title: Analysis of water channels by molecular dynamics simulation of heterotetrameric sarcosine oxidase.
abstract: 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 average hydropathy indices of the residues of the channels, and the number of migration events of water molecules through the channels were consistent with the selective transport hypothesis whereby tunnel T3 is the pathway for the exit of the iminium intermediate of the enzyme reaction.
authors: School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan.
authors: Go
authors: G
authors: Watanabe
authors: School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan.
authors: Daisuke
authors: D
authors: Nakajima
authors: School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan.
authors: Akinori
authors: A
authors: Hiroshima
authors: School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan.
authors: Haruo
authors: H
authors: Suzuki
authors: School of Science, Kitasato University, Sagamihara, Kanagawa 252-0373, Japan.
authors: Shigetaka
authors: S
authors: Yoneda
keywords: channelling; enzyme reaction; flavo-protein; selective transport