Muilu J, Törrönen A, Peräkylä M, Rouvinen J
Department of Chemistry, University of Joensuu, Finland.
Proteins. 1998 Jun 1;31(4):434-44.
Recent crystallographic studies have revealed a range of structural changes in the three-dimensional structure of endo-1,4-xylanase (XYNII) from Trichoderma reesei. The observed conformational changes can be described as snapshots of an open-close movement of the active site of XYNII. These structures were further analyzed in this study. In addition, a total of four 1 ns molecular dynamics (MD) simulations were performed representing different states of the enzyme. A comparison of the global and local changes found in the X-ray structures and the MD runs suggested that the simulations reproduced a similar kind of active site opening and closing as predicted by the crystal structures. The open-close movement was characterized by the use of distance difference matrixes and the Hinge-find program (Wriggers and Schulten, Proteins 29:1-14, 1997) to be a 'hinge-bending' motion involving two large rigidly-moving regions and an extended hinge. This conformational feature is probably inherent to this molecular architecture and probably plays a role in the function of XYNII.
最近的晶体学研究揭示了里氏木霉内切-1,4-木聚糖酶（XYNII）三维结构中的一系列结构变化。观察到的构象变化可描述为XYNII活性位点开闭运动的瞬间状态。本研究对这些结构进行了进一步分析。此外，总共进行了四次1纳秒的分子动力学（MD）模拟，代表该酶的不同状态。对X射线结构和MD模拟中发现的全局和局部变化进行比较表明，模拟重现了与晶体结构预测相似的活性位点开闭情况。通过使用距离差异矩阵和Hinge-find程序（Wriggers和Schulten，《蛋白质》29:1-14，1997）对开闭运动进行表征，结果表明这是一种“铰链弯曲”运动，涉及两个大的刚性移动区域和一个延伸的铰链。这种构象特征可能是这种分子结构所固有的，并且可能在XYNII的功能中发挥作用。
