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Published on 30 November 2016 on http://pubs.rsc.org | doi:10.1039/9781782626695-FP001
Computational Biophysics of Membrane Proteins

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Computational Biophysics of
Membrane Proteins
Edited by
Carmen Domene
King’s College London, UK
Email: carmen.domene@kcl.ac.uk
Published on 30 November 2016 on http://pubs.rsc.org | doi:10.1039/9781782626695-FP001 View Online
RSC Theoretical and Computational Chemistry Series No. 10
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Contents
Chapter 1 Introduction to the Structural Biology of Membrane

Proteins 1
Mary Luckey
1.1 Introduction 1
1.2 Membrane Features 2
1.3 Lipid Polymorphism 5
1.4 Classes of Membrane Proteins 7
1.4.1 a-Helical Bundles 7
1.4.2 b-Barrels 8
1.5 Functions of Membrane Proteins 9
1.5.1 Channels 10
1.5.2 Transporters 11
1.5.3 Enzymes 14
1.5.4 Receptors 14
1.6 Membrane Protein Complexes 15
1.7 Conclusions 17
References 17
Chapter 2 Molecular Dynamics Simulations: Principles and

Applications for the Study of Membrane Proteins 19
Victoria Oakes and Carmen Domene
2.1 Introduction 19
2.2 Classical Molecular Dynamics 20
2.2.1 Additive Force Fields 22
2.2.2 Polarisable Force Fields 24

Edited by Carmen Domene
Published by the Royal Society of Chemistry, www.rsc.org
v
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vi Contents
2.2.3 Practical and Technical Considerations 25

2.2.4 Applications 29
2.3 Coarse-grained Molecular Dynamics
Simulations 30
2.4 Ab initio Molecular Dynamics 33

2.5 Enhanced Sampling Techniques and Free Energy
Methods 34
2.6 Conclusions 40
References 40
Chapter 3 Free Energy Calculations for Understanding Membrane

Receptors 59
Andrew Pohorille
3.1 Introduction 59
3.2 The Basics of Free Energy Calculations 60
3.2.1 The Parametric Formulation of Free Energy
Calculations 60
3.2.2 Ergodicity, Variance Reduction Strategies,
and the Transition Coordinate 63
3.3 Free Energy Perturbation Methods 65
3.3.1 Theoretical Background 65
3.3.2 Alchemical Transformations 70
3.4 Probability Distribution Methods 73
3.5 Thermodynamic Integration 75
3.5.2 Adaptive Biasing Force Method 78
3.6 Replica Exchange for Enhanced Sampling in
Configurational Space 80
3.7 Applications of Free Energy Calculations:
Case Studies 81
3.7.1 Binding of Anesthetic Ligands to
Receptors 82
3.7.2 Free Energies of Ions across Channels 84
3.7.3 Conformational Transitions in Receptors 86
3.8 Non-equilibrium Properties from Free Energy
Calculations 88
3.8.2 Example – the Leucine–Serine Channel 93
3.9 Summary and Conclusions 96
References 98
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Contents vii
Chapter 4 Non-atomistic Simulations of Ion Channels 107

Claudio Berti and Simone Furini
4.1 Introduction 107

4.2 Methods Based on Continuum Distributions

of Ions 111
4.2.1 Poisson–Boltzmann 112
4.2.2 Poisson–Nernst–Planck 117
4.2.3 Improvements of Classical Continuum
Theories of Electrolytes 119
4.3 Particle-based Methods 122
4.3.1 Brownian Dynamics 124
4.3.2 Monte Carlo 127
4.4 Methods to Include Atomic Detail in
Non-atomistic Models 128
4.4.1 Atomic Detail in Brownian Dynamics 129
4.4.2 Atomic Detail in Continuum Models 132
4.5 Concluding Remarks 133
References 133
Chapter 5 Experimental and Computational Approaches to Study

Membranes and Lipid–Protein Interactions 137
Durba Sengupta, G. Aditya Kumar, Xavier Prasanna and
Amitabha Chattopadhyay

5.1.1 Membrane Components 138
5.2 Role of Membrane Lipids in Membrane Protein
Organization and Function 139
5.3 Mechanisms for Lipid Regulation of Membrane
Proteins 140
5.3.1 Specific Membrane Effects 140
5.3.2 Non-specific Membrane Effects 142
5.4 Range of Time Scales Exhibited by Membranes 142
5.5 Lipid–Protein Interactions: Insights from
Experimental Approaches 144
5.5.1 Determining Near-neighbor Relationships in
Membranes: Interaction of Melittin with
Membrane Cholesterol utilizing FRET 144
5.5.2 Interaction of the Actin Cytoskeleton with
GPCRs: Application of FRAP 147
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viii Contents
5.6 Computational Approaches to Study Membrane

Organization and Lipid–Protein Interactions 149
5.6.1 Simulating Single Component and
Multi-component Bilayers 151
5.6.2 Atomistic Simulations Elucidating

Lipid–Protein Interactions 151
5.6.3 Coarse-grain Methods to Analyze Membrane
Protein Interactions 153
5.6.4 Enhanced Sampling Methods 154
5.7 Future Perspectives: The Road Ahead 155
Acknowledgements 155
References 155
Chapter 6 Computer Simulation of Ion Channels 161

Ben Corry
6.1 Introduction to Ion Channels 161

6.2 Questions that can be Addressed and Associated
Timescales 165
6.3 Ion Permeation 169
6.4 Ion Selectivity 174
6.4.1 Na1/Ca21 Selection 174
6.4.2 Na1/K1 Selection 177
6.5 Channel Gating 181
6.6 Interactions of Channels with Drugs
and Toxins 184
6.6.1 Toxin–Channel Interactions 184
6.6.2 Channel Blockage by Small Molecules 187
6.7 Conclusions 189
References 190
Chapter 7 Computational Characterization of Molecular

Mechanisms of Membrane Transporter Function 197
Noah Trebesch, Josh V. Vermaas and Emad Tajkhorshid
7.1 Membrane Transport – A Fundamental Biological

Process 197
7.2 Substrate Binding and Unbinding 200
7.2.1 Spontaneous Binding Simulations Revealing
a Binding Mechanism and Site 201
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Contents ix
7.2.2Proposing Substrate Binding Sites through

Molecular Docking 202
7.2.3 Unraveling Substrate Release Pathways 204
7.3 Capturing Localized Transporter Motions with
Equilibrium Molecular Dynamics 205

7.3.1 Substrate-induced Structural Changes of an
Antiporter 206
7.3.2 Gating Elements in a Neurotransmitter
Transporter 206
7.4 Computational Description of Global Structural
Transitions in Membrane Transporters 209
7.4.1 Nonequilibrium Simulation of Structural
Changes 210
7.4.2 Application to an ABC Transporter 212
7.5 Water within Transporters 215
7.5.1 Water Leaks in Transporters 216
7.5.2 Water in Proton Pathways 216
7.6 The Lipid Frontier 219
7.6.1 Why Now? Initial Barriers to Simulating
Lipid–Protein Interactions 219
7.6.2 Computational Probes of Lipid–Protein
Interactions 220
7.7 Concluding Remarks 221
References 223
Chapter 8 Computational Studies of Receptors 237

Maria Musgaard and Philip C. Biggin

8.2 Network Models Can Provide Insight into
Large-scale Conformational Changes 239
8.3 Network Models to Examine Gating 241
8.4 Network Models to Compare Dynamics 242
8.5 Network Models to Suggest Novel Mechanisms
for Modulation 244
8.6 Molecular Dynamics to Aid Crystallographic
Interpretation 245
8.7 Molecular Dynamics to Move between States 247
8.8 Molecular Dynamics to Refine Working
Models 249
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x Contents
8.9 Molecular Dynamics to Explain the Effects of

Ions and Water 251
8.10 Molecular Dynamics to Quantify Free Energy
Requirements 253
8.11 Conclusions 255

References 255
Subject Index 259

Published on 30 November 2016 on http://pubs.rsc.org | doi:10.1039/9781782626695-00001
CHAPTER 1
Introduction to the Structural

Biology of Membrane Proteins
MARY LUCKEY
Department of Chemistry and Biochemistry, San Francisco State

University, 1600 Holloway Ave., San Francisco CA 94132, USA
Email: luckey@sfsu.edu
1.1 Introduction
The biomembrane is an essential feature of life, defining the interior of cells
and controlling the entry and exit of molecules and ions.1 Lipids in the
membrane make a hydrophobic barrier for aqueous solutes; this barrier is
semipermeable due to the presence of membrane proteins. In addition to
transport functions, membrane proteins have roles as receptors, enzymes,
and structural components. Biomembranes also contain glycolipids and
glycoproteins, whose carbohydrate constituents are external to the cell
and are important in recognition. This introduction focuses on membrane
proteins in the context of their lipid environment.
Membrane proteins share some features with soluble proteins, for
example the protein interior (excluding channel walls) is tightly packed with
mostly nonpolar residues. However, the surface of membrane proteins is
amphiphilic, allowing interactions with both the polar exterior and the
nonpolar interior of the membrane. The need to maintain this amphiphilic
structure increases the difficulty of purifying and handling membrane pro-
teins. In addition, their localization in the membrane often impedes their
overexpression. These difficulties hampered their structural characterization
for many years, so that X-ray crystallography of membrane proteins lagged

1
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2 Chapter 1
25 years behind that of soluble proteins. In 1988, Harmut Michel, Johann

Deisenhoffer, and Robert Huber received a Nobel Prize for the first crystal
structures of membrane proteins, those from the photosynthetic reaction
center of Rhodopseudomonas viridis.2 (Rhodospeudomas viridis has been
renamed Blastochloris viridis.) Over the next two decades, new membrane
protein crystal structures were sufficiently rare to grace the covers of Nature
and Science when they did appear. However, their number rose exponen-
tially; the data base now contains more than 650 unique structures of
membrane proteins determined with X-ray crystallography or NMR
spectroscopy,3 with good overall agreement in structures that have been
solved by both. The availability of detailed membrane protein structures
allows researchers to further probe their function and dynamics using
genetic, biochemical, biophysical, and computational tools.
1.2 Membrane Features

The native environment of membrane proteins is dynamic and asymmetric,
described by Singer and Nicolson as fluid and mosaic in their 1972 model
that became the paradigm for membrane structure (Figure 1.1).4 Lipids
consisting of polar head groups and nonpolar acyl chains form a two-
dimensional fluid bilayer (Figure 1.2). Lipid composition is diverse, with
most of the lipids randomly distributed in the bulk phase of the bilayer while
Figure 1.1 The Fluid Mosaic Model of Singer and Nicolson views the membrane as a
fluid lipid bilayer with a mosaic of intrinsic proteins. The fatty acyl chains
from each leaflet form the nonpolar interior, while the aqueous periphery
contains extrinsic proteins and carbohydrate chains (not shown).
From S. J. Singer and G. L. Nicolson, Science 1972, 175, 720. r 1972,
American Association for the Advancement of Science. Redrawn with
permission from AAAS.
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Introduction to the Structural Biology of Membrane Proteins 3

Figure 1.2 Phospholipid bilayers may exist in the liquid disordered phase (Ld, left) or
the liquid ordered phase (Lo, right). Ld and Lo phases are depicted with
representative snapshots from coarse-grained simulations using the Martini
force-field. DPPC (dipalmitoyl phosphatidylcholine) is shown in green,
DOPC (dioleoyl phosphatidylcholine) in orange, cholesterol in purple,
with portions of headgroups visible as beads. Water is not shown for clarity.
Kindly provided by Dr Svetlana Baoukina, University of Calgary.
Undulations
(10-6-1s)
Flip-flop
(10-3-104 s) cis-trans isomerization
(10-10s)
Bond vibrations
(10-12s)
Rotational diffusion wobble

Protrusion
(10-8s)
(10-9 s)
Lateral diffusion
(10-7s)
Figure 1.3 A variety of lipid motions create disorder in the fluid lipid bilayer. Several
kinds of lipid motions are shown here with their approximate correlation
times.
Kindly provided by Prof. Carmen Domene, King’s College London.
some are localized by specific interactions with proteins and/or other lipids,
often in regions of ordered lipids called rafts (see below).
In the lipid disordered phase (Ld, also called La), fluidity of the bilayer
results from the constant and varied motion of lipids (Figure 1.3). Although
the lateral diffusion rate in pure lipid bilayers is very fast, the measured
mobility of bulk lipids on the surface of cells is much slower. This difference
has been explained by single-particle tracking on the surface of cells con-
taining cytoskeletons: single-molecule trajectories are fast within small
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4 Chapter 1
regions, where they are confined until they hop to a contiguous region,
producing a slower overall progression.5
The mosaic distribution of membrane proteins results from wide vari-
ations in lateral mobility, from those that diffuse rapidly on the surface to
those anchored by the cytoskeleton. A large proportion of membrane

proteins function in protein assemblies, which themselves have varying
lifetimes. Some complexes of membrane proteins are very stable, such as the
respiratory complexes involved in energy transduction (see below), while
others are the result of transient interactions such as those involved in signal
transduction. Many lipid-anchored proteins are observed in membrane rafts
enriched in sphingomyelin and cholesterol in the lipid-ordered (Lo) state
(see Figure 1.2). The presence of rafts varying in size (diameters from 10 to
200 nm) and in duration (from o1 ms to fairly stable lifetimes) enhances
nonrandom distributions and dynamic interactions in the membrane.6
Lipid–lipid interactions probably drive raft formation, given that even
simple lipid mixtures reveal fluid immiscibility (Figure 1.4). The fused
Figure 1.4 A ternary phase diagram showing that concentrations of three lipid
components can reveal regions with lipid compositions that produce
immiscible fluid phases. Using giant vesicles of POPC (palmitoyl oleoyl
phosphatidylcholine)/PSM (palmitoyl sphingomyelin)/cholesterol tagged
with fluorescent markers, separation into two distinct liquid phases is
observed at 25 1C for compositions within the gray region of this phase
diagram. Several representative vesicles are shown with compositions
near the edges of the phase boundary, with the dark phase being highly
enriched in PSM and moderately enriched in cholesterol, while the
bright phase is strongly enriched in POPC. Scale bars are 20 mm and
the vesicles were imaged before the domains fully coalesced.
Kindly provided by Prof. Sarah Veatch, University of Michigan.
View Online
hydrocarbon rings of cholesterol are nearly rigid, allowing the sterol to align
with lipids containing saturated acyl chains, especially sphingomyelins, and
promote the tight packing of the Lo phase.
1.3 Lipid Polymorphism

Of the possible physical states for lipid aggregates, only a few are present at
biological conditions, while others are useful in the laboratory. A pure lipid
bilayer (constituted by only one lipid species) can be in lamellar crystalline
(Lc), lamellar gel (Lb), or lamellar liquid crystalline (called fluid, La, or
disordered, Ld) states, depending on the temperature and pressure. The shape
of the lipid molecule may introduce significant curvature to the bilayer, an
important force during some membrane processes.7 Since excessive curvature
disrupts the bilayer, biological membranes contain a significant fraction of
non-bilayer lipids (lipids such as phosphatidylethanolamine that do not form
bilayers in the pure state) to minimize the curvature tension. Non-bilayer
states include hexagonal phases (hexagonally packed arrays in long cylinders)
and cubic phases (cubic packing of rod-like elements, Figure 1.5). Hexagonal
phases may be important in biological transitions, such as pore formation
and membrane fusion. The lipidic cubic phase (LCP) has become an
important tool in the crystallization of membrane proteins.8
In contrast to the simplified mixtures employed for physical studies, the
lipid composition of most membranes is very complex: a typical membrane
has about a hundred lipid species, and over 1000 different species of lipids
have been identified in biological samples.9 Prokaryotic organisms vary
the fatty acid content of their membranes to maintain fluidity at extreme
Figure 1.5 Lipid polymorphism results in lamellar, hexagonal, and cubic phases. The
lipid bilayers shown in Figure 1.2 are of lamellar phase. The hexagonal
phase may be normal, HI (not shown) with nonpolar regions inside the
tubes, or inverted, HII (left) with polar groups and water inside. In cubic
phases, a variety of three-dimensional systems of lipid channels or
networks are interpenetrated by water channels, represented here by the
bicontinuous type (right).
Kindly provided by Dr Simone Aleandri and Prof. Ehud Landau, University
of Zurich.
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6 Chapter 1
temperatures (longer and more saturated fatty acids have higher melting
points than shorter and unsaturated fatty acids). Eukaryotic organisms have
markedly different lipid contents of their envelope and organellar mem-
branes due to the sites of lipid synthesis and patterns of lipid trafficking.
Prokaryotes lack cholesterol and other steroids, while some eukaryotic

membranes possess very high sterol contents (cholesterol in animals,
ergosterol in yeast and fungi, and stigmasterol and sitosterol in plants.)
Clearly, the membrane composition is mosaic in the plane of the bilayer,
with dynamic mixing of its lipid species. The membrane also presents
significant variations normal to the bilayer plane. The lipid headgroups
make up the polar exterior of the bilayer, with the acyl chains extending
across the nonpolar interior. Elegant probability maps for the positions of
each constituent have been achieved by joint refinement of X-ray and
neutron diffraction data (Figure 1.6). The penetration of water molecules
defines the two interfacial regions of the membrane; water is completely
absent from the hydrocarbon core. In addition to their functional import-
ance, such as exclusion of charged molecules from the interior, these
variations are important considerations for the structures of proteins that
span the bilayer.
Figure 1.6 The joint refinement of X-ray and neutron diffraction data provides the
structure of a DOPC bilayer (indicated normal to the bilayer) as density
peaks for portions of the DOPC molecule [methyl (CH3), methylene
(CH2), double-bonds (C¼C), carbonyls, choline, glycerol, and phosphate]
and water. The hydrocarbon core of the bilayer, which lacks water, is
sandwiched between two interfacial regions.
From S. H. White et al., J. Biol. Chem. 2001, 276, 32395. r 2001 by the
American Society for Biochemistry and Molecular Biology. Reprinted by
permission of the ASBMB.
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1.4 Classes of Membrane Proteins

The amphiphilic membrane proteins described above are classed as integral
membrane proteins (also called intrinsic proteins) because they are
embedded in the membrane: they interact extensively with membrane

lipids10 and cannot be purified without disrupting the membrane using
detergents or mechanical rupture. In contrast, peripheral membrane pro-
teins (also called extrinsic proteins) can be washed off the membrane
without disrupting it. They bind to membrane lipids, other membrane
proteins, or both by a combination of electrostatic and nonpolar inter-
actions. Some proteins insert into the membrane or bind it transiently, with
binding being enhanced by calcium ions, lipid anchors, and/or repeats of
small peptide domains. Amphitropic proteins are proteins whose activities
are regulated by binding to the membrane, such as some phospholipases
and blood clotting factors. Some phospholipases undergo significant con-
formational changes in order to bind their lipid substrates, while others
simply trap them by dimerization.
Integral membrane proteins are adapted to an environment that varies
from the cytosol in viscosity, dielectric constant, and isotropy, and contains
gradients of pH, redox potential, and pressure. They are described by their
number of transmembrane segments (TMSs). Bitopic membrane proteins
with one TMS tend to form dimers (such as glycophorin A) or associate with
larger, polytopic membrane proteins (such as the H protein in the photo-
synthetic reaction center). Monotopic membrane proteins do not cross the
bilayer but insert into one leaflet; an example is prostaglandin H2 synthase, an
important target of nonsteroidal anti-inflammatory drugs. In addition, pro-
teins may bind to the membrane via one or more lipid anchors (myristoyl,
palmitoyl, farnesyl, geranylgeranyl, and glycosylphosphatidylinositol groups)
added by post-translational modifications.
Integral membrane proteins are classified by their overall structure into
two dominant classes: a-helical bundles and b-barrels, which are discussed
below. Other structural patterns can occur, such as the Wza protein that
spans the bilayer with a barrel of amphipathic a-helices.11 A governing
principle is the need for secondary structure in the TMS to satisfy the
hydrogen-bonding of peptide groups, since in the low dielectric bilayer the
cost of disrupting these hydrogen bonds is B4 kcal per residue, producing a
prohibitive DG of B80 kcal to unfold a twenty-residue TM a-helix.12
1.4.1 a-Helical Bundles

In the majority of integral membrane proteins each TMS is an a-helix of
twenty or more predominantly nonpolar residues. The presence of one or
two polar residues is tolerated within the overall hydrophobicity needed.
Charged amino acids are positioned for functional purposes, they may form
ion pairs, or they may be present in their uncharged states with altered pKas
due to low dielectric environments. Alternatively, charged or polar side
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8 Chapter 1
chains can fold towards the membrane interface, snorkeling to orient their
polar groups beyond the nonpolar core of the bilayer. Snorkeling is most
commonly observed with lysine residues, but has also been seen with other
amino acids (Arg, Tyr, Asp, Glu, Asn, and Gln). Another role for polar side
chains near the TMS ends is the formation of hydrogen bonds with peptide
bond groups to cap the ends of the helices.
Tryptophan and tyrosine residues play a special role at the interface of the
polar and nonpolar domains due to electrostatic interactions of their aro-
matic rings with the hydrocarbon core; often their presence in a ring around
the protein structure helps to define the location of the interface. Another
informative aspect of the primary structure derives from the ‘positive inside
rule’: positively charged amino acids predominate on the cytoplasmic
portions of integral membrane proteins due to some restrictions in their
insertion during biogenesis. Numerous algorithms utilize the positive inside
rule combined with hydropathy plots to predict the structure of a-helical
membrane proteins.13
The first membrane protein observed (by electron microscopy) to consist
of an a-helical core was bacteriorhodopsin (bR), a light-driven proton pump
from Halobacteria. bR contains seven roughly parallel TM helices with a
covalently bound retinal cofactor near the center (Figure 1.7). Character-
ization of bR intermediates at different stages of its photocycle has revealed
small structural shifts accompanying the electronic transitions.14 Sophisti-
cated folding studies of bR have defined folding transitions as well as the
effect of curvature stress.15
bR is a bacterial homolog of rhodopsin, a photoreceptor in the retina.
Rhodopsin belongs to the large class of G protein-coupled receptors (GPCRs)
that respond to a variety of stimulants by binding to G proteins (see below)
and triggering signaling cascades. The TM a-helices in many GPCRs and in
bR are quite regular and oriented fairly perpendicular to the bilayer. How-
ever, most a-helical bundle membrane proteins contain some tilted a-helices
as well as TM helices with distortions due to kinks and bulges, short un-
wound portions, or stretches of 310 helices, in addition to half helices that
stack to span the bilayer.
1.4.2 b-Barrels
Membrane-spanning b-barrels are found in the outer membranes of Gram
negative bacteria as well as mitochondria and chloroplasts, where they
function in transport, phage binding, catalysis, and adhesion.16 Varying
from monomers to oligomers and from open barrels to tightly packed in-
teriors, most form pores that dissipate ion gradients. b-barrels typically
consist of an even number (8 to 26) of amphiphilic b-strands crossing the
bilayer at a tilt of B451, each containing 9 to 11 residues hydrogen-bonded to
the adjacent strands. Exceptions include VDAC (voltage-dependent anion
channel), a mitochondrial b-barrel with an odd number of strands
(Figure 1.8), and OmpX, an adhesion protein with several long b-strands
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Figure 1.7 The fold of a typical a-helical membrane protein is represented by the
high resolution structure of bacteriorhodopsin, showing its seven trans-
membrane helices [labeled A to G and colored from the N terminus
(blue) to the C terminus (red)] and the bound cofactor retinal.
Kindly provided by Prof. Eva Pebay-Peyroula, University Grenoble Alpes.
extending past the bilayer. Porins, a family of trimers with three open pores,
vary in their selectivity towards ions and solutes due to their pore archi-
tecture. Larger b-barrels that facilitate diffusion of specific large solutes
contain internal plug domains that may be displaced in conformational
changes driven by an energized complex linked to the inner membrane.
1.5 Functions of Membrane Proteins

The tremendous progress in the structural biology of membrane proteins
supported by countless genetic, biochemical, and biophysical studies now
provides exciting details of their different molecular functions. Specificity of
channels is illuminated by their architecture and gating mechanisms.
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10 Chapter 1
Figure 1.8 The fold of a b-barrel membrane protein is represented by the X-ray
structure of the mitochondrial porin VDAC, again colored from the N
terminus (blue) to the C terminus (red). This b-barrel is unusual in that it
has an odd number of b-strands (19, numbered in the figure), which
makes the N- and C-termini b-strands parallel.
From M. Bayrhuber et al., Proc. Natl. Acad. Sci. U. S. 2008, 105, 15370.
r 2008, National Academy of Sciences, U.S.A. Reprinted with permission.
Fundamental transport mechanisms are shared among transporters of

widely varying families. Capturing intermediates in the reaction cycles of
membrane enzymes provides details of their mechanism. An atomic picture
of a receptor interaction with signaling transducers provides vital clues to
the molecular transmission of information. Before looking at examples of
these membrane functions, it is worth remembering that the classes overlap:
for example, many receptors form ion channels and some enzymes also
transport substrates or ions.
1.5.1 Channels
Channels carry out passive diffusion (down concentration gradients), hence
passage of solutes does not require energy-driven conformational changes;
however, channel proteins may undergo conformational changes when
gated by voltage, pH, calcium ions, or other ligands. Although the selectivity
of channels varies, some exhibit exquisite specificity while maintaining very
fast permeation rates. The first X-ray crystal structure of an ion channel, that
of a truncated potassium channel called KcsA, revealed how residues lining
View Online

Figure 1.9 Channels may be highly selective, as first observed at high resolution in
the selectivity filter of the potassium channel KcsA. In this cutaway view
of the filter with the extracellular surface at the top, the electron density
(blue mesh) observed for dehydrated K1 ions is shown within the
channel in addition to a hydrated K1 ion in the central cavity.
Reprinted from, R. MacKinnon, Potassium Channels, FEBS Lett., 555,
62–65, Copyright 2003 with permission from Elsevier.
the channel transfer dehydrated potassium ions while excluding sodium and
other ions (Figure 1.9).17 Structures of aquaporins, such as the glycerol
channel GlpF, similarly revealed how water channels can prevent the
passage of protons: hydrogen bonding to channel-lining residues requires
the reorientation of each water molecule as it passes through the center of
the channel.18 Other elegant channel structures include those for connexin
found in gap junctions, TRP (transient receptor potential) channels im-
portant in neurological sensing, and mechanosensitive channels of both
vertebrates and prokaryotics.
1.5.2 Transporters
Transporters are generally considered a separate class from passive chan-
nels, even though the evolution of highly similar chloride transporters and
View Online
12 Chapter 1
19
chloride channels erodes this distinction. Active transporters are classified
as primary, those that rely on exergonic chemical reactions such as the
hydrolysis of ATP, and secondary, those that are driven by ion gradients.
The prototype for secondary transport is the extremely well characterized
lactose permease, the Lac carrier called LacY.20 The LacY protein can
accumulate lactose up to 100-fold inside Escherichia coli when coupled with
the obligatory uptake of protons. The LacY structure exhibits a two-fold
pseudosymmetry with the N-terminal and C-terminal domains forming two
distinct but similar lobes. Each domain spans the bilayer with six a-helices
and a central sugar-binding site open to the cytoplasm (Figure 1.10). Despite
the low sequence homology between the two domains of LacY, they likely
resulted from gene duplication since inverted topology repeats are seen in
the structures of many transporters.
Other transporters in the same family have been crystallized in con-
formations open to the periplasm. Much evidence has established that the
change between outward-facing (co) and inward-facing (ci) conformations
effects solute uptake. This alternating access model for the mechanism of
transport is a general model for transporter action, employed by exporters as
well as importers.21 In addition to the two states ci and co, intermediate
states that are closed (occluded) or partially open (gated) are often observed.
While the LacY structure makes it easy to visualize the transition as a rocker
Figure 1.10 The first high resolution structure of LacY protein (a C154G mutant)
clearly shows the transporter open to the cytoplasm, with the substrate
analog thiodigalactoside bound between the two domains. The twelve
a-helices are colored from the N terminus (blue) to the C terminus (red).
From J. Abramson et al., Science 2003, 301, 610. r 2003, American
Association for the Advancement of Science. Reprinted with permission
from AAAS.
View Online
switch («), alternating access can involve quite dissimilar shape chan-
ges, such as the up-and-down motion of an interior domain in the ‘elevator
mode’ of a glutamate transporter, GltPh.22
Alternating access occurs in larger, more complex proteins that carry out
primary transport, such as the maltose transporter from Escherichia coli.

Crystal structures of the entire complex of five subunits (MalF, MalG, MalK2,
and MalE, and the periplasmic maltose-binding protein) have been obtained
in both ci and co conformations, showing the role of the MalF and MalG
TMSs in alternating access (Figure 1.11).23 The structures reveal key inter-
actions between the subunits and indicate that the maltose-binding protein
covers the opening on the periplasmic side in co. These and additional
conformations also reveal the effect of binding analogs of ATP to the MalK
subunits (on the cytoplasmic side) and suggest how the binding and
hydrolysis of ATP drive the conformational changes that activate the com-
plex to enable maltose uptake. The maltose transporter is representative of a
large family of ABC transporters that include the human protein CFTR
Figure 1.11 High resolution structures of the maltose transporter in ci (left) and co
(right) conformations show how it utilizes the alternating access mech-
anism of transport, with the transition between states dependent on
ATP binding and hydrolysis. Details of the subunit interactions reveal
critical links involved in the conformational changes (not shown). The
internal cavities are shaded (grey) and the MalK (red and green), MalF
(blue), MalG ( yellow), and MalE (MBP, pink) subunits are labeled.
Kindly provided by Dr Michael Oldham and Prof. Jue Chen, Rockefeller
University.
View Online
14 Chapter 1
(the cystic fibrosis transmembrane conductance regulator) and the drug

exporter P-glycoprotein.
1.5.3 Enzymes
Membrane enzymes are wonderfully diverse, from the phospholipases

mentioned above and other enzymes such as diacylglycerol kinase that act on
lipid soluble substrates, to proteases including those involved in processing
amyloid precursor proteins, to redox complexes that carry out electron
transfers and generate proton gradients (see below). Structural biology is now
able to characterize the various steps of the enzymatic reaction cycle, beau-
tifully done with a P-type ATPase called SERCA (the sarcoplasmic reticulum
calcium pump), which uses the hydrolysis of ATP to transport calcium ions.24
SERCA is a very large protein with ten TMSs and three large cytoplasmic
domains involved in major conformational changes (Figure 1.12). The two
major states of SERCA are called E1, with two high affinity Ca sites exposed to
the cytoplasm, and E2, with two low affinity Ca sites exposed to the lumen.
The reaction cycle involves the binding of calcium and ATP to the E1 enzyme,
the hydrolysis of ATP with phosphorylation of the enzyme as a high-energy
state with the calcium sites occluded, a conformational change to E2 re-
leasing the calcium, and the release of the bound phosphate allowing the
enzyme to revert to E1. Over 20 crystal structures of SERCA bound to different
ligands have contributed to the understanding of the detailed reaction cycle.
This successful approach has now been applied to the Na, K-ATPase and
other membrane enzymes.
1.5.4 Receptors
The first GPCR to have a high resolution crystal structure was rhodopsin (see
above), which became an elegant prototype for other GPCRs. Now, the crystal
structures of many GPCRs allow the comparison of detailed ligand-binding
sites to provide fundamental understanding of their physiological roles as well
as valuable information for pharmaceutics.25 Once a ligand has docked, con-
formational changes allow a GPCR to bind to its G protein(s) at the other side
of the membrane. In a biological tour de force, this initial interaction was
captured in crystals of the b2-adrenergic receptor (b2AR) with its G-protein, Gs,
and the inverse agonist carazolol (Figure 1.13).26 The structure shows the
conformational changes in b2AR as well as in Gs that are the first steps of the
signal transmission.
The mechanism of signal transduction is also targeted in structural work
on neurotransmitter receptors, such as the beautiful crystal structures of
glutamate, serotonin, and GABA (g-aminobutyric acid) receptors.27,28 Intense
studies of these and other receptors (such as those for epidermal growth
factor, dopamine, and acetyl choline) are laying the foundation for the
fundamental understanding of brain functions along with insight into
neurological disorders and bases for rational drug design.29
View Online

Figure 1.12 Key intermediates of the reaction cycle of SERCA have been captured in
high resolution structures using different ligands. The structures of E1
bound to phosphate, two Ca21 ions, and an ADP analog; E2 bound to
the phosphate analog BeF3; and E2 bound to an ATP analog, in
addition to either AlF4 or the inhibitor thapsigargen (TG), are shown
in the cycle. Significant shifts are evident in the domains of SERCA
(A domain, yellow; N domain, red; P domain, blue; TM segments M1–2,
purple, M3–4 green, M5–6 wheat, and M7–10 grey.)
Reproduced by permission from Macmillan Publishers Ltd: Nature,
Copyright 2007.
1.6 Membrane Protein Complexes

Many membrane proteins contain multiple subunits or form complexes to
carry out their functions. This is especially true for energy transducing
complexes. The photosynthetic complexes PS1 and PS2 are the largest
complexes to have crystal structures. The high resolution crystal structures
of the respiratory chain complexes provide astonishing mechanistic insights
that reveal striking differences in the modes of coupling electron transport
and proton transport. Complex I couples the flow of electrons through its
View Online
16 Chapter 1
Figure 1.13 The interaction of a G protein-coupled receptor (the b2-adrenergic recep-

tor) with its G protein is captured in the high resolution structure of the
ternary complex of b2AR (green), the agonist BI-167107 (yellow spheres),
and the Gs heterotrimer. Only the aRas domain (gold) of Gs makes
extensive contact with the receptor as it swings away from aAH (also
gold) and the other subunits of the Gs protein, Gb (cyan) and Gg (blue).
Copyright 2011.
hydrophilic domain to a concerted piston-like movement in its membrane

domain that allows the passage of protons (Figure 1.14).30 In contrast, Com-
plex III utilizes the separation of two centers of electron carriers that oxidize
ubiquinol in a cycle called the Q cycle concomitant with the ejection of pro-
tons. Complex IV (cytochrome oxidase) accepts the electrons from cytochrome
c and protons from the cytosol to reduce O2 to H2O, while ejecting additional
protons.31 Finally, the protons reenter on a rotating ring of subunits of the ATP
synthase, whose rotor is mechanically coupled to a stator causing rotation of
the catalytic a and b subunits, changing their conformation to effect the
catalysis.32 Membrane structural biology has contributed greatly to under-
standing each of these very large molecular machines.
View Online

Figure 1.14 A membrane protein complex composed of B2000 amino acids in 14

polypeptide chains is shown in the high resolution structure of complex
I from T. thermophilus. The overall shape and subunit interactions
suggest a coupling mechanism in which the lateral helix acts as a piston
to drive the conformational changes that open proton channels in
response to the reduction of the bound quinone (Q).
Copyright 2013.
1.7 Conclusions
Building on this remarkable progress, the field of membrane protein
structural biology is moving to address many more challenges. Researchers
are studying even larger complexes, such as the nuclear pore with as many as
a thousand proteins; more proteins from eukaryotes, especially humans,
such as CFTR; more dynamic processes, such as fusion. The rest of this
volume illustrates the contribution of biophysical and computational re-
search to these studies. It is axiomatic that the interplay between simu-
lations and experiments enhances both.
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8. (a) V. Cherezov, Curr. Opin. Struct. Biol., 2011, 21(4), 559; (b) P. Nollert,
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13. K. D. Tsirigos, A. Hennerdal, L. Kall and A. Elofsson, Proteomics, 2012,
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21. L. R. Forrest, R. Krämer and C. Ziegler, Biochim. Biophys. Acta, 2011,
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T. S. Kobilka, F. S. Thian, P. S. Chae, E. Pardon, D. Calinski,
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Biophys. Acta, 2010, 1797(8), 1343.
CHAPTER 2
Molecular Dynamics
Simulations: Principles and
Applications for the Study of
Membrane Proteins
VICTORIA OAKESa AND CARMEN DOMENE*a,b
a
Department of Chemistry, Britannia House, 7 Trinity Street,
King’s College London, London SE1 1DB, UK; b Chemistry Research
Laboratory, Mansfield Road, University of Oxford, Oxford OX1 3TA, UK
*Email: carmen.domene@kcl.ac.uk
2.1 Introduction
Research into novel chemical problems is now commonly facilitated by
computational methods in order to supplement experimental data, instruct
future work and, in many cases, provide details for which no experimental
methods are applicable. This is of particular importance in the context
of membrane proteins, where the complexity of the membrane prevents
established techniques to be utilised in order to understand structure–
function relationships for soluble proteins.1 Three-dimensional structures of
membrane proteins have only began to emerge in the last two decades, due
to the difficulty in their expression and purification, and their instability
when removed from their native environment.2 Progress in this field3 and
the emergence of new techniques for structure determination, such as cryo-
electron microscopy,4 have led to a wealth of available structures from many

19
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sprinkling of persons of a higher grade, who formed the small
Opposition. Though the opinions of these were of the most moderate
shade of what would now be called “liberalism,” the slightest
expression of them was attended with positive risk. Spies were
employed to watch such of them as had any social position; in several
cases there were trials for sedition, with sentences of transportation;
and only the impossibility of finding grounds for indictment
prevented more. The negative punishment of exclusion from office,
and from every favour of Government and its supporters, was the
least; and it was universally applied. Burns nearly lost his
excisemanship for too free speaking; and a letter is extant, addressed
by him to one of the commissioners of the Scottish Board of Excise,
in which, without denying his Liberalism, he protests that it is within
the bounds of devout attachment to the Constitution, and implores
the commissioner, as “a husband and a father” himself, not to be
instrumental in turning him, with his wife and his little ones, “into
the world, degraded and disgraced.” Part of the poet’s crime seems to
have been his having subscribed to an Edinburgh Liberal paper
which had been started by one Captain Johnstone. This Johnstone
was imprisoned after the publication of a few numbers; and the very
printer of the paper, though himself a Tory, was nearly ruined by his
connection with it. No subsequent attempt was made during the
Dundas reign to establish an Opposition newspaper. From 1795 to as
late as 1820, according to Lord Cockburn, not a single public meeting
on the Opposition side of politics was, or could be, held in
Edinburgh. Elections of members of Parliament, whether for burghs
or for counties, in Scotland, were a farce: they were transacted
quietly, by those whose business it was, in town-halls or in the
private rooms of hotels; and the people knew of the matter only by
the ringing of a bell, or by some other casual method of
announcement. Abject Toryism, or submission to Dundas and the
existing order of things, pervaded every department and every corner
of established or official life in Scotland,—the Church, the Bench, the
Bar, the Colleges and Schools; and so powerfully were any elements
of possible opposition that did exist kept down by the pressure of
organised self-interest, and by the fear of pains and penalties, that
the appearance at last from the Solway to Caithness was that of
imperturbable political stagnation.
Once, indeed, a crisis occurred which put the Scottish people
nearly out in their calculations. This was in March 1801, when Pitt
resigned office, and Dundas along with him, and a new ministry was
formed under Pitt’s temporary substitute, Mr. Addington, afterwards
Lord Sidmouth. Dundas out of power was a conception totally new to
the Scottish mind,—an association, or rather a dissociation, of ideas
utterly paralysing. “For a while,” says Lord Brougham, “all was
uncertainty and consternation; all were seen fluttering about like
birds in an eclipse or a thunderstorm; no man could tell whom he
might trust; nay, worse still, no man could tell of whom he might ask
anything.” Dundasism, which had hitherto meant participation in
place and patronage, now seemed in danger of losing that meaning;
and the bulk of the Scottish population feared that they might have
to choose between the name and the thing. They were faithful to
Dundas, however; and they were rewarded. The Addington ministry,
which had come into power principally to conclude peace with
France by the Treaty of Amiens, came to an end after that Treaty had
been rendered nugatory by the recommencement of the war; and in
May 1804 Pitt returned to the helm. Dundas, who had in the interim
been raised to the peerage by the title of Viscount Melville, then
resumed his place in his friend’s cabinet, to yield his Parliamentary
service thenceforward in the Upper House, and official service
mainly in the First Lordship of the Admiralty. Scotland then rolled
herself up comfortably once more for her accustomed slumber,—the
only difference being that her bedside guardian had to be thought of
no longer as her Harry Dundas, but less familiarly now as her Lord
Melville. So for another year; but then what a reawakening! It was in
April 1805 that, in consequence of the report of a Committee of the
House of Commons that had been appointed for the investigation of
alleged abuses in the naval service, the Whigs, through Mr.
Whitbread as their spokesman, opened an attack on Lord Melville on
charges of malversation of office, and misappropriation of public
moneys, during his former Treasurership of the Navy, either directly,
or by collusion with his principal financial subordinate. The attack
grew fiercer and fiercer, as well as more extensive in its scope; and,
although it was evidently inspired mainly by the political
vindictiveness of a party made furious by long exclusion from office,
it became more formidable from the fact that some of Pitt’s own
friends either abetted it fully or thought that the irregularities in
account-keeping which had been disclosed ought not to pass without
Parliamentary censure. Pitt reeled under such a blow at once to his
private feelings and his administration; and, after doing his best to
resist, he had to consent that Lord Melville should quit office, and
that Lord Melville’s name should be struck off from the list of His
Majesty’s Privy Council till the charges against him were formally
and publicly tried. The trial was to be in the shape of an
impeachment before the House of Lords. Before it could come on Pitt
was dead. He died on the 23d of January 1806; and the longexcluded
Whigs had then their turn of power for somewhat more than a year
in what is remembered as the Fox and Grenville ministry,—a name
accurate only till the 13th of September 1806, when Fox followed his
great rival to the grave, and Lord Grenville became Premier singly. It
was in April and May 1806, when this Fox and Grenville ministry
was new in office, that the great trial of Lord Melville in Westminster
Hall was begun and concluded. The charges against him had been
formulated into ten articles; and he was acquitted upon all the ten,—
unanimously on the only one which vitally impeached his personal
integrity, by overwhelming majorities on five of the others, and by
smaller but still decisive majorities on the remaining four. On the
whole, it was a triumphant acquittal; and it was received as such
throughout Scotland,—where, at one of the dinners held in honour of
the event by the jubilant Scottish Tories, there was sung a famous
song beginning with this stanza:—
“Since here we are set in array round the table,
Five hundred good fellows well met in a hall,
Come listen, brave boys, and I’ll sing as I’m able
How innocence triumphed and pride got a fall.
But push round the claret,—
Come, stewards, don’t spare it;
With rapture you’ll drink to the toast that I give:
Here, boys,
Off with it merrily:
‘Melville for ever, and long may he live!’”
Melville did live for some time longer, restored to his place in the
Privy Council, and rehabilitated in honour, but never again in office,
hardly caring to concern himself further with politics, and spending
his last years mainly in Scotland. He died on the 27th of May 1811, in
the seventieth year of his age.
That system of the government of Scotland by proconsulship of
which he had been so conspicuously the representative did not by
any means die with him. It was continued, with variations and
modifications, through those successive ministries of the later part of
the reign of George III. and the whole of the reign of George IV.
which fill up the interval between the death of Pitt and the eve of the
Reform Bill; nay, not only so continued, but continued with the
accompanying phenomenon that it was still a Dundas that exercised,
occasionally at least, what did remain of the proconsulship. Robert
Dundas, 2d Viscount Melville, who died as late as 1851, was a
member of most of the successive administrations mentioned, from
Perceval’s of 1809–12, through Liverpool’s of 1812–27, to Canning’s
and the Duke of Wellington’s of 1827–30, holding one or other of his
father’s old posts in these administrations, and so or otherwise
maintaining the hereditary Dundas influence in Scottish affairs while
Toryism kept the field. But, while this prolongation of the Dundas
influence in the second Lord Melville is not to be forgotten, it is the
father, Henry Dundas, 1st Lord Melville, that has left the name of
Dundas most strikingly impressed upon the history of Scotland, and
it is the stretch of two-and-twenty years between 1783 and 1806,
during which this greatest of the Dundases exercised the
proconsulship, that has to be remembered especially and
distinctively in Scottish annals as the time of the Dundas Despotism.
“The Dundas Despotism!” O phrase of fear, unpleasing to a

modern ear! What a Scotland that must have been which this phrase
describes! A country without political life, without public meetings,
without newspapers, without a hustings: could any endurable
existence be led in such a set of conditions,—could any good come
out of it?
Incredible as it may seem, there is evidence that the Scottish
people did contrive, in some way or other, to lead not only an
endurable but a very substantial and jolly existence through the
Dundas Despotism, and that not only a great deal of good, but much
of what Scotland must now regard as her best and most
characteristic produce, had its genesis in that time, though the
exodus has been later. The various liberties of the human subject
may be classified and arranged according to their degrees of
importance; and a great many of them may exist where the liberty of
voting for members of parliament and of openly talking politics is
absent. So it was in Scotland through the reign of Henry Dundas and
his Toryism. The million and a half of human beings who then
composed Scotland, and were scattered over its surface, in their
various parishes, agricultural or pastoral, and in their towns and
villages, went through their daily life with a great deal of energy and
enjoyment, notwithstanding that Dundas, and the lairds and the
provosts and bailies as his agents, elected the members of parliament
and transacted all the political business of the country; nay, out of
the lairds and the bailies themselves, and all the business of
electioneering, they extracted a good deal of fun. What mattered it to
them that now and then some long-tongued fellow who had started a
newspaper was stowed away in jail, or that an Edinburgh lawyer like
Muir was transported for being incontinent in his politics? Could not
people let well alone, obey the authorities, earn their oatmeal, and
drink their whisky in peace? Few of Scott’s novels come down so far
as to this period of Scottish life, and it has not been much described
in our other literature of fiction; but till lately there were many alive
who remembered it, and delighted in recalling its savageries and its
humours. O the old Scottish times of the lairds, the “moderate”
ministers, the provosts and the bailies!—the lairds speaking broad
Scotch, farming their own lands, carousing together, seeing their
daughters married, and writing to London for appointments for their
sons; the “moderate” ministers making interest for their sons,
preaching “Blair and cauld morality” on Sundays, and jogging to
christenings or to Presbytery dinners through the week; the provosts
and bailies in their shops in the forenoon, or meeting in the morning
at their “deid-chack” after a man was hanged! Every considerable
town then had its hangman, who was frequently a well-to-do person
that sold fish or some such commodity. And then, all through society,
the flirtations, the friendships, and the long winter evenings at the
fireside, with the cracks between the “gudeman” and his neighbours,
and the alternative of a hand at cards or a well-thumbed book for the
young folks! What stalwart old fellows, both of the douce and of the
humorous type, oracular and respected in their day, and whose
physiognomies and maxims are still preserved in local memory, lived
and died in those days and made them serve their turn! Nay, of the
Scotsmen who have been eminent in the intellectual world, what a
number belong by their birth to the reign of Dundas, and were
nurtured amid its torpid influences! Burns closed his life in the midst
of it; Dugald Stewart and James Watt lived through it; Scott, Jeffrey,
Chalmers, Wilson, Hamilton, and Carlyle are all, more or less,
specimens of what it could send forth. Vixere fortes ante
Agamemnona: there was pith in Scotland before there was
Parliamentary Reform.
Naturally it was in Edinburgh that the various elements of
Scottish life at this time were seen in their closest contact and their
most intimate union or antagonism. It was here that Dundas lived
when he was in Scotland; and here were the central threads of that
official network by which, through Dundas, Scotland was connected
with the English Government. Edinburgh was then still the chief city
of Scotland, even in population; for, though now Glasgow has far
outstripped it in that particular, then the two cities were happy in
numbering little more than 80,000 each. At least, in the census of
1801 Edinburgh stands for 82,000, or almost exactly neck to neck
with Glasgow, which stands for 83,000. Dundee, which came next,
reckoned but 29,000; Aberdeen, 27,000; and Leith and Paisley each
about 20,000. Few other Scottish towns had a population of more
than 10,000.
Was there ever another such city to live in as Edinburgh?
“And I forgot the clouded Forth,
The gloom that saddens heaven and earth,
The bitter east, the misty summer,
And gray metropolis of the North.”
One regrets that this is all that our noble Laureate’s experience of
Edinburgh enabled him to say. The east winds do bite there fearfully
now and then, and blow a dust of unparalleled pungency in your eyes
as you cross the North Bridge; but, with that exception, what a city!
Gray! why, it is gray, or gray and gold, or gray and gold and blue, or
gray and gold and blue and green, or gray and gold and blue and
green and purple, according as the heaven pleases, and you choose
your ground! But, take it when it is most sombrely gray, where is
another such gray city? The irregular ridge of the Old Town, with its
main street of lofty antique houses rising gradually from Holyrood
up to the craggy Castle; the chasm between the Old Town and the
New, showing grassy slopes by day, and glittering supernaturally
with lamps at night; the New Town itself, like a second city spilt out
of the Old, fairly built of stone, and stretching downwards over new
heights and hollows, with gardens intermixed, till it reaches the flats
of the Forth! Then Calton Hill in the midst, confronted by the
precipitous curve of the Salisbury Crags; Arthur Seat looking over all
like a lion grimly keeping guard; the wooded Corstorphines lying soft
away to the west, and the larger Pentlands looming quiet in the
southern distance! Let the sky be as gray and heavy as the absence of
the sun can make it, and where have natural situation and the hand
of man combined to exhibit such a mass of the city picturesque? And
only let the sun strike out, and lo! a burst of new glories in and
around. The sky is then blue as sapphire overhead; the waters of the
Forth are clear to the broad sea; the hills and the fields of Fife are
distinctly visible from every northern street and window; still more
distant peaks are discernible on either horizon; and, as day goes
down, the gables and pinnacles of the old houses blaze and glance
with the radiance of the sunset. It is such a city that no one, however
familiar with it, can walk out in its streets for but five minutes at any
hour of the day or of the night, or in any state of the weather, without
a new pleasure through the eye alone. Add to this the historical
associations. Remember that this is the city of ancient Scottish
royalty; that there is not a close or alley in the Old Town, and hardly
a street in the New, that has not memories of the great or the quaint
attached to it; that the many generations of old Scottish life that have
passed through it have left every stone of it, as it were, rich with
legend. To an English poet all this might be indifferent; but hear the
Scottish poets:—
“Edina! Scotia’s darling seat!
All hail thy palaces and towers!”
was the salutation of Burns, when first brought from his native
Ayrshire to behold the Scottish capital. “Mine own romantic town,”
was the outburst of Scott, in that famous passage where, after
describing Edinburgh as seen from the Braids, he makes even an
English stranger beside himself with rapture at the sight:—
“Fitz-Eustace’ heart felt closely pent;
As if to give his rapture vent,
The spur he to his charger lent,
And raised his bridle hand,
And, making demi-volte in air,
Cried, ‘Where’s the coward that would not dare
To fight for such a land?’”
Here, though it is an Englishman that is supposed to speak, it is a

Scotsman that supplies the words; but there can be no such objection
in the case of the following lines from a sonnet, entitled “Written in
Edinburgh,” by Tennyson’s friend, Arthur Hallam:—
“Even thus, methinks, a city reared should be,
Yea, an imperial city, that might hold
Five times a hundred noble towns in fee ...
Thus should her towers be raised; with vicinage
Of clear bold hills, that curve her very streets,
As if to indicate, ’mid choicest seats
Of Art, abiding Nature’s majesty,—
And the broad sea beyond, in calm or rage
Chainless alike, and teaching liberty.”
At the time with which we are concerned this city had the
advantage of containing, as has been said, only about eighty
thousand people. For comfortable social purposes, that is about the
extreme size to which a city should go. The size of London is
overwhelming and paralysing. There can be no intimacy, no unity of
interest, in such a vast concourse. Ezekiel might be preaching in
Smithfield, Camberwell might be swallowed up by an earthquake,
and the people of St. John’s Wood would know nothing of either fact
till they saw it announced in the newspapers next morning. Hardly
since the days of the Gordon Riots has London ever been all agitated
simultaneously. In Ancient Athens, on the other hand, we have an
illustration of what a town of moderate size could be and produce.
That such a cluster of men as Pericles, Socrates, Æschylus,
Sophocles, Euripides, Aristophanes, Plato, Phidias, Alcibiades,
Xenophon, and others,—men of an order that we only expect to see
now far distributed through space and time, nantes rari in gurgite
vasto,—should have been swimming contemporaneously or nearly so
in such a small pond as Athens was, and that this affluence in
greatness should have been kept up by so small a population for
several ages, seems miraculous. The peculiar fineness of the Hellenic
nerve may have had something to do with the miracle; but the
compactness of the place,—the aggregation of so many finely and
variously endowed human beings precisely in such numbers as to
keep up among them a daily sense of mutual companionship,—must
also have had its effect. In “Modern Athens” the conditions of its
ancient namesake are not all reproduced. To say nothing of any
difference that there may be in respect of original brain-and-nerve
equipment between the modern and the ancient Athenian, “Modern
Athens” is, unfortunately, not a separate body-politic, with separate
interests and a separate power of legislation. There are no walls now
round the Edinburgh territory; nor have the Edinburgh people the
privilege of making wars and concluding treaties with even the
nearest portions of the rest of Great Britain. They cannot meet
periodically on the Castle Esplanade to pass laws for themselves in
popular assembly, and hear consummate speeches beginning “O men
of Edinburgh.” But, with many such differences, there are some
similarities. Everybody in Edinburgh knows, or may know,
everybody else, at least by sight; everybody meets everybody else in
the street at least once every day or two; the whole town is within
such convenient compass that, even to go from one extremity of it to
the other extremity, there is no need to take a cab unless it rains. It is
a city capable of being simultaneously and similarly affected in all its
parts. An idea administered to one knot of the citizens is as good as
administered to the whole community; a joke made on the Mound at
noon will ripple gradually to the suburbs, and into the surrounding
country, before the evening. If such is the case even now, when the
population is over 260,000, must it not have been still better when
the population was only 80,000, and that population was more shut
in within itself by the absence as yet of telegraphs and railroads?
Moreover, the eighty thousand people who were in Edinburgh
when Henry Dundas ruled Scotland were people of a rather peculiar,
and yet rather superior, mixture of sorts. There never has been any
very large amount of trade or of manufacture in Edinburgh, nor
much of the wealth or bustle that arises from trade and manufacture.
For the roar of mills and factories, and for a society ranging
correspondingly from the great millionaire uppermost to crowds of
operatives below, all toiling in the pursuit of wealth, one must go to
Glasgow. In Edinburgh the standard of the highest income is much
lower, and the standard of the lowest is perhaps higher, than in
Glasgow; nor is wealth of so much relative importance in the social
estimate. Roughly classified, the society of Edinburgh in the days to
which we are now looking back consisted, as the society of
Edinburgh still consists, of an upper stratum of lawyers and resident
gentry, college officials, and clergy, reposing on, but by no means
separated from, a community of shopkeepers and artisans sufficient
for the wants of the place. Let us glance at these components of the
society of Old Edinburgh in succession:—
First, The Lawyers and Resident Gentry.—These two classes
may be taken together, as to a certain extent identical. From the time
of the Union, such of the old nobility of Scotland as had till then
remained in their native country, occupying for a part of the year the
homely but picturesque residences of their ancestors in the Old Town
of Edinburgh, had gradually migrated southwards, leaving but a few
families of their order to keep up their memory in the ancient capital
of Holyrood and St. Giles. In the room of this ancient nobility, and,
indeed, absorbing such families of the old nobility as had remained,
there had sprung up,—as might have been expected from the fact
that Edinburgh, though it had parted with its Court and Legislature,
was still the seat of the supreme Scottish law-courts,—a new
aristocracy of lawyers. The lawyers,—consisting, first, of the judges
as the topmost persons, with their incomes of several thousands a
year, and then of the barristers, older and younger, in practice or out
of practice, but including also the numerous body of the “Writers to
the Signet” and other law-agents,—are now, and for the last century
or two have been, the dominant class in the Edinburgh population.
From the expense attending education for the legal profession, the
members of it, till within a time comparatively recent, were generally
scions of Scottish families of some rank and substance; and, indeed,
it was not unusual for Scottish lairds or their sons to become
nominally members of the Scottish bar, even when they did not
intend to practise. The fact of the substitution of the legal profession
for the old Scottish aristocracy in the dominant place in Edinburgh
society is typified by the circumstance that the so-called “Parliament
House,”—retaining that name because it enshrines the hall where the
Estates of the Scottish Kingdom held their meetings during the last
eighty years of the time when Scotland had no Parliaments but her
own,—is now the seat of the supreme Scottish law-courts, and the
daily resort of the interpreters of the laws in these courts. Any day
yet, while the courts are in session, the Parliament House, with its
long oaken ante-room, where scores of barristers in their wigs and
gowns, accompanied by writers in plainer costume, are incessantly
pacing up and down, and its smaller inner chambers, where the
judges on the bench, in their crimson robes, are trying cases, is the
most characteristic sight in Edinburgh. Even now the general hour of
breakfast in Edinburgh is determined by the time when the courts
open in the morning; and, dispersed through their homes, or at
dinner-parties, in the evening, it is the members of the legal
profession that lead the social talk. In the old Dundas days it was the
same, with the addition that then the lawyers were perhaps more
numerous in proportion to the rest of the community than they are
now, and were more closely inter-connected by birth and marriage
with the Scottish nobility and lairds.
Of hardly less importance socially was the Academical Element.
As Edinburgh possesses a University, as its University has long been
in high repute, and as, by reason of the comparative cheapness of
board and education in Edinburgh, many families, after a residence
in England or the Colonies, have been attracted thither for the sake
of the education of their sons, or, without going thither themselves,
have sent their sons thither, the business of education has always
been prominent, if not paramount, among the industries of the city.
The teachers of the public and of other schools have always formed a
considerable class numerically, as well as in rank; while to the
University professors, partly from the higher nature of their
teaching-duties, partly from the traditional dignity conferred on
them by the great reputation of some of their body in past times, and
partly from some superiority in their emoluments, there has alway
been accorded a degree of social consideration not attached to the
same function anywhere out of Scotland. The reputation of the
Medical School of Edinburgh, in particular, has always invested the
professors in the Medical Faculty of the University with special
distinction; and, as these professors have been generally also at the
head of the medical practice of the city, the Medical element, and
with it the Scientific element, in Edinburgh society have from times
long past been, to a considerable extent, in union with the
professorial.
In all Scottish cities The Clergy have, from time immemorial,
exercised an amount of social influence not willingly allowed to any
other class of persons. This arises partly from the same causes which
give the clergy influence in other parts of Britain, but partly from the
peculiar affection of the Scottish people for the national theology
with which they have been saturated through so many centuries of
clerical teaching. In Edinburgh, in consequence of the perpetuation
there of relics of that old Scottish aristocracy which never was
completely brought into subjection to Presbytery, and in
consequence of the presence in society of a distinct intellectual
element in the lawyers, the clergy have not perhaps had, relatively,
the same weight as in other towns. Still they were powerful even in
the old Edinburgh of the Dundas rule. At the very least, a negative
respect was paid to them by the preservation throughout the place of
an external Presbyterian decorum and strictness; and in all houses
“the minister” was treated with distinction. Add to this that there
generally were among the Edinburgh clergy men possessing claims
to respect in addition to those belonging to their profession. Some,
even in that age of “Moderatism,” were remarkable for their
eloquence and zeal as preachers and as pastors; others had literary
pretensions; and others were professors in the University as well as
parish clergymen. More, indeed, than now, the professorial and the
clerical elements were then intermixed in Edinburgh. Perhaps,
however, that which gave the greatest dignity to the clerical or
ecclesiastical element in Edinburgh was the annual meeting in that
city, every May, of the General Assembly of the Church of Scotland.
In the history of Scottish society since the Union there is, perhaps, no
one fact of greater importance than the regular and uninterrupted
succession of those annual “General Assemblies” in Edinburgh for
the discussion of the affairs of the National Church. Let an
Englishman fancy that during the last two centuries there had been
no Parliament in England, no meetings of the House of Lords or of
the House of Commons, but that regularly during that period there
had been annual convocations of representatives of the whole body
of the English Clergy, together with such leading members of the
laity as churchwardens or the like from all the English parishes, and
that these convocations had sat ten days in every year, discussing all
public matters in any way bearing on the Church, and making laws
affecting the entire ecclesiastical organisation of England, and he will
have an idea of the extent to which the national history of Scotland
since her union with England is bound up in the records of her
“General Assemblies.” The General Assembly, in fact, from the year
1707 to the Disruption of the Scottish Church in 1843, was, to some
extent, a veritable Parliament, in which, though the secular
Parliament had been abolished, the united people of Scotland still
saw their nationality preserved and represented. All through the year
the clergy individually, in the thousand parishes or so into which
Scotland was divided, managed their own parochial affairs with the
assistance of select laymen called elders; these clergymen, again,
with some of their elders, held frequent district meetings, called
“presbyteries,” in order to regulate by deliberation and voting the
church affairs of their districts; there were still larger meetings,
periodically held, called “provincial synods”; but the grand
rendezvous of all, the supreme court of appeal and ecclesiastical
legislation, was the annual General Assembly in Edinburgh. The time
of its meeting was one of bustle and excitement. Black coats
swarmed in the streets; the Assembly was opened with military
pomp and circumstance by a Lord High Commissioner representing
the Crown; this Commissioner sat on a throne during the meetings,
and held levees and dinner-parties in Holyrood Palace all through
the ten days; the clergy, with lay representatives, some of whom were
usually noblemen or baronets, deliberated and debated during those
ten days, under a president of their own choosing called the
“Moderator”; the proceedings were in parliamentary form, and the
decisions by a majority of votes; and in many cases,—as in trials of
clergymen for moral or ecclesiastical misdemeanour,—barristers
were called in to plead professionally, as they did in the secular law-
courts. As was natural in a deliberative assembly almost all the
members of which were of the speaking class, the speaking was of a
very high order,—far higher, indeed, than has ever been heard in
these later days in the British Parliament; while at the same time
there was ample opportunity for the exercise of business talent and
of all the tact and skill of party-leadership. Much of the general
politics of Scotland took necessarily the form of church politics; and,
indeed, the connections between church politics and state politics
were pretty close. The vast majority of the clergy were adherents of
Dundas in general politics, and bent on swaying church polity in the
same direction; while the small minority of “Evangelicals” or “High-
Fliers,” as they were called, corresponded to the proscribed
“Liberals” in secular politics. The leading clergymen of both parties
were to be found in or near Edinburgh.
Respecting the Mercantile and Artisan classes it need only be
repeated that they were by no means separated by any social
demarcation from the fore-mentioned classes, but were intertwined
with these by family-relationships, and often also by the sympathies
belonging to superior natural intelligence and superior education.
Booksellers and printers were more numerous in Edinburgh
proportionally than in any other British town.
In a population of such dimensions, composed as has been
described, there was necessarily a good deal of leisure; and leisure
leads to sociability. Edinburgh in those days was one of the most
sociable towns in the world. By that time “society,” in the
conventional sense, had, with a few lingering exceptions, shifted
itself out of the Old Town into the New, or into the suburbs; and,
with this change, there had been a considerable change of manners.
Much of the formality, and at the same time much of the coarseness,
of an older stage of Scottish life had been civilised away,—the absurd
etiquette of the old dancing assemblies, for example, and the more
monstrous excesses of hard drinking. But the convivial spirit, and
many of the old convivial forms, remained. Dinner parties were
frequent; and the old custom of “toasts” and “sentiments” by the
hosts and the guests over their wine was still in fashion. Lord
Cockburn’s description of those dinner parties of his youth is one of
the best passages in his book. But it is on the supper parties that he
dwells with most evident affection. There were various kinds of
supper parties: the oyster supper at taverns, the bachelor supper in
lodgings, and the real domestic supper, to which both sexes were
invited; which last Lord Cockburn vaunts as a delightful institution
of Edinburgh, which the advancing lateness of the dinner-hour had
unhappily superseded. In short, in every form and way, from the set
dinner party, with its immense consumption of claret, in the houses
of the more wealthy, to the homely tea parties of gentlewomen of
moderate means, living in the suburbs of the Old Town, or in flats in
the New Town, and the roystering suppers of young men, where
culinary deficiencies were compensated by good humour and the
whisky punch, people were in the habit of incessantly meeting to
spend the evenings together. Lord Cockburn mentions, as illustrative
of the continuance of those sociable habits of the Edinburgh folks to
a somewhat later period than that with which we are immediately
concerned, the fact that for a great many years after his marriage,
which was in 1811, he had not spent above one evening in every
month, on the average, in solitude, i.e. without either being out as a
guest, or having friends with him at home. Even Sydney Smith,
though not native and to the manner born, and, with his English
tastes, more fastidious in his ideas of conviviality, retained to the last
a pleasant recollection of those Edinburgh hospitalities, as
experienced by him during his stay in Edinburgh from 1797 to 1802.
“When shall I see Scotland again?” he says in one of his letters:
“never shall I forget the happy days passed there, amidst odious
smells, barbarous sounds, bad suppers, excellent hearts, and the
most enlightened and cultivated understandings.”
Sydney Smith’s allusion to “the enlightened and cultivated
understandings” he encountered amid such roughish surroundings,
suggests the mention of what was, all in all, the most characteristic
feature of Edinburgh society at the close of the eighteenth century
and the beginning of the nineteenth—its intellectualism. In a
community composed in so large a measure of practitioners of the
learned professions, it was inevitable that there should be more of
interest in matters intellectual than is common, more of a habit of
reasoning and discussion, more play and variety in the choice of
topics for conversation. What mattered it that many of the most
intellectual men and women gave expression to their ideas in broad
Scotch? Ideas may be expressed in broad Scotch, and yet be the ideas
of cultivated minds; at all events, it was so then in Edinburgh, where
many excellent lawyers, University professors, and medical men kept
up the broad Scotch in their ordinary conversation, though the
majority had gone over to the English in all save accent, and some
were sedulous in trying to Anglicise themselves even in that. But,
whether the dialect was English or Scotch, there was a great deal of
very pleasant and very substantial talk. True, in Sydney Smith’s
recollection of the conversation of the Edinburgh people at the time
he moved among them, two great faults are specified. It ran too
much, he records, to that species of jocosity, perfectly torturing to an
Englishman, which the Scotch themselves called wut; and it also ran
too much, he records, into disputation and dialectics. “Their only
idea of wit,” he says, speaking of the Scotch generally, but of the
Edinburgh people in particular, “or rather of that inferior variety of
the electric talent which prevails occasionally in the North, and
which, under the name of wut, is so infinitely distressing to people of
good taste, is laughing immoderately at stated intervals.” And again
—“They are so imbued with metaphysics that they even make love
metaphysically: I overheard a young lady of my acquaintance, at a
dance in Edinburgh, exclaim, in a sudden pause of the music, ‘What
you say, my lord, is very true of love in the abstract, but——,’ here
the fiddlers began fiddling furiously, and the rest was lost.” This is
somewhat unfair. Wut, in its place, is as good as wit, and may be a
great deal heartier. As practised in the north, it corresponds more
with what is properly humour. It consists in a general openness to
the ludicrous view of things, a general disposition to call each other
Tam and Sandy, a general readiness to tell and to hear Scottish
stories the fun of which lies in the whole series of conceptions (often
too local) that they call up, rather than in any sudden flash or quip at
the close. At all events, the Scotch like their wut, and find it
satisfying. As for the dialectics, there is, perhaps, too much of that.
The excess in this direction is due, doubtless, in part to the
omnipresence of the lawyers. But wut and dialectics make a very
good mixture; and, dashed as this mixture is and always has been in
Edinburgh with finer and higher ingredients, there has been no town
in Britain for the last century and a half of greater deipnosophistic
capabilities, all things considered.
One element which Englishmen who do not know Edinburgh
always imagine as necessarily wanting in it never has been wanting.
Whether from the influence of the lawyers, and of the relics of the old
Scottish baronage and baronetage, acting conjointly as a
counterpoise to the influence of the clergy, or from other less obvious
causes, there has always been in Edinburgh a freer undercurrent of
speculative opinion, a tougher traditional scepticism, a greater
latitude of jest at things clerical and Presbyterian, than in other
Scottish towns. From the early part of the eighteenth century, when
Allan Ramsay, Dr. Archibald Pitcairn, and others, did battle with the
clergy in behalf of theatrical entertainments and other forms of the
festive, there has never been wanting a strong anti-clerical and even
free-thinking clique in Edinburgh society; and towards the end of the
century, when David Hume and Hugo Arnot were alive or
remembered, no city in Britain sheltered such a quantity of cosy
infidelity. Of hundreds of stories illustrative of this, take one of the
mildest:—Pitcairn, going about the streets one Sunday, was obliged
by a sudden pelt of rain to take refuge in a place he was not often in,
—a church. The audience was scanty; and he sat down in a pew
where there was only another sitter besides,—a quiet, grave-looking
countryman, listening to the sermon with a face of the utmost
composure. The preacher was very pathetic; so much so that at one
passage he began to shed tears copiously, and to use his pocket-
handkerchief. Interested in this as a physiological phenomenon for
which the cause was not apparent, Pitcairn turned to the
countryman, and asked in a whisper, “What the deevil gars the man
greet?” “Faith,” said the man, slowly turning round, “ye wad maybe
greet yoursel’ if ye was up there and had as little to say.” Pitcairn was
the type of the avowed Edinburgh infidel; of which class there were
not a few whose esoteric talk when they met together was of an out-
and-out kind; but the countryman was the type of a still more
numerous class, who kept up exterior conformity, but tested all
shrewdly enough by a pretty tough interior instinct. Indeed, long
after Pitcairn’s time, a kind of sturdy scepticism, quite distinct from
what would be called “infidelity,” was common among the educated
classes in Edinburgh. Old gentlemen who went duly to church, who
kept their families in great awe, and who preserved much etiquette in
their habits towards each other, were by no means strait-laced in
their beliefs; and it was not till a considerably later period, when a
more fervid religious spirit had taken possession of the Scottish
clergy themselves, and flamed forth in more zealous expositions of
peculiar Calvinistic doctrine from the pulpit than had been
customary in the days of Robertson and Blair, that evangelical
orthodoxy obtained in Edinburgh its visible and intimate alliance
with social respectability. Moreover, even those who were then
indubitably orthodox and devout by the older standard were devout
after a freer fashion, and with a far greater liberty both of conduct
and of rhetoric, than would now be allowable in consistency with the
same reputation. There is no point on which Lord Cockburn lays
more stress than on this. “There is no contrast,” he says, “between
those old days and the present that strikes me so strongly as that
suggested by the differences in religious observances, not so much by
the world in general, as by deeply religious people. I knew the habits
of the religious very well, partly through the piety of my mother and
her friends, the strict religious education of her children, and our
connection with some of the most distinguished of our devout
clergymen. I could mention many practices of our old pious which
would horrify modern zealots. The principles and feelings of the
persons commonly called evangelical were the same then that they
are now; the external acts by which these principles and feelings
were formerly expressed were materially different.”
Among the differences, Lord Cockburn notes in particular the
much laxer style, as it would now be called, in which Sunday was
observed by pious people and even by the most pious among the
clergy. There seems also to have been more freedom of speech, in the
direction of what would now be called profane allusion, among the
admittedly pious. One of the gems of Lord Cockburn’s book is his
portrait of one venerable old lady, a clergyman’s widow, sitting
neatly dressed in her high-backed leather chair, with her
grandchildren round her, the very model of silver-haired serenity, till
one of her granddaughters, in reading the newspaper to her,
stumbled on a paragraph which told how the reputation of a certain
fair one at the court of the Prince Regent had suffered from some
indiscreet talk of his about his own relations with her, but then
starting up, and exclaiming, with an indignant shake of her
shrivelled fist,—“The dawmed villain! does he kiss and tell?” There
were not a few old ladies of this stamp in Edinburgh in Lord
Cockburn’s boyhood and youth; some of whom survived far into the
present century, too old to part with their peculiarities, even to
please the clergy. “Ye speak, sir, as if the Bible had just come oot,”
said one such old lady, who lingered long in Edinburgh, to a young
clergyman who was instructing her on some point of Christian
practice on which she was disposed to differ from him. The
continuation in the society of Edinburgh of a considerable sprinkling
of such free-speaking gentlewomen of the old Scottish school,
intermingled with as many of the other sex using a still rougher
rhetoric, imparted, we are told, a flavour of originality to the
convivial conversation of the place for which there is now no exact
equivalent.
Presided over by such seniors, the young educated men of the
time did not stint themselves in the choice or the range of their
convivial topics. They discussed everything under the sun and down
to the centre. Who has not heard of the Speculative Society of
Edinburgh, founded in 1764 in connection with the University, and
kept up from that time to this by successive generations of students;
of which Lord Cockburn says that it “has trained more young men to
public spirit, talent, and liberal thought, than all the other private
institutions in Scotland”? Between 1780 and 1800 this society was in
all its glory, discussing, week after week, as its minutes inform us,
such topics as these:—“Ought any permanent support to be provided
for the poor?” “Ought there to be an established religion?” “Was the
execution of Charles I. justifiable?” “Should the slave trade be
abolished?” “Has the belief in a future state been of advantage to
mankind, or is it ever likely to be so?” “Is it for the interest of Britain
to maintain what is called the balance of Europe?” Here surely was
scepticism enough to keep thought alive; and that such questions,
discussed not only in the Speculative Society, but also in minor
associations of the same kind, and carried doubtless also, with other
more scientific topics, into private assemblages, should have been
ventilated in Edinburgh at that day, shows that, even under the
Dundas Despotism, there was no lack of intellectual freedom.
It is but a continuation of what we have been saying to add that
the old Edinburgh of those defunct decades had already an
established reputation as a literary metropolis. The rise of the
literary reputation of Edinburgh may date, for all purposes except
such as shallow present scholarship would call merely antiquarian,
from the time when Allan Ramsay set up his circulating library in the
High Street, and supplied the lieges furtively with novels, plays, and
song-books, including his own poems. This was about the year 1725,
when his countryman, Thomson, was publishing in London the first
portion of his Seasons. Thomson himself, and his contemporaries or
immediate successors, Mallet, Smollett, Armstrong, Meikle,
Macpherson, and Falconer, all rank in the list of literary Scots; but
they were Scoti extra Scotiam agentes, and had, most of them, but
an incidental connection with Edinburgh. The poets Robert Blair and
James Beattie, the philosopher Reid, and the theologian and critic
Dr. George Campbell, were not only literary Scots, but literary Scots
whose lives were spent on their own side of the Tweed; but, with the
exception of Blair, none of them were natives of Edinburgh, and even
Blair did not live there. After Ramsay, in short, the early literary
fame of Edinburgh is associated with the names of a cluster of men
who, born in different parts of Scotland, had, from various chances,
taken up their abode in Edinburgh, and who resided there, more or
less permanently, during the latter half of the eighteenth century.
The most prominent men of this cluster were these:—David Hume
(1711–1776), known as a philosophical writer since the year 1738, and
who, though he spent a good many years of his literary life in
England and in France, was for the last twenty years of it, and these
the most busy, a resident in Edinburgh; Hume’s senior and survivor,
Henry Home, Lord Kames (1696–1782), one of the judges of the
Court of Session, still remembered for the contrast between the
coarse Scottish facetiousness of his manners and the studied fineness
of his writings; the learned and eccentric Burnet, Lord Monboddo
(1714–1799), also a judge of Session, at whose Attic suppers in the
Old Town all the talent and beauty of Edinburgh were for many years
regularly assembled; the pompous but sensible Dr. Hugh Blair
(1718–1799), Professor of Belles Lettres in the University, and one of
the clergymen of the city; his more celebrated colleague, Dr.
Robertson the historian (1722–1793), Principal of the University, and
likewise one of the city clergymen; the minor historical writers and
antiquarians, Tytler of Woodhouselee (1711–1792), Dr. Henry (1718–
1790), Lord Hailes (1726–1792), Dr. Adam Ferguson (1724–1816),
and Dr. Gilbert Stuart (1742–1786); the poet John Home, author of
the tragedy of Douglas (1722–1808), once the Rev. Mr. Home, but
long bereft of that title, and known since 1779 as a retired man of
letters in Edinburgh; the illustrious Adam Smith (1723–1790),
settled in Edinburgh during the last twenty years of his life in the
post of commissioner of customs; the hardly less illustrious Dugald
Stewart (1753–1828), elected Professor of Mathematics in the
University as early as 1774, but thence transferred in 1785 to the
chair of Moral Philosophy, where he completed his fame; and, lastly,
not to overburden the list, the novelist and essayist Henry Mackenzie
(1745–1831), an acknowledged literary celebrity ever since 1771,
when he had published his Man of Feeling. In a class by himself,
unless we choose to associate him with the Creeches, Smellies, and
other “wuts” of a lower grade, whose acquaintance Burns made in his
leisure hours during his first visit to Edinburgh in 1786, we may
mention Burns’s immediate predecessor in the poetry of the Scottish

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Computational Biophysics of

Membrane Proteins Carmen Domene

Life as a matter of fat lipids in a membrane biophysics

Fundamentals of Membrane Bioreactors Materials Systems

Introduction to the Fast Multipole Method Topics in

Modern Tools of Biophysics 1st Edition Thomas Jue

Membrane Characterization Nidal Hilal

Membrane processes pervaporation vapor permeation and

Aging Research Methodological Issues Carmen García-Peña

Fictions of Migration in Contemporary Britain and

Computational Biophysics of Membrane Proteins

RSC Theoretical and Computational Chemistry Series

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RSC Theoretical and Computational Chemistry Series No. 10

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Chapter 1 Introduction to the Structural Biology of Membrane

Chapter 2 Molecular Dynamics Simulations: Principles and

RSC Theoretical and Computational Chemistry Series No. 10

2.2.3 Practical and Technical Considerations 25

2.4 Ab initio Molecular Dynamics 33

Chapter 3 Free Energy Calculations for Understanding Membrane

Chapter 4 Non-atomistic Simulations of Ion Channels 107

4.1 Introduction 107

4.2 Methods Based on Continuum Distributions

Chapter 5 Experimental and Computational Approaches to Study

5.1 Introduction 137

5.6 Computational Approaches to Study Membrane

5.6.2 Atomistic Simulations Elucidating

Chapter 6 Computer Simulation of Ion Channels 161

6.1 Introduction to Ion Channels 161

Chapter 7 Computational Characterization of Molecular

7.1 Membrane Transport – A Fundamental Biological

7.2.2Proposing Substrate Binding Sites through

Equilibrium Molecular Dynamics 205

Chapter 8 Computational Studies of Receptors 237

8.1 Introduction 237

8.9 Molecular Dynamics to Explain the Eﬀects of

8.11 Conclusions 255

Subject Index 259

Introduction to the Structural

Department of Chemistry and Biochemistry, San Francisco State

RSC Theoretical and Computational Chemistry Series No. 10

25 years behind that of soluble proteins. In 1988, Harmut Michel, Johann

1.2 Membrane Features

Introduction to the Structural Biology of Membrane Proteins 3

Rotational diffusion wobble

those anchored by the cytoskeleton. A large proportion of membrane

Introduction to the Structural Biology of Membrane Proteins 5

1.3 Lipid Polymorphism

Prokaryotes lack cholesterol and other steroids, while some eukaryotic

Introduction to the Structural Biology of Membrane Proteins 7

1.4 Classes of Membrane Proteins

embedded in the membrane: they interact extensively with membrane

1.4.1 a-Helical Bundles

Introduction to the Structural Biology of Membrane Proteins 9