Paper Citing NAMD - Abstract
Wang, Beibei; Weng, Jingwei; Wang, Wenning
Multiple conformational states and gate opening of outer membrane protein ToIC revealed by molecular dynamics simulations
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 82:2169-2179, SEP 2014
Outer membrane protein TnIC serves as an exit duct or exporting substances out of cell. The occluded periplasmic entreance of ToIC is required to open for substrate transport, although the opening mechanism were performed to explore the conformational dynamics of ToIC. The periplasmic gate was shown to sample multiple conformational states with various degree of gating opeing. The gate opeing was facilitated by all mutations expcept Y362F, which adopts an even more closed state thatn wild type ToIC. The interproteomer salt-briedge R367-D153 is traned out to be crocial for periplasimc gate opeing. The mutations that dirupt the interactins at the periplamic tip may affect the stablity of the trimeric assemly of ToIC. Structual asymmerty of the periplasmic gate was observed to be opeing sized dependen. Asymmetric conformations are found in moderately opening states, while the most and the least opening states are often more symmetric. Finally. it is shown that lowering pH can remarkably stabilize the closed state of the periplasmic gate
