Free-energy analysis of protein solvation with all-atom molecular dynamics simulation combined with a theory of solutions.
The structure of a protein is strongly influenced by solvation. In the present review, the solvation effect is treated within the framework of statistical thermodynamics. The key quantity is the solvation free energy of protein and a fast method for its computation with explicit solvent is introduced. The applications of the method to the structural fluctuation of protein in water, structure determination of protein-protein complex, and urea effect on protein structure are then described, and the roles of solvent water and cosolvent are discussed from the standpoint of energetics.
Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan; Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Katsura, Kyoto 615-8520, Japan. Electronic address: nobuyuki@cheng.es.osaka-u.ac.jp.
Nobuyuki
N
Matubayasi
D056004:Molecular Dynamics Simulation; D011489:Protein Denaturation / Q000187:drug effects; D011506:Proteins / Q000737:chemistry*; D012996:Solutions; D012997:Solvents / Q000737:chemistry*; D013816:Thermodynamics
D011506:Proteins; D012996:Solutions; D012997:Solvents