The role of water in protein folding, self-assembly and molecular recognition

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The role of water in protein folding, self-assembly and molecular recognition / Arieh Ben-Naim

資料種別:: 図書
出版情報:: Hackensack, N.J. : World Scientific, c2011
形態:: xxvii, 452 p. ; 24 cm
シリーズ名:: Molecular theory of water and aqueous solutions / Arieh Ben-Naim ; pt. 2 <BA90975599>
著者名:: Ben-Naim, Arieh, 1934- <DA0216053X>
ISBN:: 9789814350532 [9814350532] (: hbk)
9789814350549 [9814350540] (: pbk)
書誌ID:: BB07974244

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注記:

Includes bibliographical references (p. 443-450) and index

主題:

Molecular theory; Solution (Chemistry); Water

言語:

英語

目次情報:

Quotations

List of Abbreviations

Preface

Acknowledgements

Introduction, the Main Problem and the Main Tools / 1：

The General Problem / l.l：

Forces and Driving Forces / 1.2：

Definition of the Solvation Process and the Corresponding Thermodynamic Quantities / 1.3：

The Conditional Solvation Process / 1.4：

Some Numerical Values of Solvation Thermodynamics / 1.5：

Solvation of hydrophilic molecules or groups / 1.5.1：

Solvation of hydrophobic molecules or groups / 1.5.2：

Hydrophobicity Scales / 1.6：

Some Numerical Values of the Pairwise Hydrophobic and Hydrophilic Interactions / 1.7：

Pairwise hydrophobic{H?0)interaction / 1.7.1：

Pairwise hydrophilic (H?I)interaction / 1.7.2：

Potential of average force for pairs of side chains of amino acids / 1.7.3：

Dissection of the Solvation Gibbs Energy of a Globular Protein / 1.8：

Dissection of the Solvation Gibbs Energy of a Denatured Protein / 1.9：

The Relationship between the Standard Gibbs Energy of a Reaction and Solvation Gibbs Energies / 1.10：

The Various Solvent-Induced Contributions to the Driving Force for Protein Folding / 1.11：

The solvation of the hard part / 1.11.1：

The solvation of the soft part / 1.11.2：

The contribution of the functional groups (FGs) exposed to the solvent / 1.11.3：

Concluding Remarks and Some Suggestions for the Future / 1.12：

Solvation and Solubility of Globular Proteins / 2：

Definition of Solubility and its Relationship to the Solvation Gibbs Energy / 2.1：

Solvation Gibbs Energy of a Model Globular Protein / 2.2：

Estimation of the Solvation Gibbs Energy of Real Proteins / 2.3：

The Relation between Solubility and Solvation Gibbs Energy for Moderately Soluble Proteins / 2.4：

A Possible Explanation for an Apparently Paradoxical Experimental Finding / 2.5：

The Effect of the Addition of a Solute on the Solvation Gibbs Energy / 2.6：

Concluding Remarks and Suggestions for Future Research / 2.7：

Protein Folding / 3：

The Chemical Equilibrium / 3.1：

Definition of the Folded and Unfolded Forms / 3.2：

Formal Dissection of the Solvent-Induced Effect on Protein Folding into "Small" Ingredients / 3.3：

Methods of Studying and Estimating the Various Contributions to $G / 3.4：

Summary of the Factors Involved in the Stability of the Native Protein / 3.5：

The Problem of the Preferential Protein Folding Pathways of Proteins / 3.6：

Energy Landscapes, Gibbs Energy Landscapes and Forces in Protein Folding / 3.7：

What Kind of Forces are Exerted on the Protein in the Process of Protein Folding? / 3.8：

The Forces in Action / 3.9：

Is there a "Folding Code"? / 3.10：

Association and Self-Assembly of Biomolecules / 3.11：

Thermodynamics and Statistical Thermodynamics of the Association Process / 4.1：

The Factors Involved in the Association of two Biomolecules / 4.2：

Association of two Hypothetical Globular Proteins / 4.3：

The "driving force" for dimerization / 4.3.1：

Virtual dimers, probabilistic considerations / 4.3.2：

Some numerical estimates of various contributions to the total PMF / 4.3.3：

H?0 or, H?I Interaction: Which is More Important in the Association Process? / 4.4：

Association of P and L in an ideal gas phase / 4.4.1：

Association in an organic liquid / 4.4.2：

Association in aqueous solutions / 4.4.3：

Enhancement of the H?O Mode by Strengthening the H?I Effects / 4.4.4：

Association by the Complete Absorption of a Small Solute into a Big Solute / 4.5：

Absorption without conformational changes in P / 4.5.1：

Absorption with conformational changes in P / 4.5.2：

Specificity of the Binding Mode; Molecular Recognition / 4.6：

The lock-and-key model for molecular recognition / 4.6.1：

Molecular recognition through the solvant / 4.6.2：

Self-Assembly of Macromolecules / 4.7：

Strong Solvent-Induced Forces between Macromolecules / 4.8：

Solvent-induced force by means of one-water bridges / 4.8.1：

Solvent-Induced Force by Means of Two-Water Bridges / 4.8.2：

Stronger forces between H?I surfaces / 4.8.3：

The General Statistical Mechanical Expression for the Chemical Potential and the Pseudo-Chemical Potential / 4.9：

The Pseudo-Chemical Potential and the Solvation Helmholtz Energy of a Molecule Having Internal Rotational Degrees of Freedom / Appendix B：

The Potential of Mean Force (PMF) and the Solvent-Induced Force / Appendix C：

Conditional Solvation and Conditional Correlation / Appendix D：

Non-Additivity of the Potential of Mean Force and of the Solvation Gibbs Energy / Appendix E：

The Statistical Mechanical Definition of Independence of Solvation and of Conditional Solvation / Appendix F：

Approximate Estimates of the H?I Interaction between Two, Three and Four H?I Groups at a Distance of 4.5 A / Appendix G：

Evaluating The Inadequacy of Kauzmann's Model for the Role of the H?O Effect in Protein Folding / Appendix H：

The Cracks in the Hydrogen Bond Inventory Argument / Appendix I：

Can "Statistical Potential," Derived from Protein Structures, be Interpreted as a Potential of Mean Force? / Appendix J：

Work of Creating a Cavity and the Probability of Finding a Cavity in a Solvent / Appendix K：

H?I Interactions and Solubility of Isomeric Compounds / Appendix L：

Further Inflating the Already Inflated Value of the H?0 Effect / Appendix M：

The Anfinsen Dogma and the "Thermodynamic Hypothesis" Applied to the Process of Protein Folding / Appendix N：

Entropy-Enthalpy Compensation; from an Exact Theorem to an Approximate Manifestation / Appendix O：

Probability of Finding a Specific Configuration of a Protein and the Work Required to Obtain that Configuration / Appendix P：

The Many Faces of Reversibility and Irreversibility / Appendix Q：

Cooperativity in Protein Folding? / Appendix R：

Local Densities of Water Molecules near H?I Groups / Appendix S：

What Drives the "Driving Force?" / Appendix T：

References

Index

Quotations

List of Abbreviations

Preface

Acknowledgements

Introduction, the Main Problem and the Main Tools / 1：

The General Problem / l.l：

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