A highly parallelizable integral equation theory for three dimensional solvent distribution function: application to biomolecules.
Three dimensional (3D) hydration structure is informative to clarify the functions of hydrated waters around a protein. We develop a new approach to calculate 3D solvation structure with reasonable computational cost. In the present method, the total solvation structure is obtained using conventional one dimensional reference interaction site model (RISM) followed by integrating the 3D fragment data, which are evaluated around each atom (site) of solute. Thanks to this strategy, time-consuming 3D fast Fourier transformation, which is required in 3D-RISM theory, can be avoided and high-parallel performance is achieved. The method is applied to small molecular systems for comparison with 3D-RISM. The obtained results by the present method and by 3D-RISM show good agreement. The hydration structures for a large protein computed by the present method are also consistent with those obtained by x-ray crystallography.
Yokogawa
Daisuke
D
Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan.
Sato
Hirofumi
H
Imai
Takashi
T
Sakaki
Shigeyoshi
S
D003198:Computer Simulation; D018360:Crystallography, X-Ray; D006859:Hydrogen / Q000737:chemistry; D008958:Models, Molecular; D010100:Oxygen / Q000737:chemistry; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000737:chemistry
D011506:Proteins; D012997:Solvents; D014867:Water; D006859:Hydrogen; D010100:Oxygen