Myths and verities in protein folding theories:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Hackensack, NJ
World Scientific
[2016]
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| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | xxiv, 421 Seiten Diagramme |
| ISBN: | 9789814725996 |
Internformat
MARC
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| 300 | |a xxiv, 421 Seiten |b Diagramme | ||
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Datensatz im Suchindex
| _version_ | 1804176902258163712 |
|---|---|
| adam_text | Contents
Preface xvii
Acknowledgements xxi
List of Abbreviations xxiii
Chapter 1 Introduction: The Protein
Folding Problem — Some of the
Myths Associated with the Protein
Folding Theories 1
Chapter 2 From Frank and Evans’
Iceberg Formation Conjecture
to the Explanation of the
Hydrophobic Effect 13
2.1 Abstract...................... 13
2.2 The Origin of the Myth and Some
Historical Notes .................. 14
2.3 The Evolution of the Myth . . . 24
2.4 Some Theoretical Questions . . 27
2.4.1 How Can a Simple
Nonpolar Solute, Such as
Argon, Form “Icebergs”? 28
vii
Myths and Verities in Protein Folding Theories
viii
2.4.2 The General
Statistical-Mechanical
Expressions for the
Thermodynamics
of Solvation of Nonpolar
Solutes in Water .... 37
2.4.3 Application of the
Two-Structure Model for
Water; the Low- and
High-Local-Density
Components.................. 41
2.4.4 An Exact Argument Using
a Hypothetical Hard Point
Particle.................... 46
2.4.5 An Approximate Estimate
of the Contribution of
Structural Changes to the
Solvation Entropy ... 49
2.4.6 Generalization for H pO
Interaction and for Any
Reaction.................... 52
2.5 Does the Enhancement of the
Structure of Water Explain the
Large Positive Partial Molar Heat
Capacity of Nonpolar Solutes in
Water?...................... 55
2.6 Conclusion.................. 60
Contents | ix
Chapter 3 From Schellmans Experiments
to Fersht’s Hydrogen Bond
Inventory Argument 63
3.1 Abstract.......................... 63
3.2 The Origin of the Myth and Some
Historical Notes.................. 64
3.3 The Evolution of the Myth that
HBs Are Insignificant in Protein
Stability......................... 68
3.4 Why the Hydrogen Bond
Inventory Argument is
Wrong............................. 71
3.5 Another Way to Analyze the
Gibbs Energy Change in the
Formation of an HB................ 76
3.6 The Entropy and the Enthalpy
Change Associated with the
Reaction (3.3).................... 79
3.7 Conclusion........................ 84
Chapter 4 From Kauzmanns Conjecture
to the Myth That the Hydrophobic
Effect is the Dominant Factor
in Protein Stability 85
4.1 Abstract ......................... 85
4.2 The Origin of the Myth and Some
Historical Notes.................. 87
X
Myths and Verities in Protein Folding Theories
4.3 The Evolution of the
Hydrophobic Effect in Protein
Folding....................... 91
4.4 Cracks in the Kauzmann
Conjecture About the
Hydrophobic Effect................ 94
4.5 An Inventory of All Possible
Solvent-induced Effects .... 98
4.6 The “Evidence” in Favor of the
H pO Effects in Protein Folding 102
4.7 The Evidence in Favor of the H fil
Effects in Protein Folding ... 115
4.8 The Relevance of the H(f)I
Effects to Biochemical Processes
Involving Proteins............... 119
4.9 Conclusion........................ 124
Chapter 5 From Levinthal s Question to
Resolving Levinthal s “Paradox” 127
5.1 Abstract.......................... 127
5-2 The Origin of the Myth and Some
Historical Notes................. 128
5.3 Attempts to Resolve the Levinthal
Paradox.......................... 132
5.4 Target-Based Versus Cause-Based
Processes........................ 136
5.5 What Is the Answer to Levinthals
Question? ....................... 139
The Hydrophilic Forces .... 142
5.6
Contents
xi
5.7 Implementation of Forces in
Protein Folding; the Answer to
Levinthals Question.............. 153
5.8 Conclusion....................... 160
Chapter 6 From Anfinsen’s Hypothesis
to the Frenetic Pursuit of the Global
Minimum in the Gibbs Energy
Landscape 163
6.1 Abstract......................... 163
6.2 The Origin of the Myth .... 164
6.3 The Evolution of the “Folding
Code” Myth....................... 166
6.4 Why a Folding Code Is Unlikely
to Exist......................... 168
6.4.1 No One-to-One Code
Exists.................... 168
6.4.2 What Is the “Alphabet” of
the 3D Structure? ... 170
6.4.3 Did Evolution “Solve” the
Protein Folding Problem? 172
6.5 The Myth That the Native
Structure Resides in the Global
Minimum of the GEL............... 175
6.6 A Minimum of Gibbs Energy
with Respect to What?............ 176
6.7 The Evolution of the Myth ... 180
6.8 The Search for a Global
Minimum in the EL or in the
Potential Energy Surface .... 186
XII
Myths and Verities in Protein Folding Theories
6.9 The Search for the Structure of
Protein by Simulation......... 189
6.9.1 The Anfinsen-Type
Experiment............. 190
6.9.2 The Non-Anfinsen Type
of Renaturation
Experiment............. 198
6.9.3 Dependence on the Initial
Conditions................ 202
6.10 Conclusion.................... 211
Chapter 7 Some Candidates Which Can
Potentially Evolve into New Myths 213
7.1 The Landscape Theory of Protein
Folding.......................... 214
7.1.1 The Energy Landscape . 215
7.1.2 The Gibbs Energy
Landscape................. 220
7.1.3 The Thermodynamic
Potential Energy
Landscape................. 227
7.1.4 The Potential Energy
Surface................... 228
7.2 A Funnel-like Theory of Protein
Folding.......................... 231
7.3 The Principle of Consistency . . 238
7.4 The Application of Lattice Models
for Studying Protein Folding . . 243
Contents
XIII
Appendix B
Appendix C
Appendix D
7.5 The Principle of Minimal
Frustration....................
7.6 The Structure—Function
Paradigm.......................
The Definition of the Solvation
Process and the Corresponding
Thermodynamic Quantities
A. 1 The Old Definition of the
Solvation Process............
A.2 The New Definition of the
Solvation Process............
A.3 Solvation Gibbs Energy of
a Molecule with Internal
Rotations....................
A.4 The Solvation Volume ....
A. 5 The Solvation Enthalpy . . .
A.6 The Solvation Entropy . . .
The Definition of the Structure of
Water and Changes in the Structure
Induced by a Solute
Le Chatelier’s Principle Applied
to the Two-Structure Model
for Water
The Stability Condition for
a Chemical Reaction:
245
260
263
264
265
269
275
277
278
281
293
299
xiv | Myths and Verities in Protein Folding Theories
Appendix E Solvation Gibbs Energy of the Hard
Sphere and the Work of Cavity
Formation 301
Appendix F Formal Expression for the
Thermodynamic Quantities of
Solvation of a Nonpolar Solute 305
Appendix G The Solvation Entropy and Solvation
Energy; Structural Changes in the
Solvent 309
Appendix H The Solubility of a Simple Solute
in Water and Structural Changes
Induced in the Solvent 311
Appendix I Ben-Naim’s “Pitfalls”: Don Quixotes
Windmill 317
Appendix J Examples of Gibbs Energy
Landscapes and Gibbs Energy
Functionals 325
Appendix K The Existence of a Single Minimum
of the Gibbs Energy Functional 347
Appendix L Nonadditivity of the Gibbs Energy
Function
L. 1 The Source of the 359
Nonadditivity of the PMF . . 362
L.2 Conclusion......... 370
Contents
xv
ppendix M Nonadditivity in Binding Systems 371
M.l The Model and Its Partition
Function .......... 371
M.2 Probabilities and Correlations 374
ppendix N Frustration in Three Dipoles on
a Lattice: An Informational-
Theoretical Approach 381
N.l The Three Dipoles at the
Vertices of Regular Triangles . 381
N.2 Some Numerical Results . . . 388
pilogue 395
eferences 411
idex 421
|
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| isbn | 9789814725996 |
| language | English |
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| spelling | Ben-Naim, Arieh 1934- Verfasser (DE-588)138575460 aut Myths and verities in protein folding theories Arieh Ben-Naim Hackensack, NJ World Scientific [2016] xxiv, 421 Seiten Diagramme txt rdacontent n rdamedia nc rdacarrier Proteinfaltung (DE-588)4324567-5 gnd rswk-swf Proteinfaltung (DE-588)4324567-5 s b DE-604 Digitalisierung UB Regensburg - ADAM Catalogue Enrichment application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029360560&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Ben-Naim, Arieh 1934- Myths and verities in protein folding theories Proteinfaltung (DE-588)4324567-5 gnd |
| subject_GND | (DE-588)4324567-5 |
| title | Myths and verities in protein folding theories |
| title_auth | Myths and verities in protein folding theories |
| title_exact_search | Myths and verities in protein folding theories |
| title_full | Myths and verities in protein folding theories Arieh Ben-Naim |
| title_fullStr | Myths and verities in protein folding theories Arieh Ben-Naim |
| title_full_unstemmed | Myths and verities in protein folding theories Arieh Ben-Naim |
| title_short | Myths and verities in protein folding theories |
| title_sort | myths and verities in protein folding theories |
| topic | Proteinfaltung (DE-588)4324567-5 gnd |
| topic_facet | Proteinfaltung |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029360560&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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