[1]时术华 张庆刚.HIV-1蛋白酶与TMC114结合口袋内水分子作用的研究[J].山东建筑大学学报,2010,(04):359-363.
 SHI Shu-hua,ZHANG Qing-gang.Study on the function of water molecules buried within binding pocket of HIV-1 protease and TMC114[J].Journal of Shandong jianzhu university,2010,(04):359-363.
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HIV-1蛋白酶与TMC114结合口袋内水分子作用的研究()
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《山东建筑大学学报》[ISSN:1673-7644/CN:37-1449/TU]

卷:
期数:
2010年04期
页码:
359-363
栏目:
研究论文
出版日期:
2010-08-15

文章信息/Info

Title:
Study on the function of water molecules buried within binding pocket of
                 HIV-1 protease and TMC114
作者:
时术华1 张庆刚2
(1. 山东建筑大学理学院,山东 济南 250101; 2. 山东师范大学物理与电子科学学院, 山东 济南 250014)
Author(s):
SHI Shu-hua1 ZHANG Qing-gang2
(1. School of Science, Shandong Jianzhu University, Shandong Jinan 250101, China;  2. College of Physics and Electronics, Shandong Normal University, Shandong Jinan 250014, China)
关键词:
物理化学结合口袋分子动力学HIV-1蛋白酶TMC114
Keywords:
physical chemistry binding pocket molecular dynamics HIV-1 protease TMC114
分类号:
O5615
文献标志码:
A
摘要:
水分子在生物分子的稳定、动力学和功能方面发挥着重要作用。采用3ns分子动力学模拟, 从不同侧面系统地研究了HIV-1蛋白质酶与其抑制剂TMC114结合口袋内的五个水分子的功能作用。结果表明:水分子可以保持PR/TMC114的动力学和结构以及绑定特性的稳定;复合体的晶体结构和平均结构的比较表明Wat301、Wat2和Wat5在分子动力学模拟过程中是守恒的;对氢键的分析证实Wat301可以稳定PR与TMC114抑制剂柔性区域的结构,并且Wat2和Wat5能增强活动位点的稳定性。
Abstract:
Water molecules play an important role in the stability, dynamics and function of biomolecules. 3ns molecular dynamics (MD) simulations have been carried out to systematically investigate the role of five water molecules in the binding pocket of HIV-1 protease (PR) with TMC114 from different aspects. The results suggest that the water molecules can keep the stabilities of dynamics, the structure of PR/TMC114 and the binding specificity of PR/TMC114. Comparison between the crystal and average structures of the complex shows that Wat301, Wat2 and Wat5 are conserved during MD simulation. The analyses of hydrogen bonds prove that Wat301 can stabilize the structure of the flaps of,PR/TMC114 and that Wat2 and Wat5 can reinforce the stability of the active site triads.

相似文献/References:

[1]时术华.蛋白质静电势的量子化学计算[J].山东建筑大学学报,2010,(02):154.
 SHI Shu-hua.Quantum chemical calculations of electrostatic potential of protein[J].Journal of Shandong jianzhu university,2010,(04):154.
[2]时术华,陈建中,张庆刚,等.抑制剂PMI与MDM2结合模式的分子动力学研究[J].山东建筑大学学报,2013,(02):101.
 Shi Shuhua,Chen Jianzhong,Zhang Qinggang,et al.Insights into binding modes of inhibitors PMI to MDM2 based on Molecular Dynamics Simulations[J].Journal of Shandong jianzhu university,2013,(04):101.

更新日期/Last Update: 2010-09-19