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Solvation effect on the structural change of a globular protein: A molecular dynamics study
Author(s) -
Mizukami Taku,
Saito Hiroaki,
Kawamoto Shuhei,
Miyakawa Takeshi,
Iwayama Masashi,
Takasu Masako,
Nagao Hidemi
Publication year - 2012
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.23251
Subject(s) - solvation , globular protein , molecular dynamics , chemistry , structural change , chemical physics , globular cluster , implicit solvation , computational chemistry , thermodynamics , molecule , physics , crystallography , quantum mechanics , organic chemistry , galaxy , economics , macroeconomics
To investigate the relationship between structural change and the solvation effect, we estimated the solvation free energy or excess chemical potential (ECP) of a globular protein by the energy representation method for the protein structure obtained by a molecular dynamic simulation. A large fluctuation of ECP was detected. The estimated ECP along the first principal component axis of protein fluctuation was accompanied with “open–close” structural change, which indicated a smooth and progressive change in ECP. By performing a global water density analysis in the grid space, the water density at the hydration site had a strong correlation with the ECP. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012