Analysis of water channels by molecular dynamics simulation of heterotetrameric sarcosine oxidase.
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ABSTRACT:
SUBMITTER: Watanabe G
PROVIDER: S-EPMC4736832 | biostudies-literature | 2015
REPOSITORIES: biostudies-literature
Publications
Analysis of water channels by molecular dynamics simulation of heterotetrameric sarcosine oxidase.
Watanabe Go G Nakajima Daisuke D Hiroshima Akinori A Suzuki Haruo H Yoneda Shigetaka S
Biophysics and physicobiology 20151222
A precise 100-ns molecular dynamics simulation in aquo was performed for the heterotetrameric sarcosine oxidase bound with a substrate analogue, dimethylglycine. The spatial region including the protein was divided into small rectangular cells. The average number of the water molecules locating within each cell was calculated based on the simulation trajectory. The clusters of the cells filled with water molecules were used to determine the water channels. The narrowness of the channels, the ave ...[more]
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