标题：Molecular dynamics simulations of the coenzyme induced conformational changes of Mycobacterium tuberculosis L-alanine dehydrogenase
作者：Ling, Baoping; Sun, Min; Bi, Siwei; Jing, Zhihong; Liu, Yongjun
作者机构：[Liu, Yongjun] Chinese Acad Sci, NW Inst Plateau Biol, Xining 810001, Qinghai, Peoples R China.; [Ling, Baoping; Sun, Min; Bi, Siwei; Jing, Zhihong] 更多
通讯作者地址：[Liu, YJ]Chinese Acad Sci, NW Inst Plateau Biol, Xining 810001, Qinghai, Peoples R China.
来源：JOURNAL OF MOLECULAR GRAPHICS & MODELLING
关键词：L-Alanine dehydrogenase; Mycobacterium tuberculosis; Principle component; analysis; Free energy landscape; Molecular dynamics simulations
摘要：Mycobacterium tuberculosis L-alanine dehydrogenase (L-MtAlaDH) catalyzes the NADH-dependent reversible oxidative deamination of t-alanine to pyruvate and ammonia. L-MtAlaDH has been proposed to be a potential target in the treatment of tuberculosis. Based on the crystal structures of this enzyme, molecular dynamics simulations were performed to investigate the conformational changes of L-MtAlaDH induced by coenzyme NADH. The results show that the presence of NADH in the binding domain restricts the motions and conformational distributions of L-MtAlaDH. There are two loops (residues 94-99 and 238-251) playing important roles for the binding of NADH, while another loop (residues 267-293) is responsible for the binding of substrate. The opening/closing and twisting motions of two domains are closely related to the conformational changes of L-MtAlaDH induced by NADH. (C) 2012 Elsevier Inc. All rights reserved.