[Frontiers in Bioscience 14, 3419-3454, January 1, 2009]

[Frontiers in Bioscience 14, 3419-3454, January 1, 2009]

Roles of translational motion of water molecules in sustaining life

Masahiro Kinoshita

Institute of Advanced Energy, Kyoto University

TABLES OF CONTENTS

1. Abstract
2. Introduction
3. Entropic Excluded-Volume Effect: 3.1. Asakura-Oosawa theory; 3.2. Effect of microstructure of small particles formed near large particles or a large particle and a planar wall; 3.3. Effect of attractive potentials between small particles, a small particle and a large particle, or a small particle and a planar wall; 3.4. In real systems, what do small particles, large particles, and a planar wall, respectively, correspond to?; 3.5. Isochoric (constant-volume) and isobaric (constant-pressure) processes; 3.6. Cases where the asphericity of large particles is quite high; 3.7. Experimental evidence of entropic excluded-volume effect; 3.8. Comments on "hydrophobicity"; 3.9. Ordering processes entropically driven
4. Protein Folding: 4.1. What is the major driving force in protein folding?; 4.2. Statistical-mechanical analysis focused on the effect of translational motion of water molecules; 4.3. Morphometric approach to solvation thermodynamics of a protein; 4.4. Energetics of protein folding; 4.5. Relevance to experimental observations; 4.6. Construction of a novel method for predicting the native structure; 4.7. Partial molar volume of a protein; 4.8. Molecular mechanism of pressure denaturation of a protein: physical similarity to crystal nucleation known for a single-component system of hard spheres; 4.9. Heat and cold denaturations of a protein
5. Molecular Recognition between guest ligands and host enzymes: 5.1. Statistical-mechanical analysis focused on the effect of translational motion of water molecules; 5.2. Relevance to experimental observations
6. Formation of ordered structure by aggregation of protein molecules: 6.1. Regularity and symmetry of aggregates; 6.2. Molecular mechanism of amyloid-fibril formation; 6.3. Flexibility and adaptability of protein structure; 6.4. Relevance to experimental observations
7. Other ordering processes in biological systems: 7.1. Specificity in associations between lipids and proteins; 7.2. Can the motion of biomolecules be controlled?
8. Effects of salts and cosolute molecules: 8.1. Crucial importance of salts; 8.2. Effects of adding medium-size particles; 8.3. Surface-induced phase transition and long-range surface force
9. Perspective
10. Acknowledgments
11. Appendix A. Solvent density profile near a solvophobic solute
12. Appendix B. Contact of solutes immersed in water in isobaric process below 277 K
13. Appendix C. The first coefficient in the morphometric form for various components of hydration entropy
14. References

1. ABSTRACT

By reviewing the results of our analyses based on statistical-mechanical theories, we point out that the entropic effect arising from the translational motion of water molecules is a principal driving force in a variety of self-assembling and ordering processes in biological systems such as protein folding, molecular recognition, and ordered aggregation of protein molecules. The great entropic loss for the biomolecules accompanying these processes is largely compensated by a great entropic gain of the water that is present in the system. The microscopic mechanisms of protein folding and denaturation, receptor-ligand binding, and amyloid-fibril formation are discussed in detail. We describe an effort to develop a unique method for predicting the native structure of a protein. The roles of NaCl and cosolute molecules are also briefly discussed.