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

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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.