Electrostatic interactions determine entrance/release order of substrates in the catalytic cycle of adenylate kinase

腺苷酸激酶 磷酸转移酶 三磷酸腺苷 二磷酸腺苷 一磷酸腺苷 蛋白激酶A 生物物理学 腺苷 催化循环 基质(水族馆) 化学 生物化学 分子动力学 激酶 生物 计算化学 血小板聚集 免疫学 血小板 生态学
作者
Chun Ye,Yuxing Chen,Rongsheng Ma,Junfeng Wang,Zhiyong Zhang
出处
期刊:Proteins [Wiley]
卷期号:87 (4): 337-347 被引量:9
标识
DOI:10.1002/prot.25655
摘要

Abstract Adenylate kinase is a monomeric phosphotransferase with important biological function in regulating concentration of adenosine triphosphate (ATP) in cells, by transferring the terminal phosphate group from ATP to adenosine monophosphate (AMP) and forming two adenosine diphosphate (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 article, we use both conventional molecular dynamics (MD) simulation and an enhanced sampling technique called parallel cascade selection MD 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.
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