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

当以内坐标为二面角作为分子的自由度时，变量个数的减少有利于分子简正模的计算。然而，由于外自由度的处理比较复杂，多分子系统的简正波分析很难进行。为了无一例外地分析PDB中更多的蛋白质复合体，我们对迄今开发的二面角系统中的程序进行了升级，在复合体的简正模式分析中，通过对分子应用Eockart条件来获得复合体中每个原子相对于分子质心的位移，称为内部运动。外部运动是整个综合体的正常模式与内部运动之间的差异。我们将分子质心运动中的平移-转动分量定义为分子内所有原子外部运动的平均值，然后分析了具有较大平移-转动分量的束缚简正模。在分析的几十种酶抑制剂复合体和抗原抗体复合体中，几乎不存在显着的平移运动模式，转动分量仅局限于少数几种模式。根据结合简正波的分布，可以对络合物的动态结构进行分类。分析结果被登记在蛋白质正常模式分析数据库ProMODE中并向公众介绍。显示每个分子的内部运动、外部运动和相关性的网页被添加到数据库服务器。

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.