Electrostatic Interactions Determine Entrance/Release order of Substrates in the Catalytic Cycle of Adenylate Kinase.

Adenylate kinase is a monomeric phosphotransferase with important biological function in regulating concentration of ATP in cells, by transferring the terminal phosphate group from ATP to AMP and forming two ADP molecules. During this reaction, the kinase may undergo a large conformational transition, forming different states with its substrates. Although many structures of the protein are available, atomic details of the whole process remain unclear. In this paper, we use both conventional molecular dynamics simulation and an enhanced sampling technique called parallel cascade selection molecular dynamics simulation to explore different conformational states of the Escherichia coli adenylate kinase. Based on the simulation results, we propose a possible entrance/release order of substrates during the catalytic cycle. The substrate-free protein prefers an open conformation, but changes to a closed state once ATP·Mg enters into its binding pocket first and then AMP does. After the reaction of ATP transferring the terminal phosphate group to AMP, ADP·Mg and ADP are released sequentially, and finally the whole catalyze cycle is completed. Detailed contact and distance analysis reveals that the entrance/release order of substrates may be largely controlled by electrostatic interactions between the protein and the substrates. This article is protected by copyright. All rights reserved.