Paper Citing NAMD - Abstract
Li Wenzhao; Meng Wei; Tian Pu
Impact of Stable Protein-protein Interaction on Protein Conformational Space
CHEMICAL RESEARCH IN CHINESE UNIVERSITIES, 31:149-155, FEB 2015
Backbone dihedral angle based clustering approach was applied to investigate the effect of protein cornplexation on backbone conformational space and the effect on protein dynamics. Three representative enzyme-inhibitor complexes and their comprised proteins were used as models for small- and moderate-sized globular proteins to compare available backbone conformational space before and after complexation. Microsecond time scale molecular dynamic simulations were generated to ensure sufficient statistics. The result suggests that stable protein-protein interactions lead to redistribution of protein backbone mobility and restriction of the protein backbone conformational space, especially for short time scale motions. Surprisingly, these effects are found to be uncorrelated with protein-protein interaction surface. Consistent with many experimental and computational observations, our results indicate that both induced-fit and conformational selection models play roles in stable protein complexation process, with the dominant role being different for different protein complexes.
