Biophysical Chemistry

Biophysical Chemistry

Dagmar Klostermeier • Markus G. Rudolph

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Library of Congress Cataloging‑in‑Publication Data

Names: Klostermeier, Dagmar, author. | Rudolph, Markus G., author. Title: Biophysical chemistry / Dagmar Klostermeier and
Markus G. Rudolph. Description: Boca Raton, FL : CRC Press, Taylor & Francis Group, [2017] | Includes bibliographical references
and index. Identifiers: LCCN 2016035573| ISBN 9781482252231 (hardback ; alk. paper) | ISBN 1482252236 (hardback ; alk.
paper) | ISBN 9781482252255 (e-book) | ISBN 1482252252 (e-book) | ISBN 9781482252262 (e-book) | ISBN 1482252260 (e-book)
| ISBN 9781482252248 (e-book) | ISBN 1482252244 (e-book) Subjects: LCSH: Physical biochemistry. | Thermodynamics. |
Molecular structure. Classification: LCC QD476.2 .K56 2017 | DDC 572/.43--dc23 LC record available at https://lccn.loc.
gov/2016035573

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Contents

Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xvii
Acknowledgments. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xix
Authors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xxi

Part I — Thermodynamics

Chapter 1. Systems and their Surroundings. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3

Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Chapter 2. State Functions and the Laws of Thermodynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.1 General Considerations: State Variables and State Functions . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2.2 The Internal Energy U   and the First Law of Thermodynamics. . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.2.1 Internal Energy, Heat, and Work. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.2.2 The First Law of Thermodynamics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
2.2.3 The Ideal Gas: A Convenient System to Understand Thermodynamic Principles. . . . 9
2.2.4 Changes in the State of an Ideal Gas. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2.2.4.1 Irreversible Isothermal Expansion and Compression. . . . . . . . . . . . . . . . 12
2.2.4.2 Reversible Isothermal Expansion and Compression . . . . . . . . . . . . . . . . 13
2.2.4.3 Comparison of Reversible and Irreversible Changes of State. . . . . . . . . 14
2.2.4.4 Adiabatic Expansion and Compression. . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
2.2.5 Thermodynamic Cycles: Back and Forth or Round and Round. . . . . . . . . . . . . . . . 20
2.2.5.1 The Carnot Process. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
2.2.6 The Temperature Dependence of the Internal Energy U . . . . . . . . . . . . . . . . . . . . . 25
2.3 The Enthalpy H. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
2.4 The Entropy S and the Second Law of Thermodynamics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
2.4.1 Predicting Spontaneity of Processes: Dissipation of Heat and Matter. . . . . . . . . . 29
2.4.2 Entropy and Heat. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
2.4.3 Temperature Dependence of the Entropy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
2.4.4 The Third Law of Thermodynamics and Absolute Entropy . . . . . . . . . . . . . . . . . . . 33
2.4.5 Entropy and Order: The Statistic Interpretation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
2.5 The Free Energy G: Combining System and Surroundings. . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
2.5.1 Entropy- and Enthalpy-Driven Reactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
2.5.2 Pressure and Temperature Dependence of the Free Energy. . . . . . . . . . . . . . . . . . 41

v
vi   Biophysical Chemistry

2.5.3 Standard States. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43

2.5.4 Relation of Free Energy, Enthalpy, and Entropy to Molecular Properties. . . . . . . . 44
2.6 The Chemical Potential μ. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
2.6.1 The Chemical Potential as a Driving Force for Chemical Reactions. . . . . . . . . . . . 46
2.6.2 The Chemical Potential and Stable States: Phase Diagrams. . . . . . . . . . . . . . . . . . . 48
2.6.3 Pressure and Temperature Dependence of the Chemical Potential. . . . . . . . . . . . 51
2.6.4 The Chemical Potential as a Partial Molar Property . . . . . . . . . . . . . . . . . . . . . . . . . . 51
2.6.5 The Chemical Potential of Compounds in Mixtures. . . . . . . . . . . . . . . . . . . . . . . . . . 52
2.6.6 The Chemical Potential of Solutions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
2.6.7 Colligative Properties . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
Chapter 3. Energetics and Chemical Equilibria. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
3.1 The Free Energy Change and the Equilibrium Constant. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
3.1.1 Temperature Dependence of the Equilibrium Constant. . . . . . . . . . . . . . . . . . . . . . 69
3.1.2 The Principle of Le Chatelier. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
3.2 Binding and Dissociation Equilibria and Affinity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
3.3 Protolysis Equilibria: The Dissociation of Acids and Bases in Water. . . . . . . . . . . . . . . . . . . . . 74
3.4 Thermodynamic Cycles, Linked Functions and Apparent Equilibrium Constants. . . . . . . 75
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Chapter 4. Thermodynamics of Transport Processes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
4.1 Diffusion. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
4.2 The Chemiosmotic Hypothesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
4.3 Active and Passive Transport . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
4.4 Directed Movement by the Brownian Ratchet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
Chapter 5. Electrochemistry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
5.1 Redox Reactions and Electrochemical Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
5.2 Types of Half-Cells. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
5.3 Standard Electrode Potentials. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .105
5.4 The Nernst Equation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
5.5 Measuring pH values . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
5.6 Redox Reactions in Biology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
5.6.1 The Respiratory Chain. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109
5.6.2 The Light Reaction in Photosynthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
5.7 The Electrochemical Potential and Membrane Potentials . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
5.8 Electrophysiology: Patch-Clamp Methods to Measure Ion Flux through Ion Channels �������114
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 115
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116

Part II — Kinetics

Chapter 6. Reaction Velocities and Rate Laws. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119

Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
Chapter 7. Integrated Rate Laws for Uni- and Bimolecular Reactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
 Contents    vii

Chapter 8. Reaction Types . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137

8.1 Reversible Reactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
8.2 Parallel Reactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
8.3 Consecutive Reactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Reference. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Chapter 9. Rate-Limiting Steps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151
Chapter 10. Binding Reactions: One-Step and Two-Step Binding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
Chapter 11. Steady-State (Enzyme) Kinetics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
11.1 Rapid Equilibrium (Michaelis-Menten Formalism). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
11.2 Steady-State Approximation (Briggs-Haldane Formalism) . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
11.3 pH Dependence . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 167
11.4 Two or More Non-Interacting Active Sites . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
11.5 Two or More Interacting Active Sites: Cooperativity and the Hill Equation. . . . . . . . . . . . 175
11.6 Inhibition of Enzyme Activity. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
11.6.1 Product Inhibition in Reversible Reactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
11.6.2 Competitive Inhibition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
11.6.3 Non-Competitive Inhibition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 183
11.6.4 Mixed Inhibition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 185
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
Chapter 12. Complex Reaction Schemes and their Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
12.1 Binding of Two Substrates. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
12.1.1 Random Binding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
12.1.2 Ordered Binding. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
12.2 Ping-Pong Mechanism. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
12.3 Net Rate Constants and Transit Times. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
Chapter 13. Temperature Dependence of Rate Constants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
13.1 The Arrhenius Equation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
13.2 Transition State Theory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
13.3 Collision Theory. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
13.4 Kinetic and Thermodynamic Control of Reactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
Chapter 14. Principles of Catalysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
14.1 Enzyme Catalysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
14.2 Acid-Base Catalysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
14.3 Electrostatic and Covalent Catalysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
14.4 Intramolecular Catalysis and Effective Concentrations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 216
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 217
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Part III — Molecular Structure and Stability

Chapter 15. Molecular Structure and Interactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221

15.1 Configuration and Conformation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
15.2 Covalent Interactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
15.2.1 Covalent Bonds. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
15.2.2 Bond Angles and Torsion Angles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225
15.3 Non-Covalent Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227
15.3.1 Ionic Interactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
15.3.2 Interactions between Ions and Dipoles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 229
15.3.3 Hydrogen Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 232
15.3.4 Interactions between Induced Dipoles: van der Waals Interactions . . . . . . . . . . 234
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 237
Chapter 16. Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239
16.1 Amino Acids and the Peptide Bond. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 239
16.1.1 Properties of the Twenty Canonical Amino Acids. . . . . . . . . . . . . . . . . . . . . . . . . . . 239
16.1.2 The Peptide Bond . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 241
16.1.3 Side-Chain Rotamers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 243
16.1.4 Post-Translational Modifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 244
16.1.4.1 Glycosylation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
16.1.4.2 Phosphorylation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
16.1.4.3 Hydroxylation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 246
16.1.4.4 Carboxylation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 247
16.1.4.5 Disulfide Bonds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248
16.1.4.6 Metal Binding. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 248
16.2 Protein Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 251
16.2.1 Helical Secondary Structure Elements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
16.2.1.1 α-helix. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253
16.2.1.2 310-, poly-Pro, and Collagen Helices. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 255
16.2.2 β-Strands and their Super-Secondary Structures (β-Sheets). . . . . . . . . . . . . . . . . . 257
16.2.3 Reverse Turns . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 260
16.2.4 Protein Domains & Tertiary Structure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 262
16.2.5 Quaternary Structure & Protein-Protein Interactions . . . . . . . . . . . . . . . . . . . . . . . . 265
16.2.5.1 Homo-Oligomers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 265
16.2.5.2 Hetero-Oligomers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 267
16.2.6 Protein-Protein Interactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 268
16.2.6.1 Surface Complementarity and Buried Surface Area. . . . . . . . . . . . . . . . 268
16.2.6.2 Energetics of Macromolecular Interactions. . . . . . . . . . . . . . . . . . . . . . . 269
16.2.6.3 Role of Water – The Hydrophobic Effect. . . . . . . . . . . . . . . . . . . . . . . . . . 269
16.2.7 Protein-Ligand Interactions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 271
16.2.8 Membrane Proteins and their Lipid Environment. . . . . . . . . . . . . . . . . . . . . . . . . . . 273
16.2.8.1 Biological Roles of Lipids and Membranes. . . . . . . . . . . . . . . . . . . . . . . . 273
16.2.8.2 Types of Lipids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 275
16.2.8.3 Super-Structures Formed by Lipids and Detergents. . . . . . . . . . . . . . . 275
16.2.8.4 Properties and Structure of Membrane Proteins . . . . . . . . . . . . . . . . . . 277
16.3 Folding and Stability. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 279
16.3.1 Driving Forces for Protein Folding. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 280
16.3.2 First Folding Experiments and the Levinthal Paradox. . . . . . . . . . . . . . . . . . . . . . . 282
 Contents    ix

16.3.3 Energy Landscapes for Protein Folding. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 283

16.3.4 Mathematical Description of the Two-State Model . . . . . . . . . . . . . . . . . . . . . . . . . 285
16.3.5 Folding Pathways and Mechanisms of Protein Folding. . . . . . . . . . . . . . . . . . . . . . 290
16.3.5.1 Fast Steps in Protein Folding: Secondary Structure Formation. . . . . . 292
16.3.5.2 Rate-Limiting Steps and Protein Folding In Vivo. . . . . . . . . . . . . . . . . . . 293
16.3.5.3 Kinetics of Protein Folding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 295
16.3.5.4 Folding Intermediates in Monomers and Oligomers. . . . . . . . . . . . . . . 296
16.3.6 Protein Folding Diseases . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 300
Online Resources. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 302
Chapter 17. Nucleic Acids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 303
17.1 Nucleobases, Nucleosides and Nucleotides. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 304
17.1.1 Non-Standard Nucleobases in DNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 305
17.1.2 Non-Standard Nucleobases in RNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 306
17.2 Ribose and Nucleobase Conformations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307
17.2.1 Sugar Pucker. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 307
17.2.2 Syn- and Anti-Conformations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 308
17.3 Primary Structure of Nucleic Acids. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309
17.4 Base Pairing and Stacking. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311
17.4.1 H-bonds between Nucleobases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 311
17.4.2 Importance of Base Pair Stacking for Double Helix Formation. . . . . . . . . . . . . . . 313
17.4.3 Base Pair Geometries . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 314
17.5 DNA Structures and Conformations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315
17.5.1 DNA Double Helical Structures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 315
17.5.2 Triple and Quadruple DNA Helices. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 318
17.5.2.1 Triplexes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 318
17.5.2.2 Quadruplexes and Telomeres . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 319
17.5.3 Higher Order DNA Structures. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 320
17.5.3.1 Helix Junctions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 320
17.5.3.2 DNA Supercoiling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 322
17.5.3.3 DNA Bending and Kinking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 328
17.5.4 DNA Interactions with Proteins and Ligands . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329
17.5.4.1 DNA Recognition by Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 329
17.5.4.2 Small Molecule Binding to DNA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333
17.6 RNA Structure. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 334
17.6.1 RNA Secondary Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335
17.6.2 RNA Tertiary Structure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 336
17.6.3 RNA Folding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 338
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 338
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339
Online Resources . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 340
Chapter 18. Computational Biology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 341
18.1 Sequence Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 341
18.1.1 Sequence Composition, Global Properties, and Motifs. . . . . . . . . . . . . . . . . . . . . . 341
18.1.1.1 DNA Sequences. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 342
18.1.1.2 RNA Secondary Structure Prediction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 342
18.1.1.3 Protein Sequence Composition and Properties. . . . . . . . . . . . . . . . . . . 343
18.1.2 Sequence Alignment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 345
18.1.3 Secondary Structure Prediction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 348
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18.2 Molecular Modeling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 348

18.2.1 Force Fields. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 349
18.2.2 Energy Minimization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 350
18.2.3 Molecular Mechanics and Dynamics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352
18.2.3.1 Boundary Conditions and Solvation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 353
18.2.3.2 Integration of the Newtonian Equations. . . . . . . . . . . . . . . . . . . . . . . . . . 354
18.2.3.3 Trajectory Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 355
18.2.4 Applications of Molecular Modeling to Macromolecules. . . . . . . . . . . . . . . . . . . . 356
18.2.4.1 Fold Recognition. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 357
18.2.4.2 Homology Modeling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 358
18.2.4.3 Simulated Annealing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 358
18.2.4.4 Coarse-Grained Modeling. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 359
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 359
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 360
Online resources. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 360

Part IV — Methods

Chapter 19. Optical Spectroscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 365

19.1 Interaction of Light and Matter. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 365
19.1.1 Light as an Electromagnetic Wave . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 365
19.1.2 Principles of Spectroscopy: Transitions in Two-State Systems. . . . . . . . . . . . . . . . 367
19.2 Absorption. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 369
19.2.1 Electronic, Vibronic, and Rotational Energy Levels. . . . . . . . . . . . . . . . . . . . . . . . . . 369
19.2.2 Transitions and Transition Dipoles. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 370
19.2.3 The Lambert-Beer Law. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 372
19.2.4 Solvent Effects and Influence of the Local Environment. . . . . . . . . . . . . . . . . . . . . 374
19.2.5 Instrumentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 375
19.2.6 Biological Chromophores. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 375
19.2.7 Applications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 380
19.2.7.1 Concentration Determination. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 380
19.2.7.2 Spectroscopic Assays for Enzymatic Activity. . . . . . . . . . . . . . . . . . . . . . 381
19.2.7.3 Spectroscopic Tests for Functional Groups . . . . . . . . . . . . . . . . . . . . . . . 383
19.2.7.4 Absorption as a Probe for Structural Changes. . . . . . . . . . . . . . . . . . . . . 384
19.2.8 Potential Pitfalls. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 386
19.3 Linear and Circular Dichroism. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 387
19.3.1 Linearly Polarized Light and Linear Dichroism. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 387
19.3.2 Circularly Polarized Light and Circular Dichroism . . . . . . . . . . . . . . . . . . . . . . . . . . . 390
19.3.3 Instrumentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 395
19.3.4 Biological Chromophores that Show Circular Dichroism . . . . . . . . . . . . . . . . . . . . 395
19.3.5 Applications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 396
19.3.6 Potential Pitfalls. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .398
19.4 Infrared Spectroscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 398
19.4.1 Bond Vibrations: The Harmonic Oscillator. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 398
19.4.2 Molecule Geometry, Degrees of Freedom, and Vibrational Modes. . . . . . . . . . . 400
19.4.3 Instrumentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 402
19.4.4 Applications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 403
19.5 Fluorescence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 404
19.5.1 General Considerations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 404
 Contents    xi

19.5.2 Instrumentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 406

19.5.3 Quantum Yield and Lifetime. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 407
19.5.4 Fluorophores and Fluorescent Labeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 408
19.5.4.1 Biological Fluorophores. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 408
19.5.4.2 Extrinsic Fluorophores and their Introduction into Proteins,
Nucleic Acids, and Lipids������������������������������������������������������������������������������ 409
19.5.5 Applications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 418
19.5.5.1 Fluorescence as a Probe for Binding: Equilibrium Titrations . . . . . . . . 418
19.5.5.2 Fluorescence as a Probe for the Chemical Micro-
and Macro-Environment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 422
19.5.5.3 Fluorescence and Imaging: Fluorescence Recovery after
Photobleaching. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 423
19.5.6 Potential Pitfalls. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .424
19.5.7 Fluorescence Quenching. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 426
19.5.8 Fluorescence Anisotropy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 429
19.5.8.1 Principle of Fluorescence Anisotropy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 429
19.5.8.2 Applications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 431
19.5.8.3 Potential Pitfalls of Polarization/Anisotropy Measurements. . . . . . . . . 432
19.5.9 Time-Resolved Fluorescence. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 433
19.5.9.1 Measurement of Fluorescence Lifetimes . . . . . . . . . . . . . . . . . . . . . . . . . 435
19.5.9.2 Fluorescence Anisotropy Decays and Rotational Correlation Times. . . . 438
19.5.9.3 Rotational Correlation Time and Molecular Size. . . . . . . . . . . . . . . . . . . 439
19.5.9.4 Applications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 440
19.5.10 Förster Resonance Energy Transfer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 441
19.5.10.1 Principle of FRET . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 441
19.5.10.2 Experimental Determination of FRET Efficiencies. . . . . . . . . . . . . . . . . . 443
19.5.10.3 Applications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 446
19.5.10.4 Potential Pitfalls. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 449
19.5.10.5 FRET Efficiencies from Lifetimes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 449
19.5.10.6 FRET Efficiencies from Single Molecules. . . . . . . . . . . . . . . . . . . . . . . . . . 452
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 453
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 455
Chapter 20. Magnetic Resonance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461
20.1 Nuclear Magnetic Resonance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461
20.1.1 Nuclear Spins and the Zeeman Effect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461
20.1.2 A One-Dimensional NMR Spectrum: Larmor Frequency, Chemical Shift,
J-Coupling, and Multiplicity ������������������������������������������������������������������������������������������ 463
20.1.2.1 The Larmor Frequency. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 463
20.1.2.2 The Local Magnetic Field and the Chemical Shift . . . . . . . . . . . . . . . . . 463
20.1.2.3 Scalar Coupling and Multiplets. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 466
20.1.2.4 Shape of NMR Lines. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 467
20.1.2.5 Instrumentation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 468
20.1.3 The Nuclear Overhauser Effect: Distance Information. . . . . . . . . . . . . . . . . . . . . . . 468
20.1.4 Magnetization and Its Relaxation to Equilibrium: Fourier Transform-NMR
and the Free Induction Decay ���������������������������������������������������������������������������������������472
20.1.5 Two-Dimensional FT-NMR: COSY and NOESY . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 476
20.1.5.1 Principle of a 2D-FT-NMR Experiment. . . . . . . . . . . . . . . . . . . . . . . . . . . . 477
20.1.5.2 Correlated Spectroscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 478
20.1.5.3 Nuclear Overhauser Enhancement Spectroscopy. . . . . . . . . . . . . . . . . 479
20.1.5.4 Spin Systems and Sequential Assignment of Protein NMR Spectra . . . . 479
20.1.5.5 Structure Calculation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 483
xii   Biophysical Chemistry

20.1.6 Extending NMR to Structure Determination of Large Molecules. . . . . . . . . . . . . 484

20.1.7 NMR and Dynamics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 486
20.1.8 Solid State NMR and Biology. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 488
20.1.9 NMR and Imaging. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 489
20.2 Electron Paramagnetic Resonance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 490
20.2.1 Principle of Electron Paramagnetic Resonance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 490
20.2.2 Spin-Spin Interactions: Hyperfine Coupling of Unpaired Electrons with
Nuclei������������������������������������������������������������������������������������������������������������������������������491
20.2.3 EPR Probes and Spin Labeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 492
20.2.4 EPR as a Probe for Mobility and Dynamics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 494
20.2.5 EPR as a Probe for Accessibility. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 495
20.2.6 Measuring Spin-Spin Distances . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 496
20.2.7 Distance Determination by Pulsed EPR: PELDOR/DEER. . . . . . . . . . . . . . . . . . . . . . 497
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 500
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 501
Chapter 21. Solution Scattering. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 507
21.1 Light Scattering. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 507
21.1.1 Static Light Scattering. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 507
21.1.2 Dynamic Light Scattering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 511
21.1.3 Raman Scattering. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 513
21.2 Small Angle Scattering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 515
21.2.1 Scattering of X-rays and Neutrons. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 515
21.2.2 SAS Intensity Distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 518
21.2.3 Distance Distribution Function . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 522
21.2.4 Small Angle X-ray Scattering. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 523
21.2.4.1 SAXS Experiment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 523
21.2.4.2 Excluded Volume and Molecular Mass. . . . . . . . . . . . . . . . . . . . . . . . . . . 524
21.2.4.3 Kratky Plot. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 524
21.2.4.4 Modeling of Scattering Curves . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 525
21.2.5 Small Angle Neutron Scattering. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .526
21.2.5.1 Generation of Neutrons. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 526
21.2.5.2 Contrast Variation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 527
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 528
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 529
Chapter 22 . X-ray Crystallography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 531
22.1 Generation of X-rays. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 532
22.2 Phase Problem and Requirement for Crystals. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 536
22.3 Crystallization of Macromolecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 536
22.4 Symmetry and Space Groups. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 542
22.5 X-ray Diffraction from Crystals. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 547
22.6 Diffraction Data Collection and Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 551
22.7 Phasing Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 554
22.7.1 Isomorphous Replacement. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 554
22.7.2 Anomalous Diffraction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 556
22.7.3 Molecular Replacement. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 560
22.8 Electron Density and Model Building. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 562
22.9 Model Refinement and Validation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 565
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 568
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 569
Online Resources. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 570
 Contents    xiii

Chapter 23. Imaging and Microscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 571

23.1 Fluorescence Microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 571
23.1.1 Optical Principles of Microscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 572
23.1.1.1 Focusing and Collecting Light by Optical Lenses. . . . . . . . . . . . . . . . . . 572
23.1.1.2 Microscopes: How to Achieve Magnification with Optical Lenses. . . 574
23.1.1.3 The Diffraction Limit of Optical Resolution . . . . . . . . . . . . . . . . . . . . . . . 576
23.1.2 Wide-Field Fluorescence Microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 578
23.1.3 Confocal Scanning Microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 579
23.1.4 Total Internal Reflection Microscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 581
23.1.5 Fluorescence Lifetime Imaging Microscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 583
23.1.6 Fluorescence (Cross-)Correlation Spectroscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 584
23.1.6.1 Fluorescence Correlation Spectroscopy . . . . . . . . . . . . . . . . . . . . . . . . . . 585
23.1.6.2 FCS to Monitor Binding Events . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 587
23.1.6.3 Fluorescence Cross-Correlation Spectroscopy . . . . . . . . . . . . . . . . . . . . 590
23.1.7 Single-Molecule Fluorescence Microscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 592
23.1.7.1 Principles of Single-Molecule Microscopy . . . . . . . . . . . . . . . . . . . . . . . . 592
23.1.7.2 Why Single Molecules? . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 595
23.1.7.3 Localization and Tracking of Single Molecules. . . . . . . . . . . . . . . . . . . . 596
23.1.7.4 Kinetic Information from Single-Molecule Microscopy. . . . . . . . . . . . . 597
23.1.7.5 Colocalization of Molecules. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 598
23.1.7.6 Single-Molecule FRET. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 600
23.1.8 Super-Resolution Microscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 605
23.2 Electron Microscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 608
23.2.1 Principle of Electron Microscopy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 608
23.2.2 Sample Preparation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 609
23.2.3 Image Generation and Analysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 610
23.2.4 Three-Dimensional Electron Microscopy: Cryo-Electron Tomography and
Single Particle Cryo-EM ��������������������������������������������������������������������������������������������������� 611
23.2.5 Scanning Probe Microscopy: Scanning Tunneling, Scanning Force, and
Atomic Force Microscopy ����������������������������������������������������������������������������������������������� 617
Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .618
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 619
Chapter 24. Force Measurements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 623
24.1 Force Spectroscopy by AFM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 625
24.2 Optical Tweezers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 631
24.3 Magnetic Tweezers. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 638
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 642
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 642
Chapter 25. Transient Kinetic Methods. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 647
25.1 Stopped Flow. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 647
25.2 Quench Flow. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .650
25.3 Laser Flash Photolysis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 651
25.4 Relaxation Kinetics: Pressure- and Temperature-Jump . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 653
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 654
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 655
Chapter 26. Molecular Mass, Size, and Shape . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 657
26.1 Mass Spectrometry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 657
26.1.1 Ionization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 658
xiv   Biophysical Chemistry

26.1.1.1 Matrix-Assisted Laser Desorption Ionization . . . . . . . . . . . . . . . . . . . . . . 658

26.1.1.2 Electrospray Ionization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 659
26.1.2 Ion Storage and Manipulation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 660
26.1.2.1 Time of Flight Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 660
26.1.2.2 Quadrupoles and Ion Traps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 661
26.1.2.3 Orbitraps. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 664
26.1.2.4 Ion Fragmentation and Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 665
26.1.3 Detection. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 667
26.1.4 Mass Spectra. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 669
26.1.5 Applications. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 669
26.1.5.1 Mass Analysis for the Identification of Molecules. . . . . . . . . . . . . . . . . . 669
26.1.5.2 Isotope Distribution and Isotope Exchange. . . . . . . . . . . . . . . . . . . . . . . 670
26.1.5.3 Protein Identification from One- and Two-Dimensional Gels. . . . . . . 671
26.1.5.4 Native Mass Spectrometry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 671
26.1.5.5 Ion Mobility and Molecular Shape. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 672
26.1.5.6 Identifying Protein-RNA Interaction Sites after Photo-Crosslinking. . . . 673
26.1.5.7 Secondary Ion Mass Spectrometry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 673
26.1.5.8 Quantitative Mass Spectrometry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 674
26.2 Analytical Ultracentrifugation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 676
26.2.1 Instrumentation and Detection Systems. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 676
26.2.2 Behavior of a Molecule in a Gravitational Field . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 678
26.2.3 Sedimentation Velocity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 682
26.2.3.1 Determination of Sedimentation Coefficients. . . . . . . . . . . . . . . . . . . . . 683
26.2.3.2 Solvent and Concentration Dependence of the Sedimentation
Coefficient. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 684
26.2.3.3 Measuring Polydispersity and Association. . . . . . . . . . . . . . . . . . . . . . . . 685
26.2.4 Sedimentation Equilibrium. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 687
26.2.4.1 Determination of Molecular Mass Using Sedimentation
Equilibrium . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 687
26.2.4.2 Association in Sedimentation Equilibrium. . . . . . . . . . . . . . . . . . . . . . . . 689
26.2.5 Zonal, Band, or Isopycnic Centrifugation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 690
26.3 Surface Plasmon Resonance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 693
26.3.1 Physical Background of SPR. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 693
26.3.2 Principle and Information Content of an SPR Experiment . . . . . . . . . . . . . . . . . . . 695
26.3.3 Mass Transport Limitation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 697
26.3.4 Receptor Immobilization on the Sensor Surface. . . . . . . . . . . . . . . . . . . . . . . . . . . . 697
26.3.4.1 Covalent Receptor Immobilization. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 698
26.3.4.2 Non-Covalent Receptor Immobilization. . . . . . . . . . . . . . . . . . . . . . . . . . 700
26.3.5 Stoichiometry of Binding in an SPR Experiment. . . . . . . . . . . . . . . . . . . . . . . . . . . . 701
26.3.6 Specificity of Binding in an SPR Experiment. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 702
Questions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .702
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 706
Online resources. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 707
Chapter 27. Calorimetry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 709
27.1 Isothermal Titration Calorimetry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 709
27.1.1 General Principle. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 709
27.1.2 ITC Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 711
27.1.3 Origin of Enthalpic Changes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 713
27.1.4 Practical Considerations. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 715
27.1.5 Measuring High Affinities with ITC by Competition. . . . . . . . . . . . . . . . . . . . . . . . . 717
27.1.6 Measuring Michaelis-Menten Enzyme Kinetics with ITC. . . . . . . . . . . . . . . . . . . . . 717
 Contents    xv

27.2 Differential Scanning Calorimetry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 720

27.2.1 General Principle. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 720
27.2.2 Two-State Unfolding of Macromolecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 723
27.2.3 Two-State Unfolding with Subunit Dissociation . . . . . . . . . . . . . . . . . . . . . . . . . . . . 725
Questions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 726
References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 726

Appendix

Chapter 28. Prefixes, Units, Constants. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 731

28.1 Prefixes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 731
28.2 SI (Système International) or Base Units. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 732
28.3 Derived Units Used in this Book. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 732
28.4 Natural Constants Used in This Book. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 733
Chapter 29. Mathematical Concepts Used in This Book. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 735
29.1 Sums and Products. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 735
29.2 Quadratic Equation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 736
29.3 Binomial Coefficients . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 736
29.4 Trigonometry. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 737
29.5 Logarithms and Exponentials. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 737
29.6 Differentiation and Integration. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .739
29.7 Partial fractions. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 742
29.8 l’Hôpital’s rule. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 743
29.9 Vectors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 743
29.9.1 Dot Product. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 744
29.9.2 Cross Product. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 744
29.10 Complex Numbers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 745
29.11 Basic Elements of Statistics. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 747
29.12 Error Propagation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 748
29.13 Series Expansion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 749
29.13.1 Taylor Series. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 749
29.13.2 Fourier Series. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 749
29.14 Fourier Transformation. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 751
29.15 Convolution. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .753

Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 755
Preface

Writing this book, we wanted to present the concepts of physical chemistry and molecular structure that
underlie biochemical processes from a biochemist’s perspective. The content of the book is equally well
accessible to students and scientists with backgrounds in physics, chemistry or biology, but is particularly
intended for bachelor and master students of life science curricula. The book will also be useful as an
introductory text to more advanced students from other fields, and should serve as a reference for Ph.D.
students and young researchers.
The book is organized in four parts: thermodynamics, kinetics, molecular structure and stability, and
biophysical methods. To limit theoretical treatments to biologically relevant systems, we left out quan-
tum mechanics and statistical thermodynamics. Each individual chapter is followed by a set of problems
that should illustrate the principles treated in the chapter and put them into a biochemical context. The
commented solutions to the problems are collected in a separate Solutions Manual. References for the
work cited in the text are summarized at the end of each chapter, together with advanced literature that
provides additional information and may serve as a starting point for delving into a particular subject.
The first part provides background on thermodynamic principles. Early on in the text, we have tried
to illustrate the relevance of these thermodynamic concepts for biochemical systems. Electrochemistry is
also treated in this part because it is presented from a thermodynamic point of view.
The second part presents kinetics in a somewhat non-traditional way. We have chosen to start with
pre-steady state kinetics. This approach allows us to introduce many basic principles, which we can then
build upon in the subsequent treatment of the more traditional steady-state enzymology. We also included
a rather complete derivation of integrated rate laws and velocity equations.
In the third part, molecular interactions relevant for biological molecules are reviewed in light of
the thermodynamic principles from the first part of the book. The principles of protein and nucleic acid
structures are presented, striving for a balance between comprehensiveness and a focus on aspects that
are important for life sciences. This part assumes a basic knowledge of the concepts of chemical bonds,
orbitals and hybridization.
The fourth part deals with biophysical techniques and their applications to the study of biological
macromolecules and their interactions. The selection naturally reflects our own preferences and areas of
expertise. We included widely used techniques that should be accessible to most researchers when trying
to answer a particular biochemical question. Standard biochemical methods, such as gel electrophoresis
and chromatography, have been omitted. For the techniques most frequently used in a biophysical labora-
tory, a section on “potential pitfalls” may help to avoid common mistakes. Many well-established meth-
ods, among them fluorescence microscopy and mass spectrometry, have been developed much further in
recent years. We incorporated these novel developments and include specific application examples.

xvii
xviii   Biophysical Chemistry

Cross-references within and between all parts of the book serve to emphasize common themes and
to highlight recurrent principles. Boxes throughout the main text illustrate the relevance of a particular
topic, provide additional information on applications, or show derivations of formulas, but may be skipped
without breaking the flow of reading.
The appendix is specifically tailored to the requirements of the four main Parts. We only list constants
and units discussed in the text, and restrict the treatment of mathematical concepts to operations that
are used in the book. The appendix is meant to be a convenient reference, not a substitute for a thorough
training in mathematics.
We hope that this book is an enjoyable read, provides inspiration, and motivates students and research-
ers alike to dive deeper into biophysical chemistry.
Dagmar Klostermeier
Markus G. Rudolph
Muenster
Acknowledgments

We are grateful to our colleagues and friends who have taken the time to carefully read large parts of the
drafted manuscript: David Banner, Garry Crosson, Hans-Joachim Galla, Walter Huber, Jürgen Köhler,
John Ladbury, Erwin Peterman, Jochen Reinstein, Alison Rodger, Paul Rösch, Franz-Xaver Schmid,
Bernhard Schmidt, Joachim Seelig, Heinz-Jürgen Steinhoff, Dmitri Svergun, and Ian Wilson. Your con-
structive comments on how to improve the text, both scientifically and educationally, are much appreci-
ated. A special “Thank You” goes to David Banner for proof-reading of the entire manuscript. Of course,
any remaining errors in the book remain the sole responsibility of the authors.
We also thank our editors at CRC Press, Francesca McGowan and Emily Wells, for their commitment
and constructive support, and for swiftly answering any queries that came up during the writing of this
book.

xix
Authors

Dagmar Klostermeier studied Biochemistry and holds a PhD in Biochemistry. After her postdoctoral
training with David Millar at The Scripps Research Institute in La Jolla, USA, she was a junior research
group leader at the University of Bayreuth, Germany, and a Professor for Biophysical Chemistry at the
University of Basel, Switzerland. In 2011, she became Professor for Biophysical Chemistry at the University
of Muenster, Germany, and is teaching Physical and Biophysical Chemistry. Her research aims to decipher
the mechanisms of ATP-driven molecular machines by biophysical techniques, including single-molecule
fluorescence microscopy.

Markus G. Rudolph studied Biochemistry and holds a PhD in Biochemistry. He completed his postdoc-
toral training in Structural Biology in the laboratory of Ian A. Wilson at The Scripps Research Institute in
La Jolla, USA, before leading his own research group at the University of Goettingen, Germany. In 2006,
he moved to Hoffmann-La Roche Ltd. in Basel, Switzerland, as a researcher in Structural Biology and
Biophysics. His main research interests are the structural biology and catalytic mechanisms of enzymes,
and structure-based drug design.

xxi
 Part I
Thermodynamics

T
he field of thermodynamics (gr. thermos: heat, dynamis: force) is centered around energy in all
forms. It refers to the analysis of the available energy, the distribution of energy, and the con-
version of energy from one form into the other. Thermodynamic considerations are invaluable
for the understanding of the importance of energy in biological systems, its storage and availability,
and the energetic costs involved in maintaining cellular functions and stability. The thermodynamic
framework is based on four laws, simple rules that have been derived empirically from observing the
real world. These laws and concepts allow a quantitative description of complex biological systems,
and enable us to understand and, more importantly, to predict their behavior in specific circum-
stances. Before we begin to construct the building of thermodynamics, however, we will have to
start with a set of definitions.

1
 1
Systems and Their
Surroundings

A
system is the part of the universe we are currently focusing on, and that we are attempting to describe
quantitatively. Systems are separated from the rest of the universe by walls that allow them to i­nteract
with their surroundings . By surroundings we refer to that part of the rest of the universe that interacts
with the system (Figure 1.1). An isolated system is separated from its surroundings by walls that do not allow
exchange of heat or matter. A closed system exchanges heat with its surroundings, but does not exchange mat-
ter, and an open system can exchange heat and matter with its surroundings. Walls that allow heat exchange
are called diathermic, whereas walls that do not allow the exchange of heat are called adiabatic.
These definitions imply that all living organisms are open systems: they exchange heat and mat-
ter with their surroundings. Open systems are not so easy to describe quantitatively, however. We
will therefore start with isolated and closed systems in order to illustrate the underlying concepts,
before we move to open systems (Section 2.6).

FIGURE 1.1:   Systems and surroundings: open, closed, and isolated systems.  A system is the part of
the universe we want to understand (pale yellow). It is in contact with its surroundings (blue). System and
surroundings are separated by walls. Open systems exchange heat (red) and matter (green) with their sur-
roundings; closed systems exchange heat, but not matter; and isolated systems exchange neither heat nor
matter with their surroundings. Open and closed systems are separated from their surroundings by diather-
mic (heat-permeable) walls, isolated systems are surrounded by adiabatic (thermally insulated) walls.

3
4   Chapter 1. Systems and Their Surroundings

Energy exchanged between a system and its surroundings is always counted from the perspective of
the system. A negative value means energy flows from the system into the surroundings: the energy
of the system is reduced. A positive value means that energy flows into the system, and the energy of
the system is increased (Section 2.2.2).

QUESTIONS
1.1 What are open, closed or isolated systems? (1) a protein in solution in a sealed test tube,
(2) the lungs, (3) a bird, (4) a lake, (5) a biochemical reaction in a reaction tube, (6) coffee in a
thermos flask, (7) the sample chamber of a differential scanning calorimeter, (8) the sample
chamber of an isothermal titration calorimeter, (9) a cuvette in a photometer (no lid).
1.2 What is the sign of the transferred energy from the perspective of the system and the sur-
roundings for
(1) a swimmer in a pool with cold water?
(2) a heated house?
(3) a coffee cup?
(4) an ice cold drink in a warm bar?
(5) a cold hand shaking a warm hand?
1.3 Is the earth an isolated, closed, or open system?
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http://kinemage.biochem.duke.edu/teaching/BCH681/2013BCH681/elasticScattering
www.xtal.iqfr.csic.es/Cristalografia/index-en.html
www.doitpoms.ac.uk/tlplib/index.php
www.ysbl.york.ac.uk/~cowtan

Imaging and Microscopy

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Transient Kinetic Methods

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