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Published online before print July 27, 2007, 10.1110/ps.072909007
Protein Science (2007), 16:1927-1933. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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Theoretical study of the partial molar volume change associated with the pressure-induced structural transition of ubiquitin

Takashi Imai1, Shusaku Ohyama1, Andriy Kovalenko2, and Fumio Hirata3

1 Department of Bioscience and Bioinformatics, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
2 National Institute for Nanotechnology, National Research Council of Canada, and Department of Mechanical Engineering, University of Alberta, Edmonton, Alberta T6G 2M9, Canada
3 Department of Theoretical Studies, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan

(RECEIVED March 28, 2007; FINAL REVISION June 13, 2007; ACCEPTED June 14, 2007)

The partial molar volume (PMV) change associated with the pressure-induced structural transition of ubiquitin is analyzed by the three-dimensional reference interaction site model (3D-RISM) theory of molecular solvation. The theory predicts that the PMV decreases upon the structural transition, which is consistent with the experimental observation. The volume decomposition analysis demonstrates that the PMV reduction is primarily caused by the decrease in the volume of structural voids in the protein, which is partially canceled by the volume expansion due to the hydration effects. It is found from further analysis that the PMV reduction is ascribed substantially to the penetration of water molecules into a specific part of the protein. Based on the thermodynamic relation, this result implies that the water penetration causes the pressure-induced structural transition. It supports the water penetration model of pressure denaturation of proteins proposed earlier.

Keywords: partial molar volume; pressure denaturation; protein hydration; water penetration; 3D-RISM theory


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