3 L.

Stryer
3.4, 3.5, 3.7, 6.6 T.M. Devlin
68, 74, 76 J. Koolman


( - )

DNA

:
Figure 3.19 Amino Acid Sequences Have Direction
This illustration of the pentapeptide Tyr-Gly-Gly-Phe-Leu (YGGFL) shows the sequence from
the amino terminus to the carboxyl terminus. This pentapeptide, Leu-enkephalin, is an opioid
peptide that modulates the perception of pain. The reverse pentapeptide, Leu-Phe-Gly-Gly-Tyr
(LFGGY), is a different molecule and shows no such effects.

Figure 3.21
The formation of a disulfide bond from two cysteine residues is an oxidation reaction.

F. Sanger 1953

 : HbS

(. )

GAG--GTG

MstII,
CCTNAGG

Southern blotting

MstII DNA HbA
2 ,
DNA HbS
1

:
HbS DNA

Figure 3.23 Peptide Bonds Are Planar

In a pair of linked amino acids, six atoms (C, C, O, N, H, and
C) lie in a plane. Side chains are shown as green balls.

Figure 3.27 Rotation About Bonds in a Polypeptide

The structure of each amino acid in a polypeptide can be adjusted by
rotation about two single bonds. (A) Phi () is the angle of rotation
about the bond between the nitrogen and the -carbon atoms, whereas
psi () is the angle of rotation about the bond between the -carbon
and the carbonyl carbon atoms. (B) A view down the bond between
the nitrogen and the -carbon atoms, showing how is measured. (C)
A view down the bond between the -carbon and the carbonyl carbon
atoms, showing how is measured.

Figure 3.24 Typical Bond Lengths Within a Peptide Unit

The peptide unit is shown in the trans configuration.

Figure 3.25 Trans and Cis Peptide Bonds

The trans form is strongly favored because of
steric clashes that occur in the cis form.

Figure 3.28 A Ramachandran Diagram Showing the Values of and

Not all and values are possible without collisions between atoms. The most favorable
regions are shown in dark green; borderline regions are shown in light green. The structure
on the right is disfavored because of steric clashes.

.

( ),
- -.

- -

Figure 3.31 Ramachandran Diagram for Helices

Both right- and left-handed helices lie in regions of allowed
conformations in the Ramachandran diagram. However,
essentially all helices in proteins are right-handed.

Figure 3.35 Ramachandran Diagram For Strands

The red area shows the sterically allowed conformations
of extended, -strand-like structures.

0.35

 ( -)
- (-)

2
-

-
-
-

(R) -

 - -
CO
-

-
2
.

 -
C-

93
98

28

33
-

16

21
Cu, Zn

: ,

- - -, .
4
180 .

1 4

:
.

.
.

 :
.

-
( ) . -
7 8 -

.

- 2 -
(-) .

 - -.
-
.

- G- .
-
-. - 1 1 .

 ,-

(
,
) -
-
- .
- -
.


: ..

 PrPC PrPSc:
PrPC prion

PrPsc
PrPC

PrPc

PrPc

(a) PrPC (blue partial circles)

undergoes conformational change,
converting into PrPSc (orange partial
pentagons). PrPSc is protease
resistant and amyloidogenic, and
aggregates in the brain
(accumulation). The process is
autocatalytic, newly formed PrPSc
recruiting more PrPC, leading to
escalating conversion and deposition.
The nature of the toxic species is not
known, and may be an unknown
intermediate formed during
conversion, oligomeric PrPSc
molecules or small aggregates of
PrPSc. Depleting PrPC itself removes
the substrate for conversion and
formation of the neurotoxic species,
whatever this might be.
(b) Scheme showing that grafted wildtype (PrP-expressing; PrP+/+) neural
tissue into PrP-null (PrP0/0) brains is
the only tissue where PrPSc is
deposited and prion neurotoxicity
occurs after prion infection [13]. Hence
PrPSc only exerts its toxicity where
PrPC is also expressed.
N. C. Verity and G. R. Mallucci
Biochem. J. (2011) 433, 1929

Rabbits are the only species known

to be resistant to infection with
prions isolated from other species

Molecular surface graphs evidencing the differences

in the predicted DNA-binding sites (left panel,
colored blue) and the electrostatic potential
distribution (right panel, colored blue for positive
charge and red for negative charge) among PrP
molecules from distinct mammalian species (PDB
codes: 1QM1, 1DWZ, 1XYX, 1B10 and 2FJ3 for
human, cattle, mouse, Syrian hamster and rabbit
PrPs, respectively). Interestingly, All surface graphs
were generated using MolMol (Koradi et al., Journal
of Molecular Graphics, 1996).

PrP from rabbit, which constitutes, to date, the

only known TSE agent-resistant species,
presents a relatively small putative DNAcontacting surface. DNA-binding predictions
were performed using DISPLAR.

J.L. Silva et al., Methods (2011)

. (C,N,O)
.

Ser 177
His 40
Asp 85

S-S

(57%).
6%
- ,
10% -
27%

2. , , .
.
3. ( ) (
).


() -
().
,
* 1 ()
* (S-S) (-).



Zn++.

(
)

.. CK

.. LDH

 LDH


H

(-)
(+)




- ?
:

-
,
-

The molecular weight of hemoglobin is approximately 64,500 daltons. Hb is composed of two

pairs of dissimilar chains, and , each defined by a specific amino acid sequence and
incorporating an iron-containing heme group. Two dimers combine to form a hemoglobin
tetramer. This allows for the "hemeheme" interaction necessary for effective oxygen uptake
(deoxyhemoglobin oxyhemoglobin) and delivery (oxyhemoglobin deoxyhemoglobin). The
oxygen affinity of hemoglobin is a function of this hemeheme interaction and of pH (Bohr
effect), and is a measure of how many hemoglobin molecules have oxygen bound to them for a
given level of oxygen tension. In a normal individual the major hemoglobin is Hb A, constituting
approximately 97% of the total hemoglobin. Variations and/or amino acid substitutions in these
chains exist. Some are deleterious to the normal function of hemoglobin, whereas others may
have relatively normal oxygen affinity and stability. Hemoglobins containing different types of
chains make up the remainder of the hemoglobin content in red cells (22 = Hb A2
approximately 2%; 22 = Hb F approximately 1%).
Substitutions in the normal hemoglobin amino acid sequence may result in hemoglobins that
have different sub-unit interactions and varying affinities for oxygen. For example, a substitution
of the sixth amino acid on the beta chain causes Hb S, or sickle hemoglobin. Hb S has a lower
oxygen affinity and surrenders its oxygen more readily. Hb F, a normal minor hemoglobin
constituent, has a higher oxygen affinity.

POINT MUTATION

 (GFP).
The rearrangement and oxidation of the sequence Ser-Tyr-Gly is the source of fluorescence.

 ,-


: ..

PrPC is encoded by only one exon of the single-copy PRNP gene, which is located on human
chromosome 20 [15].
The mature PrPC is composed of 208209 amino acids and is attached to the outer leaflet of the
plasma membrane through a glycosylphosphatidylinositol (GPI) anchor [6] in a non-, mono- or diglycosylated form [6].
A signal peptide of 22 amino acids is cleaved from the N-terminal region, which has a flexible, random
coil sequence of about 100 amino acids. This region also contains four repeats of a sequence of eight
amino acids (PHGGGWGQ), named the octapeptide or octarepeat domain, which is related to copper
binding [16]. This region is also related to the binding of glycosaminoglycans and nucleic acids,
especially RNA [1719].
The C-terminal region is globular, with three alpha helices at positions 144154, 173194 and 200228.
A disulfide bond is formed between cysteine residues 179 and 214 [20].
In a general way, the conversion of PrPC to its altered isoform, PrPSc, leads to a refolding of
alpha-helical and coil structures into a beta sheet [21,22]. These structural changes confer different
physicochemical characteristics to PrPSc, such as insolubility in denaturing detergents and partial
resistance to digestion by proteinases [15]. The tendency to aggregation of this isoform is related to its
insolubility, and protease-resistant aggregates accumulate in the brain [6], which is one of the features of
TSEs.
Unlike PrPC, the three-dimensional structure of PrPSc has not yet been completely elucidated due to the
heterogeneity of aggregates and the impossibility of purifying it in a soluble form. The increased beta-sheet
content in PrPSc compared to PrPC has been detected through techniques such as Fourier Transform
Infrared Spectroscopy (FTIR) and Circular Dichroism (CD) [21,22]; thus, a cross-beta-sheet conformation
was proposed for scrapie prion rods [23]. Additionally, the overall structural organizations of fibrils from
three different species (mouse, bovine and elk) have been shown to be very similar through
hydrogen/deuterium exchange mass spectrometry. Moreover, two regions (2498) and (182212) have
been observed to be highly protected, and thus, the regions between them, with a higher solvent
accessibility, have been proposed to be involved in the formation of the fibrillar interface [24].

J.L. Silva et al., Methods (2011)

Prion Diseases

Prion diseases or transmissible spongiform encephalopathies (TSEs) are infectious

neurodegenerative conditions characterized by vacuolar degeneration of the central nervous
system (CNS) and deposition of an abnormal isoform of the host-encoded prion protein (PrP).
These diseases affect a wide variety of animal species and display limited zoonotic potential.
Usually displaying prolonged incubation periods, they are clinically recognized via progressive
neurological deterioration resulting from synaptic and neuronal loss and associated activated glial
responses to CNS damage. Identification of genetically inherited forms of these diseases
implicate further the critical role of the prion protein in disease pathogenesis and their
classification as protein-misfolding disorders, with similarities to other progressive dementias such
as Alzheimers and Parkinsons diseases and amyotrophic lateral sclerosis. Sporadic prion
diseases, with no known genetic risk factor or exposure to infection, have also been identified.
The disease-associated isoform of the prion protein gains several properties including ability to
transmit infection, limited protease resistance, and increased ability to fibrillize and form amyloid,
these observations on both etiology and biochemical nature of the agent resulted in the prion
hypothesis.
The prion hypothesis proposed that the infectious agent may be solely composed of a
proteinaceous particle, i.e., the disease-associated isoform of the prion protein (PrPSc), with the
means to self-propagate via an auto-catalytic process of template-mediated refolding of the
nascent cellular prion protein (PrPC). The pathway and mechanisms from refolding of the prion
protein to neurodegeneration are still unknown.

Viruses 2012, 4

Prion disease and the innate immune system

Viruses 2012, 4