Molecular Dynamics Simulation of Temperature-dependent Flexibility of Thermophilic Xylose Isomerase

有 D 木糖的 Thermus thermophilus 木糖 isomerase (TtXI ) 的复杂模型被构造，并且分子的动力学(MD ) 模拟被 NAMD2.5 为 10 ns 在 300 和 360 K 执行。旋转(Rg ) 的半径，子单元相互作用，和残余灵活性被分析。结果表演残余 6069， 142148， 169172，和 332340 在 300 和 360 K 有高灵活性。有在 360 K 的更高的灵活性的残余能主要在 300 K 比那被划分成二个组：一个人在由残余组成的 helix-loop-helix 区域定位 5580 在里面催化领域；其它在子单元连接。在 360 K 的催化领域的 Rg 显示出 0.16 吗？高，比那，在小 C 终端的 300 K，而是 Rg，领域没有明显的差别。结果显示催化领域的那提高的 Rg 可以导致 TtXI 的活跃地点的强烈运动并且支持 D 木糖 isomization 反应。八张氢契约和五离子对与 300 K 相比在 360 K 在子单元接口被减少，那可以是为在在在 TtXI 的高温度的活动的刚硬和增加的减少的主要原因。也，解释 TtXI E372G 异种的冷改编的现象的帮助以前报导了的这结果。我们的结果揭示在温度和 TtXI 的结构灵活性之间的关系，并且在与多重子单元理解 thermophile 蛋白质的 thermostability 起一个重要作用。

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-loophelix 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 A 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.