Statistical Mechanics and Stability of Macromolecules: Application to Bond Disruption, Base Pair Separation, Melting, and Drug Dissociation of the DNA Double Helix

Earl Prohofsky

doi:10.1017/CBO9780511524721

This book develops a statistical mechanical analysis of the stability of biological macromolecules. The author's approach is valid both for the long time-scale needed for DNA bond disruption, and also for highly co-operative transitions needed to explain helix melting. A new theoretical approach for executing macromolecule calculations is developed. In particular, the author devises a method for describing chemical bond disruption in these large systems, which are then used to determine when the helix melts and how drugs can dissociate from the helix. Melting temperatures are found to be in excellent agreement with experimental observations. The book will be of interest to biomolecular dynamics researchers, especially to graduate students in biological physics, theoretical chemistry and molecular biology.

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Contents

Frontmatter
pp i-vi
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Contents
pp vii-viii
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Preface
pp ix-x
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1 - Introduction
pp 1-16
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2 - Macromolecular stability
pp 17-46
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3 - Lattice dynamics
pp 47-59
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4 - Effective phonon theory
pp 60-77
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5 - Premelting disrupted chemical bonds
pp 78-87
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6 - Cooperative melting
pp 88-102
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7 - Strained chemical bonds: salt and pressure effects
pp 103-116
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8 - Bond disruption and conformation change: B to Z conformation change in DNA
pp 117-126
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9 - Hydration effects: structural water
pp 127-136
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10 - Helix with daunomycin intercalated: increased helix stability and daunomycin-DNA binding constant
pp 137-145
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11 - Nonrepeating DNA
pp 146-158
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12 - Cutting and splicing: junctions, inserts, and the replicating fork
pp 159-172
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13 - Interaction between a helix and a single attached molecule
pp 173-180
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14 - Energy considerations in bond opening
pp 181-192
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Appendix 1 - Helical lattice dynamics
pp 193-198
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Appendix 2 - Density matrix and effective phonon theory
pp 199-205
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Appendix 3 - Green functions
pp 206-213
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References
pp 214-222
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Index
pp 223-227
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Statistical Mechanics and Stability of Macromolecules

Application to Bond Disruption, Base Pair Separation, Melting, and Drug Dissociation of the DNA Double Helix

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Contents

Frontmatter
pp i-vi

Contents
pp vii-viii

Preface
pp ix-x

1 - Introduction
pp 1-16

2 - Macromolecular stability
pp 17-46

3 - Lattice dynamics
pp 47-59

4 - Effective phonon theory
pp 60-77

5 - Premelting disrupted chemical bonds
pp 78-87

6 - Cooperative melting
pp 88-102

7 - Strained chemical bonds: salt and pressure effects
pp 103-116

8 - Bond disruption and conformation change: B to Z conformation change in DNA
pp 117-126

9 - Hydration effects: structural water
pp 127-136

10 - Helix with daunomycin intercalated: increased helix stability and daunomycin-DNA binding constant
pp 137-145

11 - Nonrepeating DNA
pp 146-158

12 - Cutting and splicing: junctions, inserts, and the replicating fork
pp 159-172

13 - Interaction between a helix and a single attached molecule
pp 173-180

14 - Energy considerations in bond opening
pp 181-192

Appendix 1 - Helical lattice dynamics
pp 193-198

Appendix 2 - Density matrix and effective phonon theory
pp 199-205

Appendix 3 - Green functions
pp 206-213

References
pp 214-222

Index
pp 223-227

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Statistical Mechanics and Stability of Macromolecules

Application to Bond Disruption, Base Pair Separation, Melting, and Drug Dissociation of the DNA Double Helix

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