|  | Privalov, Peter L.
Microcalorimetry of Macromolecules
The Physical Basis of Biological Structures
 1. Edition August 2012
122.- Euro
2012. 404 Pages, Hardcover
ISBN 978-1-118-10451-4 - John Wiley & Sons
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| Short description
This is the first textbook on the microcalorimetry of biological molecules. The coverage starts from the basics of thermodynamics (which are unknown for many scientists working in biology), describes evolution of the calorimetric technique, explains how to analyze the calorimetric data, and illustrates these methods with a wide selection of examples. The book provides an essential resource to scientists studying biological molecular structures and the reactions between these structures.
From the contents
1 Introduction 1
2 Methodology 5
2.1 Thermodynamic Basics of Calorimetry, 5
2.1.1 Energy, 5
2.1.2 Enthalpy, 6
2.1.3 Temperature, 6
2.1.4 Energy Units, 7
2.1.5 Heat Capacity, 8
2.1.6 Kirchhoff's Relation, 9
2.1.7 Entropy, 11
2.1.8 Gibbs Free Energy, 13
2.2 Equilibrium Analysis, 13
2.2.1 Two-State Transition, 13
2.2.2 Derivatives of the Equilibrium Constant, 15
2.3 Aqueous Solutions, 16
2.3.1 Specifi city of Water as a Solvent, 16
2.3.2 Acid-Base Equilibrium, 18
2.3.3 Partial Quantities, 20
2.4 Transfer of Solutes into the Aqueous Phase, 23
2.4.1 Hydration Effects, 23
2.4.2 Hydrophobic Force, 25
2.4.3 Hydration of Polar and Nonpolar Groups, 28
References, 32
3 Calorimetry 33
3.1 Isothermal Reaction Microcalorimetry, 33
3.1.1 The Heat of Mixing Reaction, 33
3.1.2 Mixing of Reagents in Comparable Volumes, 35
3.1.3 Isothermal Titration Microcalorimeter, 36
3.1.4 ITC Experiments, 38
3.1.5 Analysis of the ITC Data, 41
3.2 Heat Capacity Calorimetry, 43
3.2.1 Technical Problems, 43
3.2.2 Differential Scanning Microcalorimeter, 44
3.2.3 Determination of the Partial Heat Capacity of Solute Molecules, 53
3.2.4 DSC Experiments, 55
3.2.5 Determination of the Enthalpy of a Temperature-Induced Process, 56
3.2.6 Determination of the van't Hoff Enthalpy, 58
3.2.7 Multimolecular Two-State Transition, 59
3.2.8 Analysis of the Complex Heat Capacity Profile, 60
3.2.9 Correction for Components Refolding, 61
3.3 Pressure Perturbation Calorimetry, 63
3.3.1 Heat Effect of Changing Pressure, 63
3.3.2 Pressure Perturbation Experiment, 65
References, 67
4 Macromolecules 69
4.1 Evolution of the Concept, 69
4.2 Proteins, 71
4.2.1 Chemical Structure, 71
4.2.2 Physical Structure, 76
4.2.3 Restrictions on the Conformation of Polypeptide Chains, 81
4.2.4 Regular Conformations of Polypeptide Chain Proteins, 82
4.3 Hierarchy in Protein Structure, 86
4.3.1 Tertiary Structure of Proteins, 86
4.3.2 Quaternary Structure of Proteins, 88
4.4 Nucleic Acids, 89
4.4.1 Chemical Structure, 89
4.4.2 Physical Structure, 91
References, 94
5 The alpha-Helix and alpha-Helical Coiled-Coil 95
5.1 The alpha-Helix, 95
5.1.1 Calorimetric Studies of alpha-Helix Unfolding-Refolding, 95
5.1.2 Analysis of the Heat Capacity Function, 99
5.2 alpha-Helical Coiled-Coils, 105
5.2.1 Two-Stranded Coiled-Coils, 105
5.2.2 Three-Stranded Coiled-Coils, 110
5.3 alpha-Helical Coiled-Coil Proteins, 113
5.3.1 Muscle Proteins, 113
5.3.2 Myosin Rod, 115
5.3.3 Paramyosin, 116
5.3.4 Tropomyosin, 117
5.3.5 Leucine Zipper, 118
5.3.6 Discreteness of the Coiled-Coils, 123
References, 124
6 Polyproline-II Coiled-Coils 127
6.1 Collagens, 127
6.1.1 Collagen Superhelix, 127
6.1.2 Hydrogen Bonds in Collagen, 129
6.1.3 Stability of Collagens, 131
6.1.4 Role of Pyrrolidine Rings in Collagen Stabilization, 133
6.2 Calorimetric Studies of Collagens, 135
6.2.1 Enthalpy and Entropy of Collagen Melting, 135
6.2.2 Correlation between Thermodynamic and Structural Characteristics of Collagens, 138
6.2.3 Role of Water in Maintaining the Collagen Structure, 140
6.3 Thermodynamics of Collagens, 141
6.3.1 Cooperativity of Collagen Unfolding, 141
6.3.2 Factors Responsible for Maintaining the Collagen Coiled-Coil, 143
6.3.3 Flexibility of the Collagen Structure, 145
6.3.4 Biological Aspect of the Collagen Stability Problem, 148
References, 150
7 Globular Proteins 153
7.1 Denaturation of Globular Proteins, 153
7.1.1 Proteins at Extremal Conditions, 153
7.1.2 The Main Problems of Protein Denaturation, 154
7.2 Heat Denaturation of Proteins, 155
7.2.1 DSC Studies of Protein Denaturation upon Heating, 155
7.2.2 Reversibility of Heat Denaturation, 155
7.2.3 Cooperativity of Denaturation, 156
7.2.4 Heat Capacity of the Native and Denatured States, 158
7.2.5 Functions Specifying Protein Stability, 161
7.3 Cold Denaturation, 167
7.3.1 Proteins at Low Temperatures, 167
7.3.2 Experimental Observation of Cold Denaturation, 168
7.4 pH-Induced Protein Denaturation, 173
7.4.1 Isothermal pH Titration of Globular Proteins, 173
7.5 Denaturant-Induced Protein Unfolding, 175
7.5.1 Use of Denaturants for Estimating Protein Stability, 175
7.5.2 Calorimetric Studies of Protein Unfolding by Denaturants, 176
7.5.3 Urea and GuHCl Interactions with Protein, 179
7.6 Unfolded State of Protein, 182
7.6.1 Completeness of Protein Unfolding at Denaturation, 182
7.6.2 Thermodynamic Functions Describing Protein States, 186
References, 190
8 Energetic Basis of Protein Structure 193
8.1 Hydration Effects, 193
8.1.1 Proteins in an Aqueous Environment, 193
8.1.2 Hydration of Protein Groups, 194
8.1.3 Hydration of the Folded and Unfolded Protein, 199
8.2 Protein in Vacuum, 202
8.2.1 Heat Capacity of Globular Proteins, 202
8.2.2 Enthalpy of Protein Unfolding in Vacuum, 204
8.2.3 Entropy of Protein Unfolding in Vacuum, 210
8.3 Back into the Water, 214
8.3.1 Enthalpies of Protein Unfolding in Water, 214
8.3.2 Hydrogen Bonds, 216
8.3.3 Hydrophobic Effect, 218
8.3.4 Balance of Forces Stabilizing and Destabilizing Protein Structure, 219
References, 223
9 Protein Folding 225
9.1 Macrostabilities and Microstabilities of Protein Structure, 225
9.1.1 Macrostability of Proteins, 225
9.1.2 Microstability of Proteins, 226
9.1.3 Packing in Protein Interior, 228
9.2 Protein Folding Technology, 233
9.2.1 Intermediate States in Protein Folding, 233
9.2.2 Molten Globule Concept, 234
9.3 Formation of Protein Structure, 241
9.3.1 Transient State in Protein Folding, 241
9.3.2 Mechanism of Cooperation, 242
9.3.3 Thermodynamic States of Proteins, 243
References, 245
10 Multidomain Proteins 249
10.1 Criterion of Cooperativity, 249
10.1.1 Deviations from a Two-State Unfolding-Refolding, 249
10.1.2 Papain, 250
10.1.3 Pepsinogen, 251
10.2 Proteins with Internal Homology, 255
10.2.1 Evolution of Multidomain Proteins, 255
10.2.2 Ovomucoid, 255
10.2.3 Calcium-Binding Proteins, 258
10.2.4 Plasminogen, 263
10.2.5 Fibrinogen, 264
10.2.6 Fibronectin, 267
10.2.7 Discreteness in Protein Structure, 268
References, 271
11 Macromolecular Complexes 273
11.1 Entropy of Association Reactions, 273
11.1.1 Thermodynamics of Molecular Association, 273
11.1.2 Experimental Verifi cation of the Translational Entropy, 275
11.2 Calorimetry of Association Entropy, 277
11.2.1 SSI Dimer Dissociation, 277
11.2.2 Dissociation of the Coiled-Coil, 283
11.2.3 Entropy Cost of Association, 285
11.3 Thermodynamics of Molecular Recognition, 286
11.3.1 Calorimetry of Protein Complex Formation, 286
11.3.2 Target Peptide Recognition by Calmodulin, 287
11.3.3 Thermodynamic Analysis of Macromolecular Complexes, 293
References, 295
12 Protein-DNA Interaction 297
12.1 Problems, 297
12.1.1 Two Approaches, 297
12.1.2 Protein Binding to the DNA Grooves, 299
12.2 Binding to the Major Groove of DNA, 300
12.2.1 Homeodomains, 300
12.2.2 Binding of the GCN4 bZIP to DNA, 307
12.2.3 Heterodimeric bZIP Interactions with the Asymmetric DNA Site, 313
12.2.4 IRF Transcription Factors, 317
12.2.5 Binding of NF-kappaB to the PRDII Site, 320
12.3 Binding to the Minor Groove of DNA, 322
12.3.1 AT-Hooks, 322
12.3.2 HMG Boxes, 326
12.4 Comparative Analysis of Protein-DNA Complexes, 331
12.4.1 Sequence-Specifi c versus Non-Sequence-Specifi c HMGs, 331
12.4.2 Salt-Dependent versus Salt-Independent Components of Binding, 336
12.4.3 Minor versus Major Groove Binding, 339
12.5 Concluding Remarks, 345
12.5.1 Assembling Multicomponent Protein-DNA Complex, 345
12.5.2 CC Approach versus PB Theory, 346
References, 347
13 Nucleic Acids 353
13.1 DNA, 353
13.1.1 Problems, 353
13.1.2 Factors Affecting DNA Melting, 354
13.2 Polynucleotides, 357
13.2.1 Melting of Polynucleotides, 357
13.2.2 Calorimetry of Poly(A)·Poly(U), 358
13.3 Short DNA Duplexes, 361
13.3.1 Calorimetry of Short DNA Duplexes, 361
13.3.2 Specifi city of the AT-rich DNA Duplexes, 366
13.3.3 DNA Hydration Studied by Pressure Perturbation Calorimetry, 372
13.3.4 The Cost of DNA Bending, 375
13.4 RNA, 376
13.4.1 Calorimetry of RNA, 376
13.4.2 Calorimetric Studies of Transfer RNAs, 378
References, 383
Index 387
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