Paper Citing NAMD - Abstract
Sun, Ting Guang; Li, Chun Hua; Chen, Wei Zu; Wang, Cun Xin
A novel back-door pathway for glutamine release from GlnBP revealed by steered molecular dynamics simulation
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 905:51-58, JUL 15 2009
The Glutamine transfer system consists of three components: glutamine binding protein (GlnBP), the transmembrame receptor (TMR) and the ATP binding subunit. it is typical of periplasmic transfer systems in Escherichia coli and belongs to the ABC (ATP-binding cassettes) super family. Until now, the mechanism of glutamine release from its receptor remains unknown, also little information is available on the interactions between the substrate-bound complex and the TMR because of a lack of structure information of the TMR. In our study, a steered molecular dynamics (SMD) method is used to explore the possible pathway for glutamine release from its receptor GlnBP. It is found that a novel back-door pathway, rather than a front-door pathway is more reasonable. This work may help understand the substrate release mechanism of the periplasmic transfer system and additionally give some clues as to how the substrate-bound complex binds to its TMR and completes the subsequent translocation of the substrate. (c) 2009 Published by Elsevier B.V.
