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Solvation effect on the structural change of a globular protein: A molecular dynamics study

✍ Scribed by Taku Mizukami; Hiroaki Saito; Shuhei Kawamoto; Takeshi Miyakawa; Masashi Iwayama; Masako Takasu; Hidemi Nagao

Publisher
John Wiley and Sons
Year
2011
Tongue
English
Weight
891 KB
Volume
112
Category
Article
ISSN
0020-7608

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✦ Synopsis

Abstract

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 β€œopen–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. Β© 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012

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