Translational-Entropy Gain of Solvent upon Protein Folding
Yuichi Harano 1 and Masahiro Kinoshita 1*
1 Institute of Advanced Energy, Kyoto University
* To whom correspondence should be addressed. E-mail: kinoshit{at}iae.kyoto-u.ac.jp.
Submitted on December 5, 2004
Revised on January 31, 2005
Accepted on 21 July 2005
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Abstract |
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We show that even in the complete absence of potential energies among the atoms in a protein-aqueous solution system, there is a physical factor which favors the folded state of the protein. It is a gain in the translational entropy (TE) of water originating from the translational movement of water molecules. An elaborate statistical-mechanical theory is employed to analyze the TE of water in which a protein or peptide with a prescribed conformation is immersed. It is shown that if the number of residues is sufficiently large, the TE gain is powerful enough to compete with the conformational-entropy loss upon folding. For protein G we have tested over one hundred compact conformations generated by a computer simulation with the all-atom potentials as well as the native structure. A significant finding is that the largest TE is attained in the native structure. The translational movement of water molecules is quite effective in achieving the tight packing in the interior of a natural protein. These results are true only when the solvent is water whose molecular size is the smallest among the ordinary liquids in nature.
Key Words:
conformational entropy, dehydration, hydrogen bond, native structure, secondary structure, water
