programs and back
calculating data from simulated diffractograms.
Chapter 2. Application for the Structural Analysis of Amyloid

74

Figure 2.7. Manually measuring the d-spacing of a peak using a zoomed-in image.
2.5 Unit Cell Determination
2.5.1 Search
The first stage of modelling is to find the unit cell and thus index the reflections.
Powder diffraction programs often assign incorrect Miller indices to amyloid fibre
diffraction patterns, since they are unable to distinguish whether a reflection is
meridional or equatorial. They also generally require far sharper reflections than are
available for amyloid. The search space is very wide since there are six variables (a,
b, c, o, ß and y). The use of prior information may limit the search. Other data, such as
electron diffraction, may show that the cell is orthorhombic. The cross- pattern
implies that the a dimension will be a multiple of 4.7 Å and b will be a multiple of a
value between approximately 10 and 11 Å. The other dimension may be a multiple of
the length of an extended -strand, calculated as the product of 3.5 Å and the number
of residues. Adjustment may be required if the cell is not orthorhombic. Most amyloid
Chapter 2. Application for the Structural Analysis of Amyloid

75
models in the literature use an orthorhombic cell and monoclinic cells are rare
(Sikorski et al. 2003); therefore not all angles need necessarily be considered. The
volume of the unit cell must also be sufficient to contain a whole number of peptides,
which further restricts the allowed values.
The program is supplied with a list of d-spacings, broken into the categories of
equatorial, meridional and other, defined by reference to restrictions on Miller indices.
Whilst a more fine-grained system was supported by the underlying code, mock-ups
of these user interfaces proved to be overcomplicated.
Unfortunately, the indexing method may output spuriously large values for the Miller
indices, if the corresponding unit cell dimension is large. It is therefore sometimes
better to restrict initially the type of input d-spacing and only use equatorial
reflections, since they correspond to the largest cell dimensions. Once this is done, the
meridionals and off meridionals can be considered.
Improvement of the user supplied unit cell uses a grid search. Given a unit cell and set
of d-spacings with appropriate constraints, the peaks are indexed by a least absolute
error between calculated and observed values. The total error for this unit cell is
calculated by summing the lowest errors for each d-spacing. Then, the process is
repeated for all possible unit cells on a six-dimensional grid. The user determines the
search width and spacing of the points on the grid. Once the optimum unit cell is
selected, the search width in every direction is halved and the process repeated a user-
specified number of iterations. The result is a table, comparing the experimental and
calculated resolutions (Figure 2.8). This table can be saved as an HTML file to be
viewed in a web browser or pasted into another program. Comparison of calculated
and back-calculated results, both with and without random error, was used to test the
veracity of the method.
Chapter 2. Application for the Structural Analysis of Amyloid

76

Figure 2.8. Indexing of reflections and determination of the unit cell is carried out using this
window. The user supplies the initial guess, how far the program should look for improved
values and the d-spacing of the experimental reflections. The component then finds the Miller
indices best matching the supplied unit cell and attempts to improve it.
2.5.2 Spot Position Predictor
After determination of the unit cell, a visual conformation of the correct values is
obtained by superimposing coloured crosses on to the empirical diffractogram. Whilst
some crosses will appear in empty regions of the pattern, perhaps due to systematic
absences, each reflection should have an accompanying marker.
Chapter 2. Application for the Structural Analysis of Amyloid

77
2.6 Simulation of Amyloid Fibre Diffraction Patterns
Amyloid diffraction data is of insufficient quality for the structure to be solved using
standard crystallographic methods. Verification of a proposed structure involves
comparison of observed and simulated diffraction patterns (Figure 2.9). Two windows
are present, one specific to fibre diffraction and another for more general use. In each
case, the same underlying routine is used.

Figure 2.9. Diffraction simulation window for MacOS X.
2.6.1 Sampling of Intensities in Reciprocal Space
The process works by tracing the diffracted beam back from the positions of the
pixels on the detector, to find the corresponding sample points on the Ewald sphere
(Figure 2.10). For each sample, the contribution from each reciprocal lattice point is
calculated, based on the shape and intensity of that lattice point. The effect of the
projection in real space is also considered. The shape of each of the reflections is
determined by the disorder in the sample and the crystallite size. The temperature,
Chapter 2. Application for the Structural Analysis of Amyloid

78
Lorentz, polarisation and structure factors govern the intensity of each reciprocal
lattice point. Factors that remain constant over the whole diffractogram are ignored.
Chapter 2. Application for the Structural Analysis of Amyloid

79
A
n
g
u
l
a
r

D
i
s
o
r
d
e
r



C
r
y
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a
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M
o
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a
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Figure 2.10. Flowchart showing the process by which simulated diffractograms are calculated.
Chapter 2. Application for the Structural Analysis of Amyloid

80
The location of the sampling points (x
sample
, y
sample
, z
sample
) on the Ewald sphere is
given by:
2
imageplate
2
imageplate
2
imageplate
sample
y x D
x
x
+ +
=
λ

2
imageplate
2
imageplate
2
imageplate
sample
y x D
y
y
+ +
=
λ

λ
λ
1
2
imageplate
2
imageplate
2
sample

+ +
=
y x D
D
z
where · is the wavelength of the incident beam, D is the distance between the image
plate and the sample and (x
imageplate
, y
imageplate
) is the position of the pixel on the
detector.
2.6.2 Reflection Shape
The shape of each reflection is determined by the region in reciprocal space swept out
by the distribution of crystallites. It is therefore dependent on the size of individual
crystallites and the angular disorder. The result is the convolution of a pair of
Gaussians expressed in polar coordinates due to the fibre orientation (Dupont et al.
1997) and another three-dimensional Gaussian from the size of the crystallite. The
convolution of a pair of Gaussians is another Gaussian. Amyloid fibres are generally
far more ordered along the direction of the fibre. The hydrogen bonding between -
strands in this direction is more ordered than the packing between -sheets. On this
basis, meridional reflections are likely to be sharper than equatorials. Angular
disorder is described by two parameters, o
c
and o
0
, as shown in Figure 2.11. We
distinguish between samples for which o
c
= , referred to as a true fibre and those
which have a preferred orientation in this direction. Whilst most amyloid fibrils
appear to be true fibres, diffraction patterns of A (11-25) taken with the beam
parallel to the fibre axis show that this is not always the case (Sikorski et al. 2003)
(Figure 1.5).
Chapter 2. Application for the Structural Analysis of Amyloid

81

Figure 2.11. Reflection shapes for a true fibre (left) and the general case (right). The vertical axis
is the fibre axis and the solid red dot represents the position of the spot before fibre disorder is
applied. The effect of crystallite size is not considered here.
2.6.3 Structure Factors
The unit cell contains a set of N atoms with coordinates ( ) { }
i i i
z y x , ,
atom
= r and
atomic scattering factors ( ) k
j
f . Atomic scattering factors can be approximated using
numerical solutions to Hartree-Fock functions (Cromer and Mann 1968) using
coefficients from XtalView (McRee and David 1999).
( ) 21 . 0 86 . 0 58 . 1 02 . 1 31 . 2
2 21 2 21 2 19 2 19
10 2 . 5 10 6 . 5 10 02 . 1 10 1 . 2
Carbon
+ + + + =
− − − −
× − × − × − × − k k k k
k e e e e f
The resulting structure factor is therefore:
( ) ( )
¯
=
=
N
j
hkl j hkl
i f F
1
*
atom
. 2 exp k r k π
If electrons rather than X-rays are used, then the atomic scattering factor should be
changed to account for scattering from the nucleus, according to the Mott formula
(Mott and Massey 1965) based on the use of Poisson’s equation relating the potential
to the charge-density distribution,
θ
σ
θ
σ
φ
σ
Chapter 2. Application for the Structural Analysis of Amyloid

82
( )
( )


=
2
Xray
2
2 2
electron
8
k
k
k
f Z
h
e m
f
e
π

using m
e
the mass of the electron, e the charge on the electron, h Planck’s constant
and Z the atomic number. A table of neutron scattering factors is also provided but has
not been tested.
2.6.4 Other Factors
The polarisation factor for an unpolarised incident beam is
( )
B
P θ 2 cos 1
2
2
1
+ =
B
θ is the Bragg angle given by ( ) λ θ k
2
1
arcsin =
B
, therefore
( ) ( )
4
8
1
2
2
1
1 λ λ k k + − = P
In the analysis of integrated intensities from a single crystal, the Lorentz factor is due
to the diffracted flux being dependent on the angular velocity with which the crystal is
moved through the reflecting position (Cella et al. 1970). Here, the sampling process
takes care of the issue; however, it is still necessary to account for the volume of the
reflection in reciprocal space. The full three-dimensional integral can be
approximated using a portion of a spherical shell.
( ) ( ) ( ) ( ) ( ) ( )
θ θ φ
σ θ σ θ σ σ σ + − − − − +
=
f f r r
L
cos cos
1
3 3
k k

In fact, constraints are necessary to prevent the introduction of negative numbers:
( ) ( ) [ ] ( ) ( ) ( ) ( ) [ ] π σ θ σ θ σ σ σ
θ θ φ
, min cos 0 , max cos 0 , max
1
3 3
+ − − − − +
=
f f r r
L
k k

Chapter 2. Application for the Structural Analysis of Amyloid

83
f
θ is the angle between the position vector of the reciprocal lattice point and the fibre
axis
r
σ is the standard deviation of the radial distribution, calculated by convolution of the
appropriate distributions.
The atomic isotropic Gaussian Debye-Waller factor accounts for atoms not being in
their mean positions; the effect is to lower the intensity of higher resolution signals.
( ) 2 exp
2
k
T T
B A − =
T
B is the atomic temperature factor, typically between 20 and 50 Å
2
for proteins.
Therefore,
T hkl hkl
LPA F I
2
=

Factors which are constant over the whole image are not calculated since only relative
intensity is considered important.
2.6.5 Optimisation
The process is very slow since every pixel on the image detector must be compared
with every reciprocal lattice point and the effect of that point calculated. Reducing the
number of pixels and reducing the number of lattice points will speed up the
simulation process. In many cases, the fibre diffraction pattern is quadrant symmetric;
this is checked since only a quarter of the calculation may be required. A general
picture of the diffractogram can be obtained without calculating every pixel; sampling
every other pixel reduces the number of pixels by a factor of four. The remaining
values can be calculated using bicubic interpolation. This allows the quality of the
output to be varied according to the user’s requirements. We can also reduce the
number of lattice points that need to be considered by each sample. Reciprocal space
can be divided into a series of spherical shells, in the manner of an onion. Shells are a
Chapter 2. Application for the Structural Analysis of Amyloid

84
few radial standard deviations in thickness and each sample point need only consider
samples in the shell at the same resolution and the shells on either side.
2.6.6 Automation
The result of diffraction simulation is the calculated diffractogram. Building and
simulating diffraction from a large number of models is excessively time consuming.
Facilities to construct a series of models and determine their X-ray and electron
diffraction patterns are available but due to their complexity, not exposed through the
user interface. These facilities were heavily used in the study of amyloid nanocrystals
(Makin et al. 2005) (Chapter 4).
2.6.7 Testing
Testing was critical to ensure that the results were reliable. The structure of A (11-
25) amyloid fibrils had previously been solved by X-ray fibre diffraction using
Cerius2 (Accelrys) (Sikorski et al. 2003). Therefore, A (11-25) diffractograms were
used for testing purposes (Figure 2.12), although testing was not limited to this
peptide (Figure 2.13). Using the published model, the X-ray diffraction pattern was
simulated with the other settings chosen to best fit the experimental data. Good
agreement was demonstrated between the calculated and observed images.
Additionally, the simulation process was broken down into stages and each verified
using data calculated using other methods. Dr P. Sikorski provided particular
assistance in finding bugs in this component.
Chapter 2. Application for the Structural Analysis of Amyloid

85

Figure 2.12. Comparison between the simulated (left) and observed (right) X-ray fibre diffraction
patterns, for amyloid formed from A (11-25), using the model from (Sikorski et al. 2003).

Figure 2.13. Observed diffraction pattern with calculated top left quadrant, for a non-amyloid
sample - cellulose triacetate I (Sikorski et al. 2004).
Chapter 2. Application for the Structural Analysis of Amyloid

86
2.7 Other Features
2.7.1 Introduction
Many other features are provided for the processing of diffractograms, in addition to
those which fit well in the process described earlier. Some facilities for the analysis of
electron micrograph data are also present. Furthermore, application programming
interfaces for general image processing allow for flexibility as necessary.
2.7.2 Fourier Space Operations
Fourier transforms are the basis of many other useful functions. The autocorrelation
function has peaks where the image repeats itself, which is useful in the analysis of
electron micrographs of single amyloid fibrils to look for repeat distances. Likewise,
the power spectrum, which is the intensity of the Fourier transform, is also used to
look for repeats. Often, the logarithm of power spectrum is more useful, owing to the
large range of intensities. Convolution can be calculated rapidly in Fourier space and
is employed in many aspects of electron micrograph processing including removal of
the background and the contrast transfer function. A Gaussian convolution filter
averages out local noise and can be used to calculate the low frequency components
of an image.
2.7.3 Determining the Repeat Distance from Micrographs
Repeat distances, in electron micrographs of fibres, can be established by calculating
the power spectrum of the micrograph. In the case of A (11-25) fibrils, only a repeat
at 4.7 Å is clear and no low-resolution information is visible. An alternative strategy
was devised based on single particle averaging techniques (Serpell and Smith 2000)
and then extended. The fibril image was first straightened, then regions of the fibril
were boxed, the boxes aligned and the aligned boxes averaged. This resulting average
was stored and the process repeated for boxes of different lengths. If the length of a
box corresponded to the repeat distance, then the average image for that length should
have been clearer than for all the other lengths. In order to be objective, some measure
of the visibility of the fibril was required. A variety of different methods were tested
and the standard deviation of the image was found to give the best measure of the
visibility. A graph of the results (Figure 2.14) showed peaks every 4.7 Å
Chapter 2. Application for the Structural Analysis of Amyloid

87
corresponding to the distance between -strands (the Measured Fibril) curve; the steps
were due to the background statistics (the other curves). Unfortunately no peak was
substantially larger than the others, so better visibility measurements and
straightening algorithms are required.
0
2
4
6
8
10
12
14
0 50 100 150 200 250
Length of Box (Å)
V
i
s
i
b
i
l
i
t
y

(
A
r
b
i
t
r
a
r
y

U
n
i
t
s
)
Theoretical Background
Measured Fibril
Measured Background

Figure 2.14. Graph relating visibility to length of box. In this case, visibility was defined as the
standard deviation of the image intensities. The statistics used for the theoretical background
were fitted to the measured fibril rather than the measured background. Screenshot shows
averaged images; the striations in some images have greater contrast.
Chapter 2. Application for the Structural Analysis of Amyloid

88
2.7.4 General Features
It is useful to be able to compare diffractograms; therefore crop, resize and rotation
transforms are required. Salt rings can prove a distraction, so there is the ability to
replace a specified annulus with the mean of its surrounding pixels. Horizontal and
vertical traces are used to obtain one-dimensional graphs of equatorial and meridional
reflections of fibre diffraction patterns. They are included in the diffractogram
centring component and the analysis of power spectra. Averaging the quadrants of a
fibre diffractogram reduces noise and the averaged quadrant can be inset into another
diffractogram for a visual comparison. The quadrants are symmetrical in the case that
the tilt angle is zero, Friedel’s law is obeyed and the fibre axis is horizontal or
vertical. Layers are useful when comparing diffractograms taken from different
samples. Images are given different colours and the layers superimposed as if they
were slides on top of one another; thus enabling two images to be viewed
simultaneously and the relative positions of spots compared (Figure 2.15).
Chapter 2. Application for the Structural Analysis of Amyloid

89

Figure 2.15. The two images on the bottom left and right are added together to give the
superposition shown in the upper display. The colouring of the images is determined by the
positions of the coloured sliders in the centre of the window.
2.7.5 PDB Display and Manipulation
The goal is to determine the structure of the amyloid macromolecule and this
necessarily involves PDB files. Therefore, facilities are provided to open and display
these files. The Jmol application was modified, so that it acts as a component within
the application purely for molecular visualisation. Detailed editing of PDB files is
best done using modelling applications such as Insight II (Accelrys); however it is
helpful to include some operations. Renumbering is necessary, after manual or
automated editing of the PDB, to ensure all atoms are numbered correctly. Building a
fibre structure is helpful when visualising a result. It is necessary to fill the unit cell
using the asymmetric unit and the space group, prior to diffraction simulation, using
equipoint transformations to generate the other symmetry related objects.
Chapter 2. Application for the Structural Analysis of Amyloid

90
2.7.6 Image Mathematics
Many functions are provided, mostly as public methods, rather than being exposed
through the user interface. Simple arithmetic is based on wrappers around the JAI
Library (Sun Microsystems) with corrections for bugs, such as handling complex
arithmetic correctly. Histograms and their standard deviations are useful in
understanding the statistics of the image. False colour applied to images such as
diffractograms gives a larger range of contrast than black to white and makes features
clearer.
2.8 Discussion
2.8.1 Comparison of Clearer with Other Programs
The purpose of our application is to facilitate and accelerate structural studies of
amyloid. As such, it complements those programs already used for amyloid fibre
diffraction analysis. Applications are offered by two of the collaborative computing
projects CCP4 and CCP13 and elsewhere. Outside of these projects, Fit2d (A.
Hammersley, ESRF) is the most prominent example. It is capable of one and two
dimensional data analysis, including powder and fibre diffraction and for the
calibration and correction of detector distortions.
CCP4 is the standard suite of programs for protein crystallography. Whilst they are
not specifically targeted at fibre diffraction studies, many of the programs have
proved useful; Mosflm was employed for the initial survey in the studies described in
Chapters 3 and 4.
CCP13 is a collection of separate programs written specifically for the analysis of
data from fibre diffraction. The programs share a common file format (BSL) and are
widely used for processing diffraction data from macromolecules and muscle tissue.
Some of them are now being rewritten in C# (Microsoft) and Java with a more unified
user interface. Linked Atom Least Squares (LALS) (Okada et al. 2003) is a CCP13
program for structure refinement. Atoms are constrained in such a way that the correct
intramolecular and intermolecular contacts are enforced and non-crystallographic
Chapter 2. Application for the Structural Analysis of Amyloid

91
repeat geometry is maintained. The model is then refined to reduce the error between
experimental and calculated fibre diffraction intensities. The method was successfully
developed as for analysing X-ray diffraction data from -poly-1-alanine (Arnott and
Wonacott 1966; Arnott et al. 1969). FX-PLOR is a patch (Denny et al. 1997), which
allows some versions of X-PLOR (Brunger et al. 1987) to be used with fibre
diffraction data. Hence, the facilities offered by X-PLOR, such as simulated annealing
and energy minimisation can be used for fibre structures.
Cerius2 (Accelrys) offers a very wide range of facilities for general simulation and
modelling. It was used for much of the early work on fibrous nanocrystals formed
from the peptide with sequence KFFEAAAKKFEE (AAAK) (Makin et al. 2005)
(Chapter 4). Much of Clearer was designed to offer improvements on Cerius2, whilst
still using other aspects of the program. Clearer’s fibre diffraction simulations offer
more detailed images both in terms of pixel size and number of pixels. The study of
amyloid nanocrystal structure also benefited from automated model building,
although Cerius does have a proprietary scripting language. Furthermore, Clearer is
available on all major operating systems. There is less apparent complexity whilst
maintaining a high degree of flexibility; including allowing a free choice of beam
direction, fibre axis and crystallite orientation, without the requirement for laborious,
complicated workarounds. Non-true fibres can be simulated and sets of parameters are
easily loaded and saved. Tests with new users showed that Clearer is relatively easy to
learn. Careful note was taken of user feedback and improvements have been
forthcoming. These include the simulation program having everything accessible from
a single summary window and the overall program not requiring any parameters or
input file formats to be learnt. Additionally, Clearer was designed specifically for
amyloid, including the use of sensible defaults, which are less likely to need
adjustment.
2.8.2 Application Use
Clearer has proved to be useful throughout our studies of amyloid structure. For IAPP
amyloid fibrils, both the electron and X-ray diffraction patterns benefited from
contrast enhancement. Equatorial and off-meridional signals not otherwise obvious
Chapter 2. Application for the Structural Analysis of Amyloid

92
were revealed. Radial averaging of the unprocessed images showed that these signals
were not artefacts due to the enhancement process. Examination of these averages
allowed their resolutions to be recorded and their nature to be analysed. Clues in the
shape of the peak helped determine whether any given peak was either single
reflection or some combination of many signals.
Fibrous nanocrystals (Chapter 4) were more highly oriented than IAPP (Chapter 3), so
the resulting X-ray and electron diffraction data is of higher quality. Whilst Mosflm
was used for the initial survey, Clearer’s radial averaging and peak finder allowed
reflection resolutions to be found efficiently and accurately. With this information, the
unit cell was determined using an earlier version of the unit cell search program. The
earlier version used the same grid search technique but had less flexibility and no user
interface. Using this program proved to be substantially faster than the manual
methods we employed during the development process.
Electron diffractograms from AAAK (Chapter 4) were made considerably clearer
using the contrast enhancement tool developed specifically for the patterns from this
peptide. We were then able to view the whole image, with even very faint spots made
visible and the background effectively eliminated.
Our simulation program was developed for AAAK to satisfy the particular
requirements of that study, including the simulation of hundreds of models. Cerius2
was used for the modelling itself and Discover for the molecular dynamics.
2.8.3 General Improvements
Our investigations have revealed several broad areas for further development.
Improvements are planned to each stage of the examination and to the overall
program.
General developments will each improve the user experience. In addition to
automating individual stages, the results from any single component may be fed into
the next. Once implemented, the application then mirrors the required workflow in
addition to processing each separate task. Less intervention from the user is required
Chapter 2. Application for the Structural Analysis of Amyloid

93
by default, only confirming steps, such as information from the peak finder being
automatically fed into the unit cell determination program.
Documentation is time consuming to produce and dates rapidly but is nonetheless
essential. As Clearer matures it should become more substantial as there are less
major changes in individual components. In the same way, user interface design is
crucial so that “it just works”; testing should be more formalised, including user
feedback and bug filing.
Individual calculations can be further optimised for speed, both in terms of removing
bottlenecks and parallelising routines. The latter being essential as multicore
processors, multiprocessor machines and techniques such as simultaneous
multithreading increase in prevalence.
2.8.4 Specific Improvements
Angular deconvolution of the fibre diffraction pattern has proved to be nontrivial,
including difficulties with the point spread function. Modelling of the pattern, such as
that provided by LSQINT (CCP13), specifically for amyloid, including overlapping
layer lines might prove a more fruitful approach.
A version of the unit cell determination program with greater sophistication would
incorporate heuristics specific to amyloid. These rules would result in less user
understanding being required and results being obtained more rapidly. Once an
approximate unit cell is known, the background removal program can be improved,
involving back calculation of the spot positions. The regions containing the spot
positions can be blanked out and the low frequency background calculated, with the
missing regions filled in using bicubic interpolation.
Next, the model building process can be improved. Although much of this stage is
beyond the scope of this application, automated adjustment of rotamers, interfacing
with other programs and a more quantitative approach to model building should prove
fruitful.
Chapter 2. Application for the Structural Analysis of Amyloid

94
Finally, analysis of the equator of the X-ray fibre diffraction pattern has been
considered elsewhere (Kirschner et al. 1987; Inouye et al. 1993; Malinchik et al.
1998; Lu et al. 2003). These analyses were quite rudimentary since they used models
based on radial densities quite different to those of cylindrically averaged -sheets or
bundles thereof. Compelling results have been obtained for other structures, in the
cylindrically symmetric (Oster and Riley 1952), bundles of cylinders (Burge 1959)
and general cases (Burge 1963). Building more complex models and then improving
them using methods such as simulated annealing may reveal much about the number
of protofilaments and their arrangements.
2.9 Conclusion
Our application comprises a series of programs for the analysis of diffraction data
from amyloid and some general image processing. Component programs are provided
for each stage of the analysis process. Each program was developed in parallel with
the studies discussed in the other chapters. This concurrency ensured that each
component was specifically targeted to aid in the examination of amyloid structure.
The application enabled much of the analysis of X-ray and electron fibre diffraction
data from amyloid formed from IAPP and was crucial in the examination of the
detailed structure of amyloid nanocrystals formed from AAAK.
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

95
3 Characterisation of Islet Amyloid Polypeptide Fibrils
3.1 Abstract
Amyloid formed from the islet amyloid polypeptide (IAPP) is found in the pancreatic
islets of 90 % of type II diabetes patients on post mortem. We have used negative
stain, platinum/carbon shadowing and cryo electron microscopy, in conjunction with
X-ray and electron diffraction. Synchrotron diffraction data from synthetic fibrils,
aligned using a stretch frame, shows a well-oriented diffraction pattern. This cross-
pattern is characteristic of amyloid and has discrete layer lines, which are clearly
visible at spacings of 4.7 Å. Electron diffraction reveals a very strong, sharp 4.7 Å
meridional reflection. The diffractogram was compared to a real space image obtained
by defocusing the diffraction beam, in order to show that the 4.7 Å signal is in the
same direction as the fibrils. A Fourier transform of a single fibre in the cryo-electron
micrograph also shows the 4.7 Å signal parallel to the fibril axis. Our evidence shows
that amyloid formed from IAPP has a structure built of laminated hydrogen-bonded -
sheets.
3.2 Introduction
IAPP is a 37-residue peptide, the deposition of which is associated with type 2
diabetes (Cooper et al. 1987; Hull et al. 2004). Approximately 100 years ago, post-
mortem studies found amyloid in the pancreatic islets of Langerhans (Opie 1901;
Weichselbaum and Stangl 1901). IAPP amyloid is deposited in 90 % of type 2 (non-
insulin dependent) diabetes cases in all ethnic groups (Westermark 1972; Clark et al.
1987; Clark et al. 1988; Westermark 1994; Kahn et al. 1999).
IAPP is normally cosecreted with insulin in beta cells (Clark et al. 1989; Sanke et al.
1991) and it may act as a hormone (Cooper et al. 1988). Whilst the peptide’s native,
monomeric structure is not known, its stable random coil structure in aqueous buffer
may indicate that the peptide is natively unfolded (Higham et al. 2000). IAPP is
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

96
formed by cleavage from pro-IAPP; it has an amidated C-terminus and a disulphide
bond between the cysteines at residues 2 and 7 (Goldsbury et al. 2000a).
Extracellular deposition of amyloid occurs between beta cells and islet capillaries.
Deposition in invaginations of the plasma membrane is likely to interfere with glucose
and hormone transport, insulin release and membrane signalling. The cytotoxicity of
the deposits (Lorenzo et al. 1994) may explain how amyloid formation and the
resulting death of beta cells results in the reduction of islet function observed in type 2
diabetes (Johnson et al. 1989; Clark et al. 1996; Butler et al. 2003).
Apple-green birefringence, characteristic of amyloid, is observed in ex vivo IAPP
fibril deposits after staining with Congo red and viewed between crossed polarisers
(Puchtler et al. 1961; Charge et al. 1995; Hull et al. 2004). In vitro fibril formation
proceeds via a process of nucleation and seeding (Kayed et al. 1999) and the kinetics
of this have been studied using a variety of truncated peptides (Westermark et al.
1990; Charge et al. 1995; Nilsson and Raleigh 1999).
Certain residues and groups of residues have particular importance for
amyloidogenesis (Moriarty and Raleigh 1999; Azriel and Gazit 2001). Whilst human,
cat, racoon, degu and macaque IAPP all form amyloid in vivo; rat, mouse, guinea pig
and hamster IAPP does not form fibrils, either in vivo or in vitro. Comparisons
between the structure and amyloid fibril-forming activity of truncated versions of the
peptides suggested that residues 20-29 were likely to be of importance to the
amyloidogenic properties of the molecule (Green et al. 2003). Amino acid residues
20-29 of the human IAPP molecule (SNNFGAILSS) have been suggested to be a
primary amyloidogenic domain (Westermark et al. 1990). Comparison to hamster
IAPP revealed a high degree of sequence divergence in this region. Investigation of
this region in cat IAPP found that the fragment formed amyloid and residues 25 and
26 are particularly important to amyloid formation (Betsholtz et al. 1990). Rat IAPP
differs from the human form by six residues in the central region between residues 18
and 29. Substitution of single residues by corresponding residues from the human
sequence allowed limited amyloidogenesis in three cases (R18H, L23F, V26I); multi-
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

97
residue substitution ensured a higher rate of amyloid formation (Green et al. 2003).
Residues 22-27 are also likely to be of importance owing to the region’s
amyloidogenic potential. An alanine scan of this region found that substitution of the
phenylalanine residue prevented amyloid formation (Azriel and Gazit 2001). These
conclusions are supported by a proline scan of the 20-29 residues. Substitution at any
of these locations inhibited fibril formation, with residues 22, 24 and 26-28 having the
most significant effect (Moriarty and Raleigh 1999). Additionally, IAPP (23-27),
IAPP (20-29) and IAPP (22-27) fibrils are toxic to pancreatic cells, unlike the soluble
forms (Tenidis et al. 2000).
The central region is not unique in its amyloidogenic potential; many other 5 to 20
residue fragments form amyloid, including IAPP (15-19) and IAPP (14-18)
pentapeptides (Mazor et al. 2002; Scrocchi et al. 2003). Other examples include the C
terminal region IAPP (30-37) (Nilsson and Raleigh 1999) and IAPP (8-20) (Jaikaran
et al. 2001). The role of each part of the sequence in the self-assembly process is not
fully understood; fibrils formed from truncated IAPP may have different
morphologies possibly modulated by the N-terminal region (Goldsbury et al. 1997;
Goldsbury et al. 2000a; Jaikaran et al. 2001). Fibrils formed in vitro from the full-
length peptide are therefore more likely to have the same morphology as in vivo
material than those formed from IAPP fragments. We have characterised the
molecular structure of these fibrils. Our study demonstrates that IAPP shares the same
cross- structural organisation assigned to other amyloid fibrils. X-ray diffraction
reveals the -sheet structure of bulk fibrils, whilst electron diffraction allows analysis
of the highly ordered, molecular arrangement of small bundles of fibres. Negative
stain and platinum/carbon shadowing shows the diversity and morphology of fibrils.
Cryo-electron micrographs enable the structure of single fibrils formed from full-
length IAPP to be examined.
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

98
3.3 Methods
3.3.1 Peptide and Incubation
IAPP (1-37) with the sequence NH
3
+-KCNTATCATQ RLANFLVHSS
NNFGAILSST NVGSNTY-NH
2
was purchased from Peninsula Laboratories (St.
Helens, UK) and the lyophilised powder dissolved in filtered water to a concentration
of 20 mg/ml. The stock solution was incubated at room temperature until required.
3.3.2 Electron Microscopy
The stock solution was diluted to 0.1 mg/ml in filtered water. A drop of solution was
placed on a 400 mesh copper pioloform (TAAB) carbon-coated, glow-discharged
grid. The grid was blotted and washed twice with filtered water. The grid was then
stained twice with 4 µl of 2 % uranyl acetate, blotted and left to dry, before being
examined with a Philips 208 electron microscope.
The stock solution diluted to 50 µg/ml in 25 % glycerol and water was sprayed onto
freshly cleaved mica and left to dry. This sample was platinum coated using 2 mm
platinum wire and then carbon coated using an Edwards coater. Replicas were floated
off onto 400 mesh copper grids and the platinum/carbon shadowed result examined
with a Philips 208 electron microscope operating at 80 kV.
3.3.3 Cryo Electron Microscopy
The solution was diluted to a concentration of 12.5 µg/ml using 22 µm filtered milliQ
distilled water. Holey carbon cryo-electron microscopy grids were prepared using 400
mesh copper grids (TAAB) and glow discharged for one minute. The solution was
applied onto the carbon coated, charged side of the grid, carefully blotted from the
underside and directly plunged into liquid ethane, cooled using liquid nitrogen. Grids
were stored in liquid nitrogen (Unwin 1995; Serpell and Smith 2000).
Frozen grids were examined using a Hitachi 2000 microscope operated at 200 kV
using a low dose mode and Gatan cryo stage at 103 K. Images were recorded on
Kodak film at 60 000 times magnification, with a defocus range between 6000 and
18 000 Å.
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

99
Micrographs were digitised using a Zeiss digitiser. Regions of interest were selected
from digitised images and Fourier transforms calculated using Ximdisp (Smith 1999).
The contrast transfer function was calculated from an amorphous region of the
micrograph using the MRC image-processing suite (Crowther et al. 1996). Defocus
correction was applied by filtering the measured intensity by the contrast transfer
function in Fourier space.
3.3.4 Electron Diffraction
20 mg/ml solution was placed on holey carbon grids and plunged into liquid ethane as
for the cryo-EM (Serpell and Smith 2000). The Hitachi 2000 microscope in low dose
mode was switched from imaging to diffraction mode. Diffractograms were recorded
on Kodak film, camera length 1.6 m. The ice was then allowed to sublime overnight,
leaving dehydrated fibrils, which were then examined in the same way.
Micrographs were digitised with a pixel size of 7 µm using a Zeiss digitiser. The
resulting image data was examined using Ximdisp.
3.3.5 X-ray Diffraction
The fibrils were aligned using a stretch frame as described in Chapter 1, Section 1.7.2.
A 10 mg/ml droplet of solution was placed between two waxed capillary tubes and
allowed to dry at room temperature. During drying, the distance between capillary
tubes was slowly increased (Sunde et al. 1997). Patterns were collected using a
synchrotron beam (ESRF BL4 ID2.2) with a wavelength of 0.9515 Å on a
Marresearch image plate. A second set of diffractograms was recorded in-house using
a Rigaku rotating anode, CuK X-ray source on a 345 mm Marresearch image plate.
The maximum sample to detector distance was 400 mm.
Diffraction patterns were examined using Mosflm (A. Leslie, Cambridge) run on a
Linux workstation and the resolutions of reflections noted.
All experimental data was provided by Dr L. Serpell.
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

100
3.4 Results
3.4.1 Negative Stain Electron Microscopy
Negative stain electron microscopy reveals fibrils approximately 100 Å in diameter.
They are long and unbranching, with a large radius of curvature (Figure 3.1). Their
morphology is similar to fibrils formed from synthetic truncated IAPP (Jaikaran et al.
2001). Polymorphic structures were observed, with species varying in both width and
shape. Some were smooth and others constructed of twisted filaments. One area of the
micrograph appeared to show a sheet of equally-spaced parallel filaments emerging
from the end of a fibril, with the appearance that the fibril was built from the curled
up sheet.
100 nm


Figure 3.1. Negative stain electron micrograph of IAPP amyloid fibrils. The insets show
magnified, higher-contrast regions of the image. Twisted fibrils with a repeat distance of 500 to
2000 Å show that the fibrils may be formed from protofilaments.
3.4.2 Platinum/Carbon Shadowed Electron Microscopy
Narrow filaments, with a minimum diameter of 50 Å, are seen on the same
micrograph as thicker fibres, with a width between 100 and 150 Å (Figure 3.2).
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

101
Fibrils appear slightly wider than with negative stain or cryo-electron microscopy,
owing to the shadowing. Whilst the narrow filaments were uniformly very smooth,
some of the thicker fibrils appear to be composed of two filaments coiled about one
another to form a helical structure. The pitch appeared to vary between 250 and
2000 Å. These thin, smooth filaments may be protofilaments. The measured diameters
are commensurate with previous studies based on negative stain and metal shadowing
electron microscopy (Goldsbury et al. 1997; Goldsbury et al. 2000a).
100 nm

Figure 3.2. Platinum/carbon shadowed electron micrograph of mature IAPP amyloid fibrils.
3.4.3 Cryo Electron Microscopy
Cryo-electron microscopy allows direct visualisation of single fibrils. The micrograph
is generated from the fibril itself, since there is no stain and therefore less probability
of distortion. Fibrils are closer to physiological conditions since they are frozen,
hydrated in vitreous ice. This is the same technique as previously applied to A (11-
25). That study revealed striations 4.7 Å apart corresponding to the spacing between
-strands (Serpell and Smith 2000).
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

102
We observe fairly straight, long, smooth, unbranching fibrils 45 to 50 Å diameter. The
morphology is similar to amyloid formed from truncated IAPP, A (11-25) and other
peptides. Regions of interest each containing a single straight section of a fibril were
selected, padded and floated in a box filled with mean intensity and then the Fourier
transform calculated (Crowther et al. 1996) (Figure 3.3). A strong 4.7 Å along the
direction of the fibril is prominent in the transformed images. Thicker fibrils are seen
to be composed of several protofilaments. In this case, a Fourier transform shows the
4.7 Å meridional and an equatorial at approximately 10 Å, corresponding to the -
sheet spacing. The absence of a 10 Å reflection in regions containing narrow
filaments is most likely due to small amount of ordered material within the beam
diameter since a single fibril contains only a few -sheets.
Contrast transfer function correction was applied to the region of the micrograph with
the best Fourier transform. This contained a fibril with a diameter of 45 Å. The
defocus (7500 Å) was calculated from the power spectrum of the amorphous carbon
surrounding the fibril. The micrograph was corrected by assuming the weak object
scattering approximation and dividing the Fourier transform of the region by the
calculated contrast transfer function. This corrected image gives a strong layer line at
4.7 Å. Although striations are not visible in the real space micrograph, the presence of
a layer line reveals that there is a repeating unit along the length of the fibril.
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

103

Figure 3.3. Cryo-electron micrographs of IAPP fibrils are shown on the left. In the centre is a
magnified region of micrograph containing a single fibril. The right hand image shows the
intensity of the Fourier transform of the centre image after boxing and floating. The arrow
indicates the 4.7 Å signal. The apparent layer line at approximately 15 Å was not observed in any
other transform or diffractogram.
3.4.4 Electron Diffraction
Low-resolution microscopy shows the field of view to be full of densely packed
fibrils with a clear preferred orientation (Figure 3.4 e). Electron diffraction of this area
shows a sharp arc in the same direction as the fibrils (Figure 3.4 a). Defocusing the
diffraction beam allows the diffraction region to be imaged (Figure 3.4 d & e). This
confirms that the 4.7 Å reflection is in the same direction as the fibrils.
Dehydrated fibrils have sharper reflections and higher orders (2.4 and 1.6 Å) with
greater intensities than the hydrated sample (Figure 3.4 b). This implies a larger order
parameter, owing to reduced Debye thermal broadening (Bonart et al. 1963).
Contrast enhancement and circular background subtraction reveal previously
unobserved, extremely faint reflections (Figure 3.4 c). Although standard contrast
stretches, combined with sufficient patience, would also have allowed individual
signals’ resolutions to be determined, this technique allows the complete
diffractogram to be examined. Reflection d-spacings were measured using peak
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

104
profiling (detailed in Chapter 2) of the image after background removal (Table 3.1).
The off-meridional reflections at 3.8 and 2 Å are hence revealed. These are
constituents of layer lines consistent with those measured using X-ray diffraction.
Unfortunately, the 9.5 Å equatorial reflection was not seen, since it would be inside
the saturated beam centre. Nevertheless, two other equatorials are observed at 5 and
2.8 Å.
Table 3.1. Electron diffraction signal spacings
Direction d-spacing (Å)
Meridional 4.7 2.4 1.6
Off meridional 3.8 2
Equatorial 4.8-5.2 (diffuse) 2.8
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

105
4.7 Å


1.6 Å


2.4 Å


2.8 Å


~5 Å


3.8 Å


2 Å
4.7 Å

4.7 Å

a

b

c

d

e


Figure 3.4. Electron diffraction patterns before and after dehydration (a & b). The diffractogram
from dehydrated fibrils has sharper reflections and higher order meridional reflections are
visible. Real space images show their corresponding fibril directions (d & e). The contrast-
enhanced version of b is shown in c, with off meridional and equatorial reflections now visible.
3.4.5 X-ray Diffraction
X-ray diffraction patterns show an oriented structure with discrete layer lines (Figure
3.5). Although layer lines may be seen in diffraction patterns from amyloid formed
from truncated peptides, they are rare in those taken from fibrils formed from full-
length precursors, since the bundles of fibrils are often too disordered (Inouye et al.
1993; Sunde et al. 1997).
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

106
The synchrotron pattern has the classic cross- structure with a sharp 4.7 Å reflection
on the meridian and a diffuse reflection equatorial at 9.5 Å. Although much of the
diffractogram appears similar to that of A (11-25) (Sikorski et al. 2003), there is no
evidence of a 9.4 Å layer line associated with an antiparallel structure. The 4.7 Å
corresponds to the interstrand spacing of -strands in a -sheet, whilst the 9.5 Å on
the equator represents the spacing between the -sheets. All the equatorials are very
diffuse, making accurate measurement difficult. It was therefore necessary to develop
methods to improve the contrast of the diffractograms including background removal,
contrast enhancement and peak profiling. The resulting d-spacings are listed in Table
3.2. Some peaks appear to be composed of series of overlapping peaks, as is indicated
from the shape of the signal. In-house small angle data down to 40 Å reveals two
further diffuse equatorial reflections at around 23 and 38 Å.
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

107

2.4 Å

4.7 Å

3.4 & 3.7 Å

4.2 Å

9.5 Å

9.5 Å

38 Å

~5 Å

1.9 & 2.3 Å


Figure 3.5. Wide angle (top) and small angle (bottom) synchrotron X-ray fibre diffraction
patterns from stretch frame aligned IAPP amyloid fibrils. Layer lines are clearly visible with a
spacing of 4.7 Å but not of 9.4 Å.
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

108
Table 3.2. X-ray diffraction signal spacings
d-spacing
(Å)
Intensity
(%)
Description
4.7 100 Sharp, meridional
2.37 9 Sharp, meridional
4.2 < 4 Diffuse, off meridional
3.7 2 Diffuse, off meridional
3.4 < 4 Diffuse, off meridional
2.25 5 Diffuse, off meridional
1.9 4 Diffuse, off meridional
38-40 < 4 Very diffuse, equatorial, low angle
20-23 < 4 Very diffuse, equatorial, low angle
15 19 Very diffuse, equatorial
11.2 < 4 Very diffuse, weak, equatorial
9.5 25 Diffuse, equatorial
4.8-5.3 18 Diffuse, equatorial
2 3 Background sample
3.4.6 Structural Interpretation
A combination of data from X-ray and electron diffraction and Fourier transforms of
cryo-electron micrographs has demonstrated that amyloid formed from IAPP has a
cross- core structure. The distinct layer lines observed in the electron diffraction
patterns and cryo-electron microscopy Fourier transforms are perpendicular to fibre
axis from ED and clearly demonstrate that -strands spaced 4.7 Å apart run
perpendicular to the fibre axis.
Analysis of the tables of reflections allows a likely unit cell to be inferred. The layer
line spacing gives one unit cell dimension as 4.7 Å in the direction of the fibre.
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

109
Equatorial indexing is difficult, owing to a limited number of diffuse reflections. Each
equatorial may be the result of overlapping peaks, which have not been individually
resolved. There are similar difficulties with off-meridionals, which are even more
diffuse. The strong 9.5 Å equatorial probably corresponds to the distance between -
sheets. If the -sheets are mutually antiparallel, so that adjacent -strands are face-to-
face, then we expect a cell dimension of 19 Å. This fits many equatorials and off-
meridionals. The lamellar repeat is the distance corresponding to length of peptide
chain in extended -conformation before -turn. This is likely to be a multiple of half
of 6.9 Å, which is the distance between every other -carbon in an extended -strand.
If there are 10 residues between turns, then the repeat is 34.5 Å; alternatively if there
are 11 residues, then the cell length is 38 Å. We therefore propose that the unit cell
may be orthorhombic with a = 4.7 Å, b = 19 Å, c = 38 Å. In this case, with a unit cell
length of 38 Å, each protofilament is composed of four -sheets. If the -sheet
stacking distance is 9.5 Å, then this is commensurate with the diameter of narrow
filaments observed in the negative stain and cryo electron micrographs.
3.5 Discussion
3.5.1 General Fibril Morphology
Amyloid formed from synthetic IAPP has a variety of morphologies. Studies have
examined the overall structure and analysed the differing arrangements of the
protofilaments that constitute the fibril (Goldsbury et al. 1997). Micrographs show
that the most common morphology is two intertwined filaments with an average
diameter of 80 Å. These are formed by the left-handed coiling of protofilaments and
have an axial crossover repeat distance of 250 Å. Species with more than two
filaments form either twisted structures or ribbons. The twisted structures are thicker
versions of the intertwined protofilaments with a cable-like appearance and a variety
of diameters. The ribbons are formed from the laterally associated protofilaments.
Our negative-stain electron microscopy results are consistent with these
measurements. However our cryo-electron microscopy shows single fibres with a
width of 50 Å. We therefore wish to know whether these narrow filaments are indeed
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

110
protofilaments or an aberration due to absence of stain. In cryo-electron microscopy,
the fibres are fixed in vitreous ice and the observed structure may be the ordered,
densely packed core. Cryo-electron micrographs often have low contrast; hence, any
less ordered region in the structure may be lost amongst the amorphous material
surrounding it. The same observation has also been made in studies of paired helical
filaments (Berriman et al. 2003).
STEM measurements of the mass per unit length give a value of 1.0 kDa/Å
(Goldsbury et al. 1997). Each -strand has a width of 4.7 Å, with the result that the
mass per strand width is 4.7 kDa. IAPP monomers have a molecular mass of 3.9 kDa;
therefore there are 1.2 monomers per strand width. Our data suggests that a
protofilament is composed of four laminated -sheets, giving 0.3 monomers in each
strand. This implies that the IAPP molecule is extended over three -strands and is
also commensurate with the protofilament width.
3.5.2 Understanding of Structure Derived from Diffraction Data
The cross- diffraction pattern is as expected for amyloid and of similar appearance to
those patterns reported in other studies (Inouye et al. 1993). Discrete, off-meridional
signals are clearly visible on layer lines, due to high orientational order in the sample.
Diffuse equatorials are observed implying a low coherence length, a relatively small
number of -sheets in each fibril and that the arrangement of fibrils with respect to
one another is disordered.
The proposed unit cell results imply a structure constructed from laterally associated,
hydrogen-bonded -strands, which form four -sheets. Each sheet is separated by
9.5 Å (half the b dimension), which is sufficient to allow the side-chains to pack
without overlapping. The 19 Å repeat implies that the -sheets are mutually
antiparallel. Further, detailed modelling of the structure and its side-chains is
impractical since the reflections are diffuse in the equatorial direction to the point of
overlapping. Additionally, the angular disorder results in more overlapping of closely
spaced signals.
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

111
The X-ray and electron diffraction patterns both show layer lines at 4.7 Å. Neither a
signal at 9.4 Å, nor any other evidence of a layer line at this resolution is apparent. If
such a layer line was present, then the -strands must be in an antiparallel
arrangement. Unfortunately, its absence does not directly imply a parallel
arrangement of strands within the -sheet. Antiparallel strands have a 2
1
symmetry,
which results in systematic absences. Furthermore, the specific arrangement of strands
may extinguish the whole layer line or render it sufficiently weak as to be invisible in
our experiments. A mixture of parallel and antiparallel strands is also possible but
would break the crystallographic symmetry. Whilst the -sheets themselves may be
parallel, the turn may be between sheets, in the manner suggested in models built for
A (1-40) (Petkova et al. 2002) and -synuclein (Der-Sarkissian et al. 2003), based
on SSNMR and SDSL, respectively. Although SSNMR data shows that IAPP (20-29)
fibrils are antiparallel (Griffiths et al. 1995), meridional profiles of X-ray fibre
diffractograms show no evidence of a 9.4 Å layer line (Sunde et al. 1997). Evidence
of antiparallel orientation from such a short peptide may not necessarily imply that
full-length IAPP should be the same. Whilst SSNMR studies of both A (10-35) and
full-length A both show a parallel structure (Benzinger et al. 1998; Antzutkin et al.
2000; Benzinger et al. 2000; Antzutkin et al. 2002; Balbach et al. 2002; Petkova et al.
2002; Antzutkin et al. 2003), SSNMR and X-ray diffraction studies on A (11-25)
found an antiparallel structure (Sikorski et al. 2003; Petkova et al. 2004). A structure
formed from parallel, extended -strands would have a diameter of 128 Å, far larger
than that observed in the electron microscope.
3.5.3 Hypothetical Modelling
Full-length IAPP has three fibrillogenic regions, each of which is independently
capable of adopting a -sheet conformation and forming fibrils in vitro. IAPP (20-29)
is the most studied intrinsically amyloidogenic region (Glenner et al. 1988;
Westermark et al. 1990; Ashburn et al. 1993; Griffiths et al. 1995). IAPP (30-37) also
forms amyloid fibrils (Nilsson and Raleigh 1999), as does IAPP (8-20) (Jaikaran et al.
2001). Thus the full-length peptide has three -strands, allowing both intramolecular
and intermolecular hydrogen bonding. These interactions may result in a folding
process that may be significantly more complex than that expected for other
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

112
amyloidogenic proteins (Griffiths et al. 1995; Serpell et al. 1997; Sunde et al. 1997).
Modelling of this process suggests that the peptide may fold into an “e” shape, with
both parallel and antiparallel arrangement of chains (Jaikaran and Clark 2001). The
three regions form the dense core of the protofilament, with an unfolded N-terminal
region forming the tail of the “e”. The C-terminus is sandwiched between the other
two strands. Such a shape requires two turns, a tight -turn and wider curved region to
accommodate a greater radius of curvature. The role of the C-terminus has been
examined using an intrinsic fluorescent probe (Padrick and Miranker 2001). Spectral,
quenching and anisotropic properties of the final tyrosine indicated that the C-
terminus is extremely rigid and well packed. The presence of a fluorescence resonant
energy transfer pathway confirms that residue 37 is within approximately 11 Å of the
phenylalanines at residues 15 and 23. If the turns are in residues 17 to 19 and 28 to 29,
then the extended -strand region covers approximately 10 residues. The distance
between corresponding -carbons is 6.9 Å, implying a strand length of approximately
35 Å.
The three-strand model is commensurate with the STEM mass per unit length data
showing 1.2 monomers per strand width (4.7 Å), if there are four -sheets per
protofilament (Goldsbury et al. 1997). A layer line at 9.4 Å is not expected since there
is no symmetric plane at this interval, the appropriate width of the true unit cell being
3 or 6 times 4.7 Å. This model has the hydrogen-bonded -strands perpendicular to
the fibre axis necessary to fit the characteristic cross- X-ray and electron diffraction
patterns. Four -sheets is consistent with the unit cell dimensions which require an
even number of sheets, in order to have a whole number of cells in a filament. Both
the width and length of such an arrangement is accommodated if the protofilaments
are 40 to 50 Å in diameter. Although the data is commensurate with the model, its
quality is insufficient for a firm confirmation or disproof of the hypothesis.
3.5.4 Conclusion
Mature amyloid fibrils formed from full-length IAPP have been examined in detail.
We have successfully combined negative stain, platinum/carbon shadowed and cryo
electron microscopy with X-ray and electron diffraction to build a probable unit cell.
Chapter 3. Characterisation of Islet Amyloid Polypeptide Fibrils

113
This result complements data from previous studies, including scanning transmission
electron microscopy and provides new insight into existing models. The fibrils have a
stable, highly ordered core structure, characteristic of the generic amyloid structure.
This core is a series of laminated -sheet ribbons composed of ladders of tightly
packed, hydrogen-bonded -strands; protofilaments based on this core structure are
intertwined to form mature amyloid fibrils.

Chapter 4. Molecular Basis for Fibril Formation and Stability

114
4 Molecular Basis for Fibril Formation and Stability
4.1 Abstract
Amyloid fibrils are highly ordered aggregates, although sufficiently disordered to be
generally considered non-crystalline. Considerable effort has been expended to
increase the order parameter, to improve the diffraction patterns. We have produced
amyloid crystals, formed from a twelve-residue sequence-designed peptide. Electron
microscopy reveals that these microcrystalline structures are composed of nanofibres.
X-ray and electron diffractograms show diffraction to beyond 1 Å. This has allowed
us to determine a detailed structure for amyloid. The structure has a P2
1
2
1
2
1
space
group in which antiparallel -sheets are arranged in a cross- manner, which is
characteristic of amyloid. Detailed modelling reveals the side-chain packing and thus
the importance of bonding between aromatic side-chains. Component -strands are
zipped together by stacks of intermeshed aromatic rings, which in conjunction with
salt bridges between pairs of charged residues, increase the stability of the structure.
These controlling interactions are commensurate with other authors’ work and are
likely to be of importance in understanding the self-assembly and stability of amyloid.
4.2 Introduction
We examined a twelve-residue designed peptide with sequence KFFEAAAKKFFE,
henceforth referred to AAAK (Hosia et al. 2004). This sequence is near palindromic
and is composed of a four-residue motif (KFFE) at each end, with a hydrophobic
central region (AAAK), designed to prevent -turn formation. The designed peptide
features many motifs found in amyloid precursors associated with the amyloidoses
(Table 4.1). The phenylalanine pair is found in A and AA, which are associated with
Alzheimer’s disease and secondary systemic amyloidosis, respectively. The AAA and
AAAxK motifs are both present in -synuclein (Parkinson’s disease). Although
amyloidogenic peptides do not share a common primary structure, they have a high
concentration of aromatic residues. These have been found to be important in the self-
assembly process of both amyloid (Gazit 2002b) and protein in general (Claessens
Chapter 4. Molecular Basis for Fibril Formation and Stability

115
and Stoddart 1997; Gillard et al. 1997). Hence the structure determined herein offers
substantial insight into the generic amyloid structure.
Our peptide forms amyloid fibrils organised into three-dimensional fibrous
nanocrystals. This high degree of order has enabled the collection of high-resolution
X-ray and electron diffraction data. Thus, it has been possible to determine the fibril
structure, including the orientation of -strands and obtain a detailed visualisation of
highly intermeshed side-chain arrangement.

Table 4.1. Similarities between the designed peptide and disease precursors.
Precursor Peptide Relevant Sequence Associated Syndrome
AAAK KFFEAAAKKFFE None
AA SFFSFLGEAFD Chronic inflammation amyloidosis
A KLVFFAE Alzheimer's disease
-synuclein
AAAxK, AAA and
AYEMPSEEGYQDYE
Parkinson's disease

2
-microglobulin DWSFYLLYYTEFT Dialysis related amyloidosis
ABri FAIRHF and FENKFAV British dementia
Calcitonin DFNKFT Medullary thyroid carcinoma
Gelsolin SFNNGDCCFILD Finnish inflammation amyloidosis
IAPP NFGAIL and NFLVHS Type II diabetes
Lactadherin NFGSVQFV Aortic medial amyloid
PrP
PQGGYQQYN and
VAGAAAAGAV
Creutzfeldt-Jakob disease
Chapter 4. Molecular Basis for Fibril Formation and Stability

116
4.3 Methods
4.3.1 Peptide and Incubation
The peptide, with sequence KFFEAAAKKFFE, was purchased from Interactiva
(Darmstadt, Germany) and purified by reversed-phase, high-pressure, liquid
chromatography using a C18 column and a linear gradient water/acetonitrile
supplemented with 0.1 % trifluoroacetic acid. The sample’s identity was verified
using electrospray ionisation mass spectrometry (Tjernberg et al. 2002; Hosia et al.
2004) and was provided by Dr J. Johansson. Amyloidogenesis was achieved by
incubation at 37 °C with shaking at 3 mM concentration in 50 mM phosphate buffer,
pH 7.0 for 7 days.
4.3.2 Electron Microscopy
The incubated solution, diluted (1:10), was examined by transmission electron
microscopy. 4 µl aliquots were placed on carbon-coated, glow-discharged, copper
grids (400 mesh, TAAB) and excess solution withdrawn after 30 s. Grids were
washed with 4 µl filtered (200 nm) water and negatively stained with 2 % (w/v)
uranyl acetate. The stained grids were examined using a Philips 208 microscope,
operated at 80 kV.
4.3.3 Electron Diffraction
Grids previously prepared for electron microscopy were examined using a Philips
EM400T microscope by electron diffraction. A grid was platinum coated and used for
calibration. Electron diffraction patterns were observed at an operating voltage of
100 kV and camera lengths of 295 to 2300 mm. Patterns were recorded on Kodak film
and real space images of the sampled areas examined. Films were scanned using an
Epson digitiser.
Electron diffraction patterns were analysed and processed using the Clearer image-
processing suite as described in Chapter 2. The background was removed and the
contrast enhanced.
Chapter 4. Molecular Basis for Fibril Formation and Stability

117
4.3.4 X-ray Diffraction
Fibres were partially aligned using a stretch frame (Serpell et al. 1999; Makin and
Serpell 2005) and a cryo-loop. The cryo-loop (Hampton) (radius 0.25 mm) was
dipped in the sample of fibrous material. This formed a film, which was allowed to
dry, resulting in a thin mat of fibrous material at many orientations within the two-
dimensional plane of the loop (Chapter 1, Section 1.7.4).
Data collection was carried out in-house using a Rigaku rotating anode, CuK X-ray
source and Marresearch image plate and at ESRF, France using a synchrotron beam
(BL4, ID2, wavelength = 0.99 Å). Images at several specimen-to-film distances were
collected.
Diffraction patterns were examined using Mosflm (A. Leslie, LMB Cambridge) run
on a Linux workstation and the d-spacings of reflections noted (Table 4.2). The
diffractogram was further processed using the Clearer image-processing suite
described earlier. The circularly symmetric background was removed using statistical
analysis of circular annuli. Peak positions were measured using Clearer’s peak finder
component, which examines radially-averaged circular sectors.
4.3.5 Structural Determination
The unit cell was determined using the d-spacings of signals measured from X-ray
diffraction patterns, which were then indexed. A grid search of possible orthorhombic
cells confirmed the result. Initial values were obtained using constraints from the
dimensions of the peptide and knowledge of the electron diffraction pattern. The unit
cell dimensions imply four chains. We built the model by first considering a single
chain, then an antiparallel pair and finally two pairs of chains. The initial single chain
in an idealised -conformation was built using Insight II (Accelrys) run on an SGI
workstation. All other manual refinement of the model used Cerius 2 (Accelrys).
Chapter 4. Molecular Basis for Fibril Formation and Stability

118
4.4 Results
4.4.1 Electron Microscopy
Fibrous nanocrystals were revealed by electron microscopy (Figure 4.1). The crystals
were observed to have a diameter of 12 nm to 240 nm and a high aspect ratio. Higher
magnification images showed the crystals to be composed of packed fibrils running in
the same direction as the crystals. These fibres were marked by faint striations parallel
to the fibre axis. The distance between striations was measured as 50 Å by integration
along the fibre axis. The striations may correspond to protofilaments since they are
similar to measurements made on other fibrils (Sikorski et al. 2003).
1 m

100 nm


Figure 4.1. Negative stain electron micrographs of AAAK amyloid. The left hand image shows
fibrous nanocrystals at low magnification. The fibrous content of the nanocrystals is shown on
the right, with striations spaced 50 Å apart parallel to the fibre axis.
4.4.2 X-ray Fibre Diffraction
High-resolution diffraction was observed to beyond 2 Å (Figure 4.2). The
characteristic cross- pattern, with a weak 4.7 Å meridional, showed equatorial
reflections substantially sharper than usually expected of amyloid. This may be due to
increased order between -sheets. Low angle data recorded down to 100 Å showed no
Chapter 4. Molecular Basis for Fibril Formation and Stability

119
observable signals at resolutions lower than 24 Å (data not shown, collected by Prof
E. Atkins).
4.76 Å

10.7 Å

24.4 Å

Fibre axis


Figure 4.2. X-ray fibre diffraction pattern from amyloid nanocrystals using synchrotron
radiation.
4.4.3 Electron Diffraction
Electron diffraction showed reflections beyond 1 Å (Figure 4.3). Layer lines were
observed at 9.5 Å and row lines at 6.9 Å. Defocusing the beam allowed the direct
image to be viewed and the observation made that the 4.7 Å reflections were along the
direction of the fibre. Tilting the sample did not reveal any other spots. No 10 to
11 Å reflection was observed owing to the crystal orientation. In conjunction with X-
ray diffraction, this pattern allowed the structure to be solved.
Electron diffraction involves dynamic and kinematic scattering and the film’s
response to electron flux density is not linear. This makes quantitative analysis of spot
intensities difficult. A more detailed model would have required significant collection
Chapter 4. Molecular Basis for Fibril Formation and Stability

120
of extra data, including obtaining many sections through reciprocal space, by means
of tilted crystals.
4.76 Å

6.9 Å

c
*


a
*


Fibre axis



Figure 4.3. Electron diffraction pattern from the fibrous nanocrystals showing diffraction out to
0.9 Å. Electron beam is parallel to the [0 1 0] zone axis. Right hand image is the contrast
enhanced version.
4.4.4 Indexing
The unit cell was determined based on the sharp X-ray diffraction reflections,
information from the electron diffractogram and the dimensions of the peptide chains.
An orthorhombic cell was found with a = 9.52 Å, b = 21.3 Å, c = 48.1 Å and a
P2
1
2
1
2
1
space group; where a is the fibre axis and hydrogen bonding direction, b the
-sheet chain stacking direction and c the chain direction. This is as expected for an
antiparallel cross- structure.
The normal to the specimen surface and the [0 1 0] zone axis are both parallel to the
electron beam direction; allowing us to conclude that b is orthogonal to the ac plane
and therefore the lattice vectors are mutually perpendicular. The strong meridional
Chapter 4. Molecular Basis for Fibril Formation and Stability

121
4.76 Å signal corresponds to the spacing between -strands; whilst the layer line in
the electron diffractogram at 9.52 Å implies an antiparallel arrangement and gives the
a unit cell dimension. A 9.3 Å meridional X-ray reflection is also present; the 9.52 Å
[1 0 0] signal is not expected or observed since this is a systematic absence if the
structure is antiparallel cross-. On the equator, the strong signal at 10.7 Å is the
spacing between -sheets, indexed to b = 21.3 Å. Even layer lines are observed to be
much stronger than their odd counterparts. These relative intensities can only be
achieved by having more than one pair of -strands in the unit cell and confirms the
-sheet spacing. A twelve-residue, extended -strand measures approximately
6.9 × 12 ÷ 2 = 42 Å. The lowest angle reflection is observed at 24 Å. Semi-automated
fitting and search in conjunction with modelling found c equal to 48 Å; many possible
unit cells could be eliminated since they would cause substantial clashing between
side-chains.
The space group was found by modelling; nevertheless certain signals are
conspicuously absent in both the X-ray and electron diffraction data. No meridional at
9.52 Å [1 0 0] is observed or any other reflections of the form [2n+1 0 0]. On the
equator, neither 21.3 Å [0 1 0] nor 48 Å [0 0 1] (low angle data) are observed. This is
suggestive of a P2
1
2
1
2
1
space group, which has systematic absences [h 0 0] [0 k 0]
[0 0 1] h, k, l = 2n. Comparison of the expected resolutions calculated using the above
unit cell and space group, and empirical values shows a strong fit (Table 4.2).
Chapter 4. Molecular Basis for Fibril Formation and Stability

122
Table 4.2. Strong agreement is shown between observed and predicted resolutions. Wide-angle
reflections are omitted, owing to indexing becoming trivial at high resolution.
Miller Indices
Measured d-spacing
(Å)
h k l
Predicted d-spacing
(Å)
24.43 0 0 2 24.06
19.94 0 1 1 19.49
13.27 0 1 3 12.82
10.66 0 2 0 10.66
9.33 1 0 1 9.34
8.69 1 1 0 8.70
7.93 0 2 4 7.98
7.19 0 2 5 7.14
6.13 1 0 6 6.14
5.65 1 3 1 5.66
5.33 0 4 0 5.33
4.91 1 3 5 4.90
4.76 2 0 0 4.76
4.66 1 0 1 4.65
4.37 1 3 7 4.38
4.00 0 0 12 4.01
3.91 1 1 11 3.91
3.79 1 5 3 3.78
4.4.5 Modelling
Modelling taking several months attempted to replicate the electron diffraction by
manually adjusting combinations of the strands and adjusting the side-chains. The
Chapter 4. Molecular Basis for Fibril Formation and Stability

123
presence of a 9.5 Å layer line in the electron diffraction data shows that the peptides
are in an antiparallel conformation. The electron diffraction patterns confirm that the
cell is orthorhombic; the a and c axes are clearly orthogonal, whilst the direction of b
is perpendicular to this plane. The strong, highly detailed pattern would only be
observed if the electron beam was parallel to that zone axis. The X-ray data implies a
chain stacking distance of 21.3 Å, indicating that there must be another pair of chains
in the unit cell. The orientation of this pair of chains can be determined from the
electron diffraction pattern in conjunction with stereochemical constraints.
The aromatic rings are heavily constrained by each other. Rings only fit side by side if
they are twisted, the angle of that twist being suggested by a large peak in the 9.5 Å
layer line. Each pair of adjacent phenylalanine residues has the same torsion angle,
which is equal and opposite to that of the pair at the opposite end of the peptide. There
is an apparent degeneracy in that it was not possible to determine the difference in the
electron diffraction pattern if all the aromatic rings were twisted by additional
radians; indeed, it is conceivable that two species of fibre exist. By extension of this
principle, the other side-chains have the same orientation as the phenylalanine groups
in that half of the chain. We concluded that the only possible rotation of the second
pair of chains with respect to the first was a rotation by about the a-axis. Only
rotation about the a-axis gave good intermeshing and the correct relative intensity
between odd and even layer lines. In this case the 9.5 Å layer line completely
disappears so an additional translation in the a-c plane is required to reintroduce it. In
the c direction, translations must be in units of 6.9 Å, which is the distance between
adjacent, -carbon atoms. This is difficult, since there is now no partner for free ends;
interleaving the chains results in a wide ribbon and reduces aromatic interactions;
alternatively a sequential slip between chains gives a non-orthorhombic unit cell and
the 9.5 Å layer line is no longer orthogonal to the fibre axis. Hence, the translation
must be in the a-direction. A slip by 4.7/2 = 2.4 Å eliminates all 2 0 x layer lines,
whilst 4.7/4 = 1.2 Å gives approximately the correct relative intensity of odd and even
layer lines.
Chapter 4. Molecular Basis for Fibril Formation and Stability

124
Unfortunately this approach failed since it was unable to replicate the experimental X-
ray pattern and whilst the simulated electron pattern had many features of the
experimental image, it was not convincing. Manual modelling had proved to be both
slow and ineffective, so a semi automated approach was developed.
Appropriate rotamers in a single chain were selected to avoid side-chain overlap.
Next, a pair of antiparallel chains was considered. Phenylalanine side-chains were
necessarily closely interlocked since the width of a benzene ring is greater than the
distance between the -strands in a -sheet. Careful attention was therefore required
to select the optimum set of phenylalanine rotamers.
Each phenylalanine has four possible rotamers; in a pair of chains there are eight
phenylalanine residues. This gives a total of 4
8
= 65 536 permutations. The aromatic
residues are concentrated into two blocks at either end of the chain. The blocks do not
interact and therefore they can be considered separately. Of the four residues in each
block, two are above the chain and two below, hence only 16 permutations need be
considered. The -strands exist in a periodic structure, hence the analysis must take
account of interactions from both sides. Models were built for each case and
examined both by inspection and clash score using Molprobity (Lovell et al. 2003).
The constraints resulted in only one permutation being reasonable. Once the correct
permutation had been determined, a pair of antiparallel chains could be modelled.
The whole cell contains two pairs of antiparallel chains 10.7 Å apart in the -sheet
stacking distance (b). We therefore wish to know the translation and rotation of the
second pair of chains relative to the first. Many models were built by hand and
diffraction patterns simulated using Cerius 2. This was very time consuming, so a
semi-automated approach was developed in which many hundreds of models were
built with many possible orientations and translations in the ac plane.
Stereochemically unlikely structures were eliminated by inspection. Simulated X-ray
and electron diffraction patterns were calculated using Clearer. These were compared
with experimental diffractograms (Figure 4.4); duplication of models ensured
consistency in evaluation. The absence of a 48 Å reflection in low-angle data
Chapter 4. Molecular Basis for Fibril Formation and Stability

125
eliminated many models owing to their shift along the chain direction. Short listed
candidates were judged on the basis of having the most signals in common with the
experimental diffractograms of the correct relative intensity and the least non-
observed signals. Only one candidate fit the criteria well, having the best similarity
between calculated and observed diffraction patterns (Figure 4.5). Side-chains were
oriented by energy minimisation in Cerius 2 and molecular dynamics in Discover
(Accelrys).

Figure 4.4. Comparison between simulated (top left) and observed fibre diffraction patterns for
an incorrect model. A 48 Å reflection is seen innermost on the equator and the 9.4 Å layer line is
far too strong.
Chapter 4. Molecular Basis for Fibril Formation and Stability

126

Figure 4.5. Comparison between observed and simulated X-ray diffraction patterns. The top left
hand quadrant shows the diffractogram calculated using the proposed model.
The final structure has a face-centred arrangement of chains with -strands
perpendicular to the fibre axis. Hydrogen-bonded, antiparallel chains are organised
into long -sheet ribbons, resembling previous structural models (Eanes and Glenner
1968; Sunde and Blake 1998; Jimenez et al. 1999; Sikorski et al. 2003). Chains in an
adjacent -sheet are shifted in the chain direction by half the unit cell direction (c/2)
with respect to one another. This gives the repeating model a brick-like appearance.
The fibril structure can be generated from the repeating single chain after application
of the space group’s equipoint transformations.
The brick-like organisation of chains leads to a banding pattern when the model is
viewed down the b axis. This may explain the striations seen in the micrographs of
Chapter 4. Molecular Basis for Fibril Formation and Stability

127
fibrils (Figure 4.1). There is sufficient room between the ends of the chains for
sodium or chloride ions, which have ionic radii of 0.95 Å and 1.7 Å respectively.
Amyloid formation and growth may be entropically driven due to the release of bound
water. The central hydrophobic region (AAAK) stabilises the extended -strand, thus
reducing the energy required for self-assembly.
Examination of the final structure shows that the -sheets are held together by side-
chain interactions (Figure 4.7). In each case, the N-terminus of any given chain is
surrounded by the C-termini of adjacent chains and vice versa. Aromatic interlocking
is a prominent feature, whilst avoiding aliphatic clashing. Aromatic rings between
strands in the -sheet are mutually parallel but displaced so that they are off centre.
Between sheets, the rings are in a T-shaped arrangement. Both are highly stable, with
parallel displaced being the preferred orientation (Figure 4.6) (Sun and Bernstein
1996; McGaughey et al. 1998). Pairs of lysine and glutamic acids alternate along the
structure, which may be responsible for the antiparallel orientation of strands. At
neutral pH, the peptide has a net charge of unity. A net charge of +1 or -1 has been
shown to be necessary for fibrogenesis from de novo hexapeptides (de la Paz and
Serrano 2004).



Figure 4.6. Parallel displaced (left) and T-shaped (right) orientations of aromatic rings are
particularly stable.
This stable, interlocked structure has intermeshed side-chains resulting in a highly
ordered organisation; thus ensuring the crystalline nature of the material and the high-
quality diffraction pattern.
Chapter 4. Molecular Basis for Fibril Formation and Stability

128













Figure 4.7. Proposed model for the structure of the amyloid nanocrystals. Insets containing more
than one strand are generated by the application of P2
1
2
1
2
1
symmetry. Chains are coloured by
either residue type or chain (Humphrey et al. 1996). (a) An extended single -strand with its
sequence, coloured by residue type (blue is basic, red is acidic and green is non-polar), viewed
down the a axis. (b) Four chains viewed down the b axis to show hydrogen bonding (light blue).
(c) Pair of chains, coloured by residue type; magnified region shows T-shaped aromatic
interaction between sheets. (d) Packing of chains within the crystals. Magnified region shows
both intersheet and interstrand interactions between phenylalanine side-chains. (e) Isosurface
representation of fibrillar structure, in which the fibre axis is vertical, showing close interlocking
of side-chains (Varshney et al. 1994). (f) Brick-like structure of crystal viewed down the a axis.
b
d
e
f
a
c
K F F E A A A K K F F E
Chapter 4. Molecular Basis for Fibril Formation and Stability

129
4.5 Discussion
4.5.1 The Role of Side-chains in Amyloid Formation and Structure
Phenylalanine residues stabilise the structure by - intersheet interactions (Figure
4.7). This is not surprising since aromatic residues have a critical role in the self-
assembly of amyloid from many disease related peptides (Table 4.1) (Gazit 2002b).
Investigations to understand the effects of charge attraction and -propensity on
tetrapeptides have demonstrated the importance of electrostatic interactions. They
showed that whilst the peptides KFFK and EFFE were not able to self-assemble, an
equimolar mixture and KFFE were both able to form amyloid (Tjernberg et al. 2002).
Hence, charge attraction is critical to amyloidogenesis.
Investigations into short truncated A peptides have demonstrated the importance of
the phenylalanine pair. A (17-21) with sequence LVFFA was shown to be of
particular significance in the process of plaque growth and maturation (Esler et al.
1996). Fibril assembly can be prevented by the addition of A (15-20) (QKLVFF),
which binds to A and appears to block further elongation. Similarly, A (17-21)
(LVFFA) also inhibited amyloid formation (Findeis et al. 1999). On this basis,
LPFFD is a -sheet breaker based on the A (17-21) template. Alanine substitution
shows that Lys16, Leu17, and Phe20 are all critical to inhibitory activity (Tjernberg et
al. 1996). Tests using a rat-brain cell model found it not only reduced fibril formation
but also disassembled preformed fibrils in vitro and prevented neuronal cell death
(Soto et al. 1998). An unbiased screen for variants of A with reduced
amyloidogenicity demonstrated the importance of Phe19 (Esler et al. 1996; Wurth et
al. 2002). Indeed, stacking of phenylalanine rings is observed in the X-ray structure of
A (11-25) (Sikorski et al. 2003).
Analogous experiments to those involving A used fragments of IAPP. IAPP (23-26)
(FGAIL), IAPP (15-19) (FLVHS) and IAPP (14-18) (NFLVH) are the shortest IAPP
fragments capable of forming amyloid (Azriel and Gazit 2001; Mazor et al. 2002).
Both IAPP (22-27) (NFGAIL) and IAPP (20–29) (SNNFGAILSS) also formed
amyloid and were cytotoxic, whilst GAIL remained soluble (Tenidis et al. 2000). An
alanine scan of NFGAIL showed that all substitutions could still form large
Chapter 4. Molecular Basis for Fibril Formation and Stability

130
multimeric assemblies with the exception of Phe23 (Azriel and Gazit 2001).
Molecular simulation of NFGAIL showed aromatic rings cementing the
macromolecular assemblies due to their aromatic chemical character and restricted
conformational flexibility (Zanuy and Nussinov 2003; Zanuy et al. 2004). This was
confirmed using near-ultraviolet CD spectra, recorded just before aggregates were
observed. It showed two positive bands at 265 and 285 nm, indicating that formation
of the conformational population just prior to fibril formation was associated with
aromatic interactions.
High concentrations of phenylalanine residues are present in other prominent
amyloidogenic fragments of disease related proteins. Examination of the human
calcitonin (hCT) fragments hCT (15-19), hCT (16-19), hCT (15-18) and hCT (15-17)
found that aromatic nature seemed to be the only common property of the various
very-short, amyloid-forming peptides (Reches et al. 2002). SSNMR revealed -
interactions in these fibrils (Naito et al. 2004). Similar interactions were postulated in
the case of lactadherin (Haggqvist et al. 1999) and AA has four phenylalanine
residues including a pair (Westermark et al. 1992).
Later studies of
2
-microglobulin fragments found no correlation between their
length, hydrophobicity, secondary structural propensity and ability to associate into
fibrils. In contrast, the presence of a relatively high content of aromatic side-chains
did correlate with amyloid formation, leading the authors to postulate that -
stacking was critical for amyloidogenesis (Jones et al. 2003). Sequences with a high
concentration of aromatic residues have also been found in PrP and Sup35.
Cumulatively, this evidence suggests that aromatic residues are likely to be critically
important in amyloidogenesis (Gazit 2002b).
Aromatic interactions are important in many areas of biology and chemistry (Gazit
2002b); Kevlar being a prominent example (McGaughey et al. 1998). Stacking of
aromatic rings provides stacking energy, order and directionality; thus driving and
stabilising structural assembly, whilst providing necessary selectivity. These non-
covalent interactions contribute to the packing of hydrophobic cores of protein, the
Chapter 4. Molecular Basis for Fibril Formation and Stability

131
formation of tertiary structure, host-guest interactions, porphyrin aggregation in
solution and DNA base packing (Waters 2002). The characteristic thermal stability of
thermophilic proteins is aided by aromatic clusters in a T-shaped, orthogonal-packing
geometry in comparisons with mesophilic homologues (Kannan and Vishveshwara
2000). Congo red forms micelles due to parallel stacking of the aromatic rings (Stopa
et al. 1997). Its interaction with the phenylalanine residues may explain how it
inhibits fibril formation from certain proteins including A (Klunk et al. 1989) and
IAPP (LeVine 1993).
Furthermore, aromatic interactions have been shown to be vital in many general self-
assembly processes (Claessens and Stoddart 1997; Gillard et al. 1997) and molecular
recognition (Shetty et al. 1996; McGaughey et al. 1998). Stable, well-ordered
nanotubes have been formed from assembly of diphenylalanine two-residue peptide,
with the order driven by aromatic interactions (Reches and Gazit 2003). Adjacent -
strands were aligned during the spontaneous molecular self-assembly process by
stacking to form polymeric tapes (Aggeli et al. 1997).
4.5.2 Conclusion
High-resolution diffraction patterns have, for the first time, enabled the determination
of the nanostructure of an amyloid fibril. Side-chain arrangements have been
revealed, allowing the detailed nature of the interactions between -sheets to be
visualised.
The structure is composed of -strands, laterally associated to form -sheet ribbons,
which layer on top of one another to form a three-dimensional lattice. Charge pairing
and a phenylalanine zipper provide stability. The staggered arrangement creates a
highly stable, crystalline structure with the capacity to extend in all three dimensions.
π-stacking supplies an energetic contribution (Hunter 1993), which may drive the
self-assembly process. Side-chain interactions result in specific directionality, order
and orientation leading to a highly ordered, stable, cross- structure, rather than
amorphous aggregate. Proteins have a unique side-chain arrangement that packs to
form the core of amyloid. Amyloidogenic protein appears to have many aromatic and
Chapter 4. Molecular Basis for Fibril Formation and Stability

132
charged residues. It is these specific side-chain interactions that control self-assembly,
its rate, the resulting order and therefore stability. This structure shows intersheet and
interstrand side-chain interactions and emphasises their significance for
amyloidogenesis and cohesion within the superstructure.
Our proposed structure for AAAK amyloid nanocrystals was derived by a process of
modelling. The modelling process used data from electron microscopy, electron
diffraction and X-ray fibre diffraction in conjunction with stereochemical constraints
to establish the most likely configuration. We were not able to determine the phases
of the structure factors experimentally, so uniqueness cannot be shown, as would be
the case in single-crystal X-ray crystallography. Comparison of experimental and
simulated fibre diffraction patterns shows good agreement at low resolutions;
however there are some differences at higher resolutions, showing that improvement
is possible. The orientation of aromatic rings is fixed owing to their width and the fact
that there are sixteen in a unit cell, making only one rotamer possible. The
arrangement of other side chains is largely unconstrained and the orientations shown
in the models are due to energy minimisation and molecular dynamics. Whilst this is
the best model tested, we cannot completely rule out the possibility of other models.

Chapter 5. Discussion

133
5 Discussion
5.1 Models of Amyloid Structure
5.1.1 Introduction
Many models have been proposed for the structure of amyloid. Most of these are
either tubular or laminated -sheets; the major exception being structures consisting
mainly of native structure (Inouye et al. 1998; Bousset et al. 2002; Serag et al. 2002).
Tubules can be built either from a cross- structure (Kirschner et al. 1987; Inouye et
al. 1993; Lu et al. 2003) or a single -sheet wrapped around a hollow core. In the
latter case, the shape can be either cylindrical, giving a nanotube or triangular
prismatic, resulting in a -helix (Lazo and Downing 1998; Perutz et al. 2002; Wetzel
2002; Wille et al. 2002; Kishimoto et al. 2004).
5.1.2 Largely Native Structures
A largely native structure does not explain amyloid formed from precursor proteins
without a high -sheet content but has been suggested in the cases of transthyretin and
Ure2p fibrils. There is some discussion as to whether Ure2p fibrils are amyloid. Some
studies implied a cross- core (Baxa et al. 2003), whilst others suggested a structure
based on interaction between monomers (Bousset et al. 2002). Disagreements could
be attributed to different conditions; since, after heating, a cross- structure was
postulated for Ure2p fibrils (Bousset et al. 2003).
Three transthyretin models have also been built in which the structure largely retains
its native structure. X-ray fibre diffraction reflection resolutions were measured and a
unit cell proposed that implied a structure composed of axially arrayed monomers
(Figure 5.2) (Inouye et al. 1998). Proximity information from site-directed spin-
labelling experiments lead to the suggestion of a head-to-head and tail-to-tail model
(Serag et al. 2002). In this model, the -sheets present in native transthyretin interact,
resulting in an infinite -sheet. The individual -sheets are able to interact owing to a
substantial conformational change, which moves the terminal -strand in native
transthyretin and thereby exposes the penultimate strand.
Chapter 5. Discussion

134
A crystal structure of a highly amyloidogenic triple-mutant of transthyretin revealed a
conformation in which there was a three-residue shift of one of the -strands. This
conformation, referred to as a -slip, creates a new packing arrangement in which the
molecules interact to form a double helical array of protein (Eneqvist et al. 2000).
Within the helix, a translation of 114.5 Å along the fibre axis results in superposition
of tetramers, similar to the meridional repeat of 115.5 Å found by fibre diffraction
(Blake and Serpell 1996). The diameter of the helix is 120 Å; close to the 130 Å
measured using electron microscopy (Serpell et al. 1995).
Largely native transthyretin structures (Figure 5.1) do not have simple -sheet
stacking. The diffraction pattern for such structures is likely to be significantly more
complex than that observed for transthyretin fibrils. Native transthyretin has two -
sheets, which are not parallel, so the -strands in the fibril cannot be perpendicular to
the fibre axis. Neither has any meridional signal with a d-spacing of 29 Å been
detected (Blake and Serpell 1996; Inouye et al. 1998).
The largely native models may explain the features of individual amyloid fibrils but
do not aid the understanding of amyloid in general. Amyloid forms from precursor
peptides without a common secondary structure; so, the relatively small
conformational changes proposed in these models do not explain how such disparate
precursors form structures with the shared characteristics described in Chapter 1.
Chapter 5. Discussion

135

Figure 5.1. Pair of transthyretin molecules (1BMZ) (Peterson et al. 1998). Two four-stranded -
sheets are present in each molecule forming a -sandwich (Blake et al. 1978).
Chapter 5. Discussion

136

Figure 5.2. Transthyretin amyloid fibrils; four protofilaments are composed of arrays of
monomers (Inouye et al. 1998).
5.1.3 Water-Filled Nanotube
Perutz’s model for amyloid formed from polyglutamine, was described as being a
water-filled nanotube with an internal radius of 6 Å and an external radius of 16 Å,
with 20 residues per turn (Figure 5.3). The number of residues per turn might explain
the dependence of Huntington’s disease on the number of glutamine repeats (Perutz
and Windle 2001). A nanotube is a particularly appealing structure, similar to carbon
75 Å
40 Å
29 Å
23 Å
Chapter 5. Discussion

137
nanotubes and thus elegant in both its simplicity and symmetry. Nevertheless
“elegance is for tailors” (Boltzmann) so careful note must be made of the
experimental data.
Recently, both the nanotube and -helix models have gained prominence, owing to
the observation of fibre diffraction patterns apparently without a 10 to 11 Å reflection.
Two possibilities were suggested for the existence of this signal in the case of A.
This distance could have represented the packing between twisted amyloid
protofilaments or the protofilaments could be modelled as being double or triple
walled nanotubes (Perutz et al. 2002). In the polyglutamine amyloid pattern, an 8.3 Å
signal was present in the same direction at the 4.7 Å signal. The movement of the
reflection from its expected place could be explained by the texture of the sample,
since the experiment used a mat rather than a bundle of fibres. The reflection is at a
higher resolution than is usually expected for the spacing between -sheets, owing to
the excellent packing made possible by the glutamine side-chains. Furthermore, the
observed diffraction pattern could be simulated using a conventional cross- model
(Sikorski and Atkins 2005).
A nanotube may not necessarily explain amyloid’s resistance to enzymatic
degradation, particularly for the larger radius models, which were also postulated.
Although glutamines are not themselves hydrophobic, much of the side-chain is
hydrophobic, suggesting that the tube may not be water filled.
Chapter 5. Discussion

138

Figure 5.3. Views of Perutz’s model of amyloid, down the fibre axis (left) and from the side
(right) (Perutz et al. 2002).
5.1.4 General -Helices
It has been suggested that the 10 to 11 Å reflection in the cross- pattern was merely
an artefact due to dehydration (Kishimoto et al. 2004) and that a -helix was a better
model (Jenkins and Pickersgill 2001; Wetzel 2002). -helices are present in globular
protein structure, including pectate lyase C and E (Yoder et al. 1993; Lietzke et al.
1994) and the tailspike protein of Salmonella typhimurium phage 22 (Steinbacher et
al. 1994). In addition, a left-handed, parallel -helix is present in the structure of
UDP-N-acetylglucosamine acyltransferase (Raetz and Roderick 1995).
A cylindrical antiparallel -helix, somewhat similar to Perutz’s model, with a radius
of 10 Å, was proposed for amyloid, formed from the peptide with sequence
KLKLKLELELELG (Lazo and Downing 1997). Modelling was based on X-ray fibre
diffraction, electron microscopy and particularly circular dichroism spectra, using
information derived from the CD spectrum of pectate lyase E (Sieber et al. 1995).
This antiparallel model was further postulated for amyloid fibrils formed from
transthyretin, A and immunoglobulin light chain (Figure 5.4) (Lazo and Downing
1998). A later study of the KLKLKLELELELG peptide using FTIR concluded that
the peptide did not form a parallel -helix and was more likely to be an extended -
strand (Khurana and Fink 2000).
Chapter 5. Discussion

139
-helices in globular proteins are not identical to those proposed as amyloid models
since the former are almost completely filled with inward-facing side-chains rather
than water. Additionally, these helices are composed of stretches of straight -strands
interspersed with sharp turns rich in glycine and proline residues, rather than a
continuous turn. Finally, amorphous aggregates of the P22 tail spike protein did not
show the same bands in circular dichroism spectra after staining with Congo red,
which were observed with amyloid fibrils; perhaps suggesting structural differences
between the -helix and amyloid (Khurana et al. 2001).
Electron crystallography of scrapie prion fragments resulted in an averaged electron
density calculated using a p3 symmetry operation on a lattice of hexagonal units
(Wille et al. 2002). Projection maps of oligomers, presumed to be protofilaments and
thus cross-sections of amyloid fibrils were calculated. Calculation of the maps used a
model based on six left-handed parallel -helices per hexagon. These projections were
then compared with the averaged image. Only models containing -helices were said
to be capable of satisfying the electron density constraints.
A -helix has also been proposed for full-length A amyloid based on hydrogen
deuterium exchange studies and a proline scan (Kheterpal et al. 2000; Wetzel 2002;
Kheterpal et al. 2003a; Kheterpal et al. 2003b; Williams et al. 2004). The exchange
data shows that hydrogen bonding is present along substantial lengths of the peptide
chain. In globular protein, -sheets are composed of exchange protected regions six to
eight residues in length, interspersed with shorter, unprotected regions. Hence the -
sheets in amyloid fibrils are either very wide or form close-to-ideal -helices.
NMR data is inconclusive, owing to the limitations on the length scales it is capable
of measuring. However a -helix built from parallel in-register -strands would have a
seam running down the fibril. If such a -helix collapsed, then the structure would be
very similar to the conventional cross- arrangement (Petkova et al. 2002). It is also
difficult to see how a three-sided -helix could fit in the electron density
reconstructions obtained for SH3. No evidence for a -helical model was obtained for
the IAPP fibrils and the AAAK structure is very different to that of a -helix.
Chapter 5. Discussion

140

Figure 5.4. The antiparallel -helix is composed of -strands running antiparallel to one another;
side-chains emerge from the core structure (Lazo and Downing 1998).
5.1.5 Cross- Tubule
Studies which reported a cross- tubular structure were generally based on analyses of
the equatorial region of X-ray diffraction patterns. Amyloid fibrils formed from a
series of short A fragments were modelled using a tube made of 5-6 crystallites, in
which each crystallite was made of less than six -sheets (Inouye et al. 1993). In some
versions of this model, the crystallites appeared to be organised like the spokes of a
wheel, so a tubule may not necessarily be the best description.
An earlier study on amyloid, formed from A (1-28), hypothesised that the fibrils
were hollow tubular structures with a mean radius of 43 Å. The data could also have
been modelled as a pair of cross- walls, 71 Å apart (Kirschner et al. 1987). The
values were obtained by calculating transforms of step function models and
comparing them to a graph of the equator of X-ray diffraction pattern. Both these
studies also proposed more conventional cross- models.
Examination of the signals of the equator of X-ray diffraction pattern and subsequent
modelling concluded that the A (1-40) amyloid fibrils were composed of 3 to 5
protofilaments. Each protofilament was a 30 Å wide tubule with a wall composed of
tilted -strands (Figure 5.4) (Malinchik et al. 1998).
Small angle X-ray and neutron scattering in combination with circular dichroism,
atomic force microscopy and electron microscopy on A (16-22) amyloid found only
hollow cylindrical particles fit the data. The proposed structure had a radius of 260 Å
with walls 40 Å thick. It was composed of laminated -sheets wrapped around a
hollow core with a pitch of 2140 Å (Lu et al. 2003). It is not known whether some of
Chapter 5. Discussion

141
these results may also be explained by considering protofilaments twisting about an
electrolucent core.
Each of these studies only considered a quite limited ensemble of possible models.
The selection of initial models to be tested and optimised appears to have greatly
influenced the results in each case. It may be that a wider choice of starting models
and more flexible adjustment of them would result in models similar to those
postulated using other techniques.

Figure 5.5. Possible structure of A (1-40) in which four double walled, tubular protofilaments
constitute the fibril (Malinchik et al. 1998).
5.1.6 Conventional Cross- Structure
The vast majority of studies have proposed conventional cross- structures (see Table
5.1 and Table 5.2), although there is substantial diversity between models. The first
major amyloid model was of transthyretin fibrils (Blake and Serpell 1996) and later
extended to amyloid in general (Sunde et al. 1997). Some models have parallel and
others antiparallel organisations of -strands, with increasing amphiphilicity shown to
change the alignment from antiparallel to parallel (Gordon et al. 2004). Full-length
A and A (10-35) both have hydrophobic regions, which are not distributed
symmetrically about the centre of the peptide (residues 17 to 21 and 29 to 40). A
parallel, in-register model will juxtapose these hydrophobic regions; unfortunately, it
will also juxtapose charged residues, which will require counter ions or interactions
between -sheets to overcome the unfavourable electrostatic interactions. In contrast,
A (16-22) and A (34-42) both have central hydrophobic regions, so antiparallel
Chapter 5. Discussion

142
extended -strands will both juxtapose the hydrophobic regions and minimise the
electrostatic energy. Both the suggested IAPP fibril model (Chapter 3) (Makin and
Serpell 2004b) and AAAK nanocrystal structure (Chapter 4) (Makin et al. 2005) fitted
well into the cross- paradigm and appeared clearly to exclude the other models.
Of particular interest is the nature of any twist in the fibril and its constituent
protofilaments (Figure 5.6). The -sheets within the protofilament may twist at the
same rate as the protofilaments twist about themselves, resulting in a twist of a few
degrees per strand (as found for insulin fibrils (Jimenez et al. 2002)). Alternatively,
the rates may be very different, which was proposed as a common core structure for
amyloid fibrils, with a twist of approximately 15° per stand (Sunde et al. 1997). The
key difference between these models is as to whether there is a region of the
protofilament that does not interact with any other protofilament. In the first case, the
cross-section rotates as a rigid unit along the helical structure; so all packing contacts
remain the same. This allows interacting regions to be in contact with one another
along the length of the fibril. By the same logic, non-interacting regions, including
large loops and folded domains, outside the cross- core do not interfere with the
packing of protofilaments. The AAAK model does not feature any twist, owing to the
absence of any evidence in the diffraction or micrographic data. This may be due to
the helical repeat distance being sufficiently large for the corresponding reflection to
be lower than that of the beamstop; alternatively the curvature in the -sheet may
limit the size of the nanocrystals (Diaz-Avalos et al. 2003a).
Many questions remain to be fully answered, at all levels of structural detail.
1. Which segments of the sequence form -strands? Is there any non- secondary
structure? If so, where and why?
2. What is the supramolecular organisation of -sheets? Strands may be mutually
parallel, antiparallel or perhaps some mixture of the two, which may or may
not be regular. What factors, including sequence, determine this organisation?
3. Are the -sheets laminated and how do the sheets interact with one another?
Chapter 5. Discussion

143
4. Why do fibrils stop growing in diameter?
5. What causes the conformational change leading to amyloidogenesis?
6. Do the -sheets form any sort of tubular structure? If so, where are the bends
along the chain?
7. Does amyloid have a well-defined backbone and side-chain organisation or is
the translational order of the peptide backbone only approximate?
8. Is the disorder static or dynamic?
9. How can the structure be used to find how and why fibrils are formed and can
we interfere with this process? Which intermolecular and intramolecular
interactions control the stability of the fibre?
10. How do specific amyloid structures relate to amyloid structure in general?
Which aspects of the amyloid structure are sequence specific?
11. How does amyloidogenesis relate to the overall phenomenon of protein
misfolding?
12. How do the structures of the native or oligomeric precursors relate to the
mature fibril?
Chapter 5. Discussion

144
a b c

Figure 5.6. (a) Model of insulin fibril, comprising four protofilaments coloured red, green, orange
and cyan, each containing a pair of -sheets. The transparent surface represents the
experimental EM density. (b) Model showing packing of a pair of protofilaments, the interacting
region of the protofilament is coloured purple. The protofilament twist matches that of the fibril
itself, so the interacting region remains in the core of the fibril. (c) Supercoiled protofilaments;
there is no correlation between the protofilament and fibril twist and the interacting region
rotates about the protofilament. Similar models may be constructed for other numbers of
protofilaments. (Jimenez et al. 2002) (Copyright 2002 National Academy of Sciences, U.S.A., used
with permission.)
Chapter 5. Discussion

145
Table 5.1. Summary of models postulated for the structure of amyloid using methods other than nuclear magnetic resonance.
Model Type of Amyloid Techniques Reference
86 Å diameter tubule or 71 Å apart walls of
cross- sheets.
A (1-28), A (18-28), A (18-28) mutant SAXS; XD; TEM
(Kirschner et al.
1987)
Antiparallel -strands A (34-42) TEM; FTIR; XD
(Halverson et al.
1990)
6 protofilaments Paired helical filaments
TEM
(reconstruction)
(Crowther 1991)
Antiparallel -strands A (6-25) A (22-35), A (1-38), A (1-40) XD; TEM
(Fraser et al.
1991a)
Antiparallel -strands
A (1-28), A (19-28), A (17-28), A (15-
28), A (13-28), A (11-28), A (9-28)
XD; TEM; FTIR
(Fraser et al.
1991b)
Antiparallel -strands, -turn between Ser-26
and Gly-29
A (10-43)
TEM; FTIR; CD;
Protease digestion
(Hilbich et al.
1991)
Cross- A (1-40) and mutants TEM; FTIR; XD
(Fraser et al.
1992b)
Cross-
A (11-28), A (13-28), A (15-28),
A (11-25)
TEM; XD
(Fraser et al.
1992a)
Chapter 5. Discussion

146
Model Type of Amyloid Techniques Reference
Hollow cylinder of 5-6 -crystallites, each of
~5 -sheets with ~6 residue strands
A (19-28), A (13-28), A (12-28),
A (11-28), A (9-28), A (1-28),
A (1-38), A (1-40), A (6-25),
A (11-25), A (34-42)
XD
(Inouye et al. 1993)

Antiparallel -strands A (11-25) and mutants FTIR; XD; TEM (Fraser et al. 1994)
Polar zipper Polyglutamine CD; TEM; XD (Perutz et al. 1994)
Cross-, twisted -strands, 115.5 Å period TTR XD (Blake 1995)
Cross- PrP (113-120), PrP (109-122), PrP (90-145) XD
(Nguyen et al.
1995)
Four protofilaments, in square array TTR
TEM
(cross-sections)
(Serpell et al. 1995)
Cross-, twisted -strands, 115.5 Å period TTR XD
(Blake and Serpell
1996)
Quarter staggered -sheets A (11-28), H1 XD
(Inouye and
Kirschner 1996)
Cross- with residual helical and disordered
fold
Lysozyme FTIR; HDX (Booth et al. 1997)
Chapter 5. Discussion

147
Model Type of Amyloid Techniques Reference
Twisted, probably not cylindrical
protofilaments, polymorphic
IAPP TEM; STEM
(Goldsbury et al.
1997)
Cross-, twisted -strands, 115.5 Å period
TTR variants, IgLC, IAPP (29-29), AA,
lysozyme variant
XD (Sunde et al. 1997)
Greek key motif with antiparallel C-termini
-strands
A (1-42) Model
(Chaney et al.
1998)
Axially-arrayed, native monomers TTR XD (Inouye et al. 1998)
Cross- Eleven-residue N-termini of apoSAA family XD; TEM
(Kirschner et al.
1998)
Protofilaments are antiparallel -helices, A
-turn between Val-24 and Asn-27
TTR, A, IgLC Model
(Lazo and Downing
1998)
Antiparallel -strands A (1-42) Model (Mager 1998)
3-5, twisted, tubular protofilaments, ~460 Å
period
A (1-40) XD; TEM
(Malinchik et al.
1998)
Beaded structure, ~210 Å period A (1-40) AFM
(Blackley et al.
1999)
Antiparallel -strands, -turn between
Gly-25 and Lys-28
A (1-43)
Model; Monte
Carlo simulations
(George and
Howlett 1999)
Chapter 5. Discussion

148
Model Type of Amyloid Techniques Reference
Double helix of 2 protofilaments, -strand
unclear, antiparallel shown
SH3
Cryo-EM
(reconstruction)
(Jimenez et al.
1999)
Antiparallel -strands, -turn between
Gly-25 and Lys-28
A (12-42)
Model; Molecular
dynamics
(Li et al. 1999)
-hairpin or compact random coil Polyglutamine Model
(Starikov et al.
1999)
Antiparallel -strands, -turn between Ile-32
and Gly-37
A (14-23), A (14-42) Model
(Tjernberg et al.
1999)
Regular association of thin filaments (TTR),
four protofilaments with left handed twist
TTR (10-19), lysozyme, SH3 AFM
(Chamberlain et al.
2000)
Antiparallel -strands with twisted
protofilaments
-synuclein
TEM; AFM; CD;
FTIR
(Conway et al.
2000a)
Twisted protofilaments IAPP AFM; STEM
(Goldsbury et al.
2000a)
Polymorphic assemblies of twisted
protofilaments
A (1-40) TEM; STEM
(Goldsbury et al.
2000b)
Not all of sequence is hydrogen bonded A (1-40) HDX (MS)
(Kheterpal et al.
2000)
Chapter 5. Discussion

149
Model Type of Amyloid Techniques Reference
Not parallel -helix, probably extended
-sheet
KLKLKLELELELG and
ELELELELELELG
FTIR
(Khurana and Fink
2000)
Cylinder or tube of -sheets, strands are in
exact register
A (11-25) Cryo-EM
(Serpell and Smith
2000)
5 to 6 protofilaments
AA, IgLC, variant apolipoprotein A-I,
variant lysozyme
Single particle EM
(Serpell et al.
2000b)
Parallel -strands Sup35 fragment XD
(Balbirnie et al.
2001)
N-terminal region not in -sheet network A (1-40) Proteolysis
(Kheterpal et al.
2001)
Parallel -strands SH3 FTIR (Zurdo et al. 2001)
Largely native structure Ure2p
AFM; FTIR;
Binding
(Bousset et al.
2002)
Most residues form rigid -sheet core
2
-microglobulin HDX (NMR)
(Hoshino et al.
2002)
Helical cross- protofilaments Insulin
Cryo-EM
(reconstruction)
(Jimenez et al.
2002)
Parallel, in-register -strands, ~1200 Å
period
A (10-35)
Molecular
dynamics; TEM
(Lakdawala et al.
2002)
Chapter 5. Discussion

150
Model Type of Amyloid Techniques Reference
Parallel -strands with substantial
fluctuations about a central core
A (10-35)
Model; Molecular
dynamics
(Morgan et al.
2002b)
Water-filled nanotube Polyglutamine XD; TEM (Perutz et al. 2002)
Mostly native, head to head, tail to tail
arrangement
TTR SDSL (Serag et al. 2002)
In-register, parallel -strands A (1-40) SDSL (Torok et al. 2002)
Parallel -helix Amyloid in general Model (Wetzel 2002)
Left-handed parallel -helix Scrapie prion fragments
Electron
crystallography
(Wille et al. 2002)
Cross- core Ure2p
Digestion;
Cryo-EM, STEM;
MS
(Baxa et al. 2003)
Antiparallel -strands, reverse turn A (31-35) XD; EM (Bond et al. 2003)
Various cross- models, unit cell found,
P2
1
2
1
2
1

GNNQQNY nanocrystals ED; Powder XD
(Diaz-Avalos et al.
2003a)
Staggered cross- Prion related XD
(Inouye and
Kirschner 2003)
Chapter 5. Discussion

151
Model Type of Amyloid Techniques Reference
Coiled tube of cross- structure A (16-22)
SANS; SAXS; CD;
AFM; TEM
(Lu et al. 2003)
Antiparallel, monoclinic cross- A (11-25) XD
(Sikorski et al.
2003)
C-terminus 30 % protected, N-terminus 50 %
protected
A (1-40) HDX (MS) (Wang et al. 2003)
Largely native structure – fibrils are not
amyloid
Ure2p
CR; Proteolysis
(MS, TEM,
microsequencing)
(Bousset et al.
2004)
Left-handed parallel -helix A (15-36) Model (Guo et al. 2004)
-helix (nanotube) Sup35 XD
(Kishimoto et al.
2004)
Cross- IAPP XD; ED; TEM
(Makin and Serpell
2004b)
Parallel -helix A (1-40) Proline scan
(Williams et al.
2004)
80 % of residues form distinct core
2
-microglobulin HDX (NMR)
(Yamaguchi et al.
2004)
Antiparallel Cross- KFFEAAAKKFFE XD; ED; TEM (Makin et al. 2005)
Chapter 5. Discussion

152
Table 5.2. Models of amyloid fibrils derived from solid-state nuclear magnetic resonance data.
Model Type of Amyloid Techniques Reference
Not classic -sheet, possible cis linkage between 37
and 38
A (34-42) RR NMR (Spencer et al. 1991)
Antiparallel -strands A (26-40) A (26-43) NMR; FTIR (Jarrett et al. 1994)
Highly pleated -sheet, may be parallel IAPP (20-29) RR NMR (Griffiths et al. 1995)
Pleated antiparallel -strands A (34-42) RR NMR; FTIR (Lansbury et al. 1995)
Extended, primarily -sheet like
Hamster prion H1
(109-122)
RR NMR (Heller et al. 1996)
Not classic -sheet, trans linkage between 37 and 38 A (34-42) Static echo RR NMR (Costa et al. 1997)
Antiparallel -helix KLKLKLELELELG
13
C MAS NMR; EM; CD
(Lazo and Downing
1997)
Parallel, in-register -strands A (10-35) DRAWS NMR (Benzinger et al. 1998)
Parallel, in-register -strands A (10-35) DRAWS NMR (Gregory et al. 1998)
Parallel, in-register -strands A (1-40) MQNMR; STEM (Antzutkin et al. 2000)
Antiparallel -strands A (16-22) MQMNR, REDOR NMR (Balbach et al. 2000)
Parallel, in-register -strands, no evidence for a turn A (10-35) DRAWS NMR (Benzinger et al. 2000)
Chapter 5. Discussion

153
Model Type of Amyloid Techniques Reference
Parallel all -sheets twisting along fibre axis A (10-35)
DRAWS NMR; EM;
SANS
(Burkoth et al. 2000)
-strand backbone A (16-22) fpRFDR-CT NMR (Ishii et al. 2001b)
Mixture of -sheet and -helical structure Mutant prion fragment
13
C NMR (Laws et al. 2001)
Parallel, in-register -strands A (1-28)
High resolution MAS
NMR
(Mikros et al. 2001)
Parallel, in-register -strands A (10-35) A (1-42)
MQNMR, dipolar
recoupling NMR; STEM;
EM
(Antzutkin et al. 2002)
Parallel -strands A (1-40) fpRFDR-CT NMR (Balbach et al. 2002)
Extended -strand, may be parallel TTR (105-115)
13
C
15
N MAS, REDOR
NMR
(Jaroniec et al. 2002)
Parallel, in-register -strands, disordered N-terminus A (1-40)
fpRFDR-CT, DQCSA
NMR; STEM
(Petkova et al. 2002)
Parallel in-register -strands, non- at residues 25,
26 and 29
A (1-40)
fpRFDR-CT, DQCSA, 2D
MAS exchange NMR
(Antzutkin et al. 2003)
Parallel, folded -sheets A (1-40) mutant
13
C
1
H MAS NMR; SDSL;
TEM; STEM; AFM
(Antzutkin 2004)
Chapter 5. Discussion

154
Model Type of Amyloid Techniques Reference
Extended -strand TTR (105-115)
13
C
15
N MAS NMR (Jaroniec et al. 2004)
Antiparallel, extended -strand, out of register
Designed seventeen-
residue peptide
XD; TEM; STEM;
REDOR NMR
(Kammerer et al. 2004)
Antiparallel, -strands, registry highly ordered,
registry shift 1 or 3 depending on pH (7.4 or 2.4)
A (11-25)
15
N-
13
C REDOR,
fpRFDR-CT, 2D MAS
exchange NMR
(Petkova et al. 2004)
Antiparallel, -strands at pH 7.5 and 4.1. Mixture of
parallel and antiparallel at pH 3.3. Random coil at C
termini.
Human calcitonin
13
C REDOR (Naito et al. 2004)
Chapter 5. Discussion

155
5.2 Conclusion
We have designed and implemented a suite of software tools for the examination of
diffraction patterns from amyloid fibrils. Background reduction and contrast
enhancement components ensure that the best use is made of the available data. The
locations of signals can be accurately determined using automated peak measurement.
With this information, the unit cell determination program enables the testing and
improvement of potential unit cells. Finally, fibre diffraction patterns from models
can be simulated. In conjunction with other modelling programs, this allows the
determination of amyloid structure.
This application was used to analyse X-ray and electron diffraction data from amyloid
fibrils formed from full-length IAPP and AAAK. The IAPP amyloid study employed
this information in conjunction with cryo, negative stain and platinum/carbon
shadowing electron microscopy. The presence of layer lines showed that the structure
was highly ordered and contrast enhancement aided the measurement of the
diffraction reflections. These lead to the suggestion of an orthorhombic unit cell with
a = 4.7 Å, b = 19 Å and c = 38 Å. Using protofilament dimensions provided by the
electron micrographs and mass per unit length data from a previous study (Goldsbury
et al. 1997), a hypothetical model was constructed. In this model, the protofilament
was composed of four mutually antiparallel -sheets. The IAPP peptide was spread
over three -strands and perhaps formed an “e” shape (Jaikaran and Clark 2001).
Amyloid nanocrystals formed from AAAK were analysed in a similar manner. The
high quality of the resulting data enabled a detailed structure to be constructed by
comparing calculated and observed diffraction patterns. - intersheet and interstrand
interactions stabilised this structure, which supported the theory of an important role
of aromatic residues in amyloid formation and stability. The theory was derived from
the importance of benzene rings in other areas of macromolecular assembly (Gazit
2002b) and studies of amyloidogenic fragments. Studies, involving both the IAPP and
A peptides, determining which fragments formed amyloid and which residues were
critical to amyloid formation, found phenylalanine residues to be critical to
amyloidogenesis. Other amyloid forming fragments also appeared to have a high
Chapter 5. Discussion

156
concentration of aromatic residues. Our studies showed cross- structures similar to
those postulated for other amyloid. The results were commensurate with and add to
those of the other studies referenced herein.

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157
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