Analyses of binding normal modes in protein complexes and registration to the database ProMode

分析蛋白质复合物中的结合正常模式并注册到数据库 ProMode

基本信息

批准号：
17510169
负责人：
ENDO Shigeru
金额：
$ 1.98万
依托单位：
Kitasato University
依托单位国家：
日本
项目类别：
Grant-in-Aid for Scientific Research (C)
财政年份：
2005
资助国家：
日本
起止时间：
2005 至 2007
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-17510169/
关键词：
protein complex dihedral angle internal motion external motion rotational vector Eckart condition ProMode energy minimization 基準振動解析 Eckert条件内部自由度同種多量体同種2量体同種3量体タンパク質 P2対称性

项目摘要

When an internal coordinate as a dihedral angle is used as the degree of freedom of a molecule, a decrease of the number of variables is favorable to calculation of normal modes in the molecule. However the normal mode analysis for a system of multiple molecules was hardly carried out because the handling of the external degree of freedom is complicated. To analyze more protein complexes in PDB without exception preferably the program in a dihedral angle system that we have developed heretofore was upgraded.In the normal mode analysis of a complex the displacement of each atom relative to the center of mass of a molecule in the complex, called internal motion, is obtained by applying an Eckart condition just to the molecule. The external motion is the difference between the normal mode of the whole complex and the internal motion. We defined the translation-rotation component in the motion of the center of mass of the molecule as the average of the external motion of all the atoms within the molecule and then analyzed binding normal modes which have large translation-rotation component. In the analyzed dozens kinds of protease-inhibitor complexes and antigen-antibody ones the mode with a significant translational motion existed hardly and the rotational component is localized only to a few modes. It is suggested that the dynamic structure of the complex could be classified from the distribution of binding normal modes. The analyzed results was registered in ProMode (the database of normal mode analyses of proteins) and introduced to the public. Web pages that display the internal motion, the external motion, and those correlation for each molecule was added to the database server.

当将内部坐标用作二面角作为分子的自由度时，变量数量的减少有利于计算分子中的正常模式。但是，由于外部自由度的处理是复杂的，因此几乎没有进行多个分子系统的正常模式分析。为了分析PDB中更多的蛋白质复合物，优选地，升级了我们所开发的二面角系统中的程序。在复合物的正常模式分析中，每个原子相对于络合物中分子的质量中心的位移（称为内部运动）的位移是通过将ECKART施加到分解条件上的。外部运动是整个复合物的正常模式与内部运动之间的差异。我们将分子质量中心运动中的翻译复合分量定义为分子内所有原子的外部运动的平均值，然后分析具有较大翻译反向分量的结合正常模式。在分析的数十种蛋白酶抑制剂复合物和抗原抗体抗体中，几乎没有具有显着翻译运动的模式，并且旋转成分仅定位于几种模式。建议可以根据结合正常模式的分布对复合物的动态结构进行分类。分析结果在宣传片（蛋白质正常模式分析的数据库）中注册，并向公众介绍。将显示内部运动，外部运动和每个分子相关的网页添加到数据库服务器中。