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Molecular Dynamics Simulation of Temperature-dependent Flexibility of Thermophilic Xylose Isomerase
Wei Xu,Ping Cai,Ming Yan,Lin Xu,Ping-kai Ouyang
Author NameAffiliationE-mail
Wei Xu School of Chemical and Biological Engineering, Yancheng Institute of Technology, Yancheng 224051, China  
Ping Cai State Key Laboratory of Materials-Oriented Chemical Engineering, College of Life Science and Phar-macy, Nanjing University of Technology, Nanjing 210009, China  
Ming Yan State Key Laboratory of Materials-Oriented Chemical Engineering, College of Life Science and Phar-macy, Nanjing University of Technology, Nanjing 210009, China ycitxuwei@hotmail.com 
Lin Xu State Key Laboratory of Materials-Oriented Chemical Engineering, College of Life Science and Phar-macy, Nanjing University of Technology, Nanjing 210009, China  
Ping-kai Ouyang State Key Laboratory of Materials-Oriented Chemical Engineering, College of Life Science and Phar-macy, Nanjing University of Technology, Nanjing 210009, China  
Abstract:
The complex model of Thermus thermophilus xylose isomerase (TtXI) with D-xylose was constructed, and molecular dynamics (MD) simulations were carried out at 300 and 360 K for 10 ns by NAMD2.5.The radius of gyration (Rg), subunit interactions, and residue flexibility were analyzed.The results show that residues 60-69, 142-148, 169-172, and 332-340 have high flexibility at 300 and 360 K. Residues with higher flexibility at 360 K than that at 300 K can mainly be divided into two groups: one locates in the helix-loop-helix region consisting of residues 55-80 in catalytic domain; the other at subunit interfaces.The Rg of catalytic domain at 360 K shows 0.16 ? higher than that at 300 K,but Rg of small C-terminal domain has no obvious difference.The results indicate that enhanced Rg of catalytic domain may lead to the intense motion of the active site of TtXI and promote the D-xylose isomization reaction.Eight hydrogen bonds and five ion pairs are reduced at subunit interfaces at 360 K compared with 300 K, that may be the main reason for the decrease in rigidity and increase in activity at high temperature of TtXI.This result also help to explain the cold-adaption phenomenon of TtXI E372G mutant reported previously.Our results reveal the relationship between temperature and structure flexibility of TtXI,and play an important role in understanding the thermostability of thermophile protein with multiple subunits.
Key words:  Molecule dynamics, Xylose isomerase, Structure, Flexibility
FundProject:
Molecular Dynamics Simulation of Temperature-dependent Flexibility of Thermophilic Xylose Isomerase
许伟,蔡萍,严明*,许琳,欧阳平凯
摘要:
构建了嗜热栖热菌木糖异构酶与底物木糖的复合物模型,并运用NAMD2.5软件对其在300 和360 K下进行了10 ns的分子动力学模拟. 对该酶的回旋半径、亚基间相互作用及残基柔性进行了计算与统计分析,确定了该酶在360 K时柔性残基及区域. 研究发现与300 K相比,360 K时木糖异构酶中B-因子增幅较大的残基主要可分为两组:一组位于催化结构域,是由残基55~80组成的helex-loop-helix区域,另一组位于其亚基界面上. 研究表明高温下该酶催化结构域回旋半径增加,可能加速了活性中心的运动从而有利于D-木糖的异构化反应.在360 K时亚基界面上减少了8个氢键和5个离子对,这可能也是高温下其整体结构刚性下降并且活性升高的主要原因,该结果也对文献报道的该酶E372G突变体冷适应的实验现象进行了解释. 研究结果揭示了嗜热栖热菌木糖异构酶温度和结构柔性之间的关系.
关键词:  木糖异构酶,分子动力学,结构,柔性
DOI:10.1088/1674-0068/22/05/467-472
分类号: