Partial molar volume of proteins studied by the three-dimensional reference interaction site model theory.
The three-dimensional reference interaction site model (3D-RISM) theory is applied to the analysis of hydration effects on the partial molar volume of proteins. For the native structure of some proteins, the partial molar volume is decomposed into geometric and hydration contributions using the 3D-RISM theory combined with the geometric volume calculation. The hydration contributions are correlated with the surface properties of the protein. The thermal volume, which is the volume of voids around the protein induced by the thermal fluctuation of water molecules, is directly proportional to the accessible surface area of the protein. The interaction volume, which is the contribution of electrostatic interactions between the protein and water molecules, is apparently governed by the charged atomic groups on the protein surface. The polar atomic groups do not make any contribution to the interaction volume. The volume differences between low- and high-pressure structures of lysozyme are also analyzed by the present method.
Imai
Takashi
T
Department of Bioscience and Bioinformatics, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan.
Kovalenko
Andriy
A
Hirata
Fumio
F
D001665:Binding Sites; D021621:Imaging, Three-Dimensional; D008024:Ligands; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D008970:Molecular Weight; D009113:Muramidase / Q000737:chemistry; D011312:Pressure; D011506:Proteins / Q000737:chemistry*; D012997:Solvents; D055672:Static Electricity; D013499:Surface Properties; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
D008024:Ligands; D011506:Proteins; D012997:Solvents; D014867:Water; D009113:Muramidase