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 Cell Boundaries

K50004_Book.indb 1 16-11-2021 21:01:43

TNF_00_K50004_PRELIMS_INFO_docbook_new_indd.indd 2 19-11-2021 22:57:03
 Cell Boundaries
How Membranes and Their Proteins Work

Stephen H. White
Gunnar von Heijne
Donald M. Engelman

K50004_Book.indb 3 16-11-2021 21:01:47

 Cover image: Wassily Kandinsky “Circles in a Circle” (1923). The Philadelphia Museum of Art: The Louise and Walter Arensberg Collection,
1950, 1950-134-104.

First edition published 2022

by CRC Press
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and by CRC Press

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© 2022 Taylor & Francis Group, LLC

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ISBN: 978-0-815-34216-8 (hbk)

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ISBN: 978-0-429-34132-8 (ebk)

DOI: 10.1201/9780429341328

Typeset in Utopia Std

by Deanta Global Publishing Services, Chennai, India

Instructors can access the Figure Slides at the Instructor Hub, upon registering (https://routledgetextbooks.com/textbooks/
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TNF_00_K50004_PRELIMS_INFO_docbook_new_indd.indd 4 17-11-2021 15:58:36

 Contents

List of Boxes.....................................................................................................................xi
Preface............................................................................................................................xv
Acknowledgements..................................................................................................... xvii

Chapter 0 The “E” Words: A Concise Guide to Thermodynamics.......................1

0.1 Work, Heat, and Energy..............................................................................................1
0.2 First Law of Thermodynamics....................................................................................2
0.3 Second Law of Thermodynamics..............................................................................6
0.4 The Second Law and Statistical Thermodynamics...................................................8
0.5 Gibbs Energy...............................................................................................................9
0.6 Chemical Potential...................................................................................................10
0.7 Boltzmann Principle.................................................................................................12
0.8 The Nernst Equation.................................................................................................12
0.9 Generalized Equations of Thermodynamics..........................................................14
0.10 Perspective................................................................................................................15

Chapter 1 Foundations of Membrane Structure.................................................17

1.1 Membranes Define Cell Anatomy...........................................................................17
1.2 Plasma Membranes Are Composed of Surface-Active Lipids...............................21
1.3 Lipid Bilayers Are the Fabric of Cell Membranes...................................................31
1.4 Proteins Penetrate the Membrane Bilayer and Are Mobile in the
Membrane Plane.......................................................................................................42
Key Concepts......................................................................................................................49
Further Reading..................................................................................................................49
Key Literature......................................................................................................................49
Exercises..............................................................................................................................50

Chapter 2 Lipid Bilayers........................................................................................51

2.1 Biological Membrane Lipids Spontaneously Form Bilayers.................................52
2.2 Diffraction Methods Give Key Insights for Understanding Bilayer
Structure and Membranes.......................................................................................68
2.3 Macroscopic Descriptions of Bilayers Define Fundamental Properties of
Biological Membranes..............................................................................................79
2.4 Lipid Interactions Shape Membrane Properties....................................................86
Key Concepts......................................................................................................................93
Further Reading..................................................................................................................94
Key Literature......................................................................................................................94
Exercises..............................................................................................................................95

Chapter 3 Interactions of Peptides with Lipid Bilayers.......................................97

3.1 Gibbs Partitioning Energies Provide a Foundation for Describing Lipid–
Protein Interactions..................................................................................................98

K50004_Book.indb 5 16-11-2021 21:01:47

 vi Contents

3.2 Lipid Bilayers Have Distinct Properties Compared with Bulk

Organic Phases........................................................................................................104
3.3 Charged Peptides Interact Strongly, and Predictably, with Charged
Interfaces.................................................................................................................112
3.4 Membrane-active Peptides Provide Clues to Secondary Structure
Formation at Membrane Interfaces......................................................................119
Key Concepts....................................................................................................................133
Further Reading................................................................................................................134
Key Literature....................................................................................................................134
Exercises............................................................................................................................135

Chapter 4 Membrane Protein Folding and Stability.........................................137

4.1 Interactions between α-Helices Are Central to 3D Structure Formation...........138
4.2 α-Helical Membrane Proteins Can Be Destabilized Using Heat,
Detergents, and Denaturants.................................................................................144
4.3 β-Barrel Membrane Proteins Can Be Reversibly Unfolded
Using Denaturants..................................................................................................151
4.4 Lipid Bilayers and Membrane Proteins Adapt to Each Other.............................154
Key Concepts....................................................................................................................157
Further Reading................................................................................................................157
Key Literature....................................................................................................................158
Exercises............................................................................................................................158

Chapter 5 Protein Trafficking in Cells................................................................161

5.1 Translocases Mediate the Transport of Proteins across the Endoplasmic
Reticulum Membrane............................................................................................162
5.2 Bacteria Have Many Systems for Exporting Proteins...........................................174
5.3 Proteins Are Imported into Mitochondria, Chloroplasts, and Peroxisomes......181
5.4 Proteins Are Transported in and out of the Nucleus through the Nuclear
Pore Complex..........................................................................................................186
Key concepts.....................................................................................................................191
Further reading.................................................................................................................191
Key Literature....................................................................................................................192
Exercises............................................................................................................................192

Chapter 6 Biosynthesis and Assembly of Membrane Proteins........................195

6.1 Cellular Mechanisms of Membrane Protein Assembly.......................................196
6.2 Energetics of Membrane Protein Assembly..........................................................210
6.3 Membrane Protein Topology.................................................................................218
Key Concepts....................................................................................................................232
Further Reading................................................................................................................232
Key Literature....................................................................................................................233
Exercises............................................................................................................................233

Chapter 7 How Proteins Shape Membranes......................................................235

7.1 The Cytoskeleton Provides a Framework for Cell Shape and Vesicle
Transport.................................................................................................................236
7.2 Many Different Proteins Act Together to Create Vesicular Compartments
in Cells.....................................................................................................................243
7.3 Surface-Binding Proteins Modulate Membrane Curvature and Cause
Vesicle Scission.......................................................................................................251
Key Concepts....................................................................................................................261

K50004_Book.indb 6 16-11-2021 21:01:47

 Contents vii

Further Reading................................................................................................................261
Exercises............................................................................................................................264

Chapter 8 Membrane Protein Bioinformatics...................................................265

8.1 Evolution of Protein Amino Acid Sequences Provides a Basis for
Bioinformatics.........................................................................................................266
8.2 Prediction Methods Allow Identification of Functional and Structural
Features of Membrane Proteins............................................................................273
Key concepts.....................................................................................................................289
Further reading.................................................................................................................289
Key literature.....................................................................................................................289
Exercises............................................................................................................................290

Chapter 9 Primer on Biomolecular Structure Determination.........................291

9.1 Microscopy and Crystallography Depend upon Diffraction and Fourier
Transformation.......................................................................................................292
9.2 Electron Microscopy Is a Versatile Tool for Molecular Structure
Determination.........................................................................................................298
9.3 X-Ray Crystallography Is the Mainstay of Structural Biology..............................300
9.4 What Is the “Phase Problem,” and How Do We Conquer It?...............................307
9.5 Crystallographic Models of Proteins Are Derived from Electron Density
Maps.........................................................................................................................311
9.6 Electron Crystallography Is Useful for Diffraction from Small Crystals.............313
Key Concepts....................................................................................................................316
Further Reading................................................................................................................317
Exercises............................................................................................................................317

Chapter 10 Small-Molecule Channels.................................................................321

10.1 Water Can Cross Membranes Either by Diffusion through the Lipid
Bilayer or through Channels..................................................................................322
10.2 Water and Other Small Molecules Move across Membranes Using
Channels: Aquaporins and Aquaglyceroporins...................................................325
10.3 Aquaporin Structure Reveals Structure–Function Relationships.......................329
10.4 Gating and Control of Aquaporin Function..........................................................332
10.5 Ammonia Channels Have Many Roles across Phyla but Similar Structures......336
10.6 Specialized Mechanosensitive Channels Relieve Osmotic Stress......................339
10.7 β-Barrels in Outer Membranes Reveal Diverse Strategies for Solute
Permeation..............................................................................................................351
Key Concepts....................................................................................................................352
Further Reading................................................................................................................353
Key Literature....................................................................................................................353
Exercises............................................................................................................................353

Chapter 11 Ion Channels......................................................................................355

11.1 Ionic Currents across Membranes Underlie Nerve Action Potentials................358
11.2 Potassium Channels Are Highly Selective and Permit Diffusion-Limited
Ion Transport..........................................................................................................372
11.3 Ligands Can Control the Opening and Closing of Channels...............................379
11.4 Changes In Transmembrane Voltage Can Gate Channels Rapidly by
Changing Charge Exposure across the Membrane Barrier.................................386
11.5 Voltage-Gated Na+ Channel Mechanism and Hydrated-Ion Selection..............391
11.6 A Voltage-Gated Porin in the Outer Membrane of Mitochondria Controls
Exchange of Metabolites with the Cytoplasm of Eukaryotes..............................393

K50004_Book.indb 7 16-11-2021 21:01:47

 viii Contents

11.7 Conclusion..............................................................................................................395
Key Concepts....................................................................................................................395
Further Reading................................................................................................................397
Key Literature....................................................................................................................397
Exercises............................................................................................................................398

Chapter 12 Primary Transporters: Transport against Electrical and

Chemical Gradients...........................................................................399
12.1 P-Type ATPases.......................................................................................................400
12.2 The Transport Principles of ABC Transporters Differ from Those of the
P-Type ATPases.......................................................................................................408
12.3 Energy-Coupling Factor Transporters Couple ATP Hydrolysis to
“Toppling” of the Substrate-Binding Subunit.......................................................420
Key Concepts....................................................................................................................422
Further Reading................................................................................................................422
Key Literature....................................................................................................................422
Exercises............................................................................................................................422

Chapter 13 Secondary Transport.........................................................................425

13.1 Requirements for Secondary Transporters..........................................................430
13.2 Rocker-Switch Transporters: Major Facilitator Superfamily (MFS)
Symporters..............................................................................................................433
13.3 Rocking-Bundle Transporters: Neurotransmitter Sodium Symporters.............438
13.4 Elevator-Like Transporters: Structural Studies of a Glutamate
Transporter, GltPh, Reveal Similar Principles........................................................448
13.5 The ADP/ATP Transporter from Mitochondria....................................................452
13.6 Uniporters (aka Facilitators) Facilitate Transport without Chemical
Gradients.................................................................................................................455
13.7 Conclusion..............................................................................................................457
Key Concepts....................................................................................................................457
Further Reading................................................................................................................458
Key Literature....................................................................................................................458
Exercises............................................................................................................................458

Chapter 14 Bioenergetics......................................................................................461
14.1 The Chemiosmotic Theory Is the Foundation of Bioenergetics..........................462
14.2 Electrons Move along a Chain of Protein Complexes..........................................469
14.3 ATP Synthase Produces ATP Using the Proton Gradient.....................................475
14.4 Photosynthesis Harvests Light to Produce Oxygen..............................................481
Key Concepts....................................................................................................................489
Further Reading................................................................................................................489
Key Literature....................................................................................................................489
Exercises............................................................................................................................490

Chapter 15 Information Transfer: Signaling in Cells..........................................491

15.1 Bacteria Sense Their Environment by Two-Component Signaling Systems......491
15.2 Eukaryotic Cells Coordinate Their Interactions Using Receptor Tyrosine
Kinases.....................................................................................................................500
15.3 G Protein Receptors Transmit Signals across the Plasma Membrane in
Response to Hormones and Other Compounds..................................................508

K50004_Book.indb 8 16-11-2021 21:01:47

 Contents ix

15.4 Cadherins and Integrins Mediate Mechanical Interactions with

Neighboring Cells and the Extracellular Matrix...................................................522
Key Concepts....................................................................................................................528
Further Reading................................................................................................................528
Key Literature....................................................................................................................528
Exercises............................................................................................................................530

Electrostatics Appendix...............................................................................................531
Index.............................................................................................................................537

K50004_Book.indb 9 16-11-2021 21:01:47

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