Affiliation:
1. Department of Physics, Nanjing University, Nanjing 210093, P. R. China
Abstract
Conformational opening coupled substrate release is believed to be related to the rate limiting step in the catalysis cycle of the adenylate kinase. However, it is still unclear how the substrate dissociates from its active site and how the substrate release is coupled to conformational changes of the kinase. In this work, by using metadynamics simulations, we investigated the ADP release process and the coupled protein dynamics. We found that the ADP release involves overcoming a high free energy barrier, and protonation of the [Formula: see text]-phosphate of the ADP molecules can drastically reduce the barrier height, therefore, promote the ADP release. We identified several key residues contributing to the high free energy barrier. We also showed that the ADP attached to LID domain leaves the binding pocket earlier than the one attached to the NMP domain. We further observed that the ADP release is accompanied by almost fully opening of the LID domain and partially opening of the NMP domain. Our results provide insight into the molecular mechanism of the substrate release of adenylate kinase and the coupled conformational motions.
Funder
National Natural Science Foundation of China
National Basic Research Program of China (973 Program)
Jiangsu Province
Publisher
World Scientific Pub Co Pte Lt
Subject
Computational Theory and Mathematics,Physical and Theoretical Chemistry,Computer Science Applications
Cited by
2 articles.
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