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Molecular dynamics simulations of the Hras‐GTP complex and the Hras‐GDP complex
Author(s) -
Miyakawa Takeshi,
Morikawa Ryota,
Takasu Masako,
Sugimori Kimikazu,
Mizukami Taku,
Kawaguchi Kazutomo,
Saito Hiroaki,
Nagao Hidemi
Publication year - 2013
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.24457
Subject(s) - hras , gtp' , molecular dynamics , hydrolysis , chemistry , crystallography , computational chemistry , organic chemistry , enzyme , biochemistry , kras , mutation , gene
We study the structures of the Hras‐GTP complex and the Hras‐GDP complex in water to investigate the mechanism of GTP hydrolysis of the Hras‐GTP complex. We performed molecular dynamics simulations of these complexes to investigate the structures of these complexes using the potential parameters of AMBER ff03 and our potential parameters around Mg 2+ . Our simulations show that the averaged structure differences between the Hras‐GTP complex and Hras‐GDP complex are found in the switch I and II regions. In particular, in the switch II region, the α 2 ‐ helix of Hras‐GDP is shorter than the α 2 ‐ helix of Hras‐GTP. The averaged number of water molecules in the first hydration sphere in Hras‐GDP complex is larger than that in Hras‐GTP complex. The occurrence ratio of the duration time of waters in the first hydration sphere of PA has long tail both in Hras‐GTP and in Hras‐GDP. In Hras‐GDP complex, β ‐phosphate is hard to be hydrolyzed, while the number of waters in the first hydration sphere is larger than those in Hras‐GTP. This suggests that there is a special direction for the hydrolysis. © 2013 Wiley Periodicals, Inc.