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

文献类型：期刊论文

作者Ye, Chun1,2,3; Ding, Chengtao1,3; Ma, Rongsheng1,3; Wang, Junfeng2; Zhang, Zhiyong1,3
刊名PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
出版日期2019-04-01
卷号87期号:4页码:337-347
关键词conformational transition domain motion enhanced sampling molecular dynamics simulation protein dynamics
ISSN号0887-3585
DOI10.1002/prot.25655
通讯作者Zhang, Zhiyong(zzyzhang@ustc.edu.cn)
英文摘要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 center dot Mg enters into its binding pocket first and then AMP does. After the reaction of ATP transferring the terminal phosphate group to AMP, ADP center dot 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.
WOS关键词MOLECULAR-DYNAMICS ; ESCHERICHIA-COLI ; CONFORMATIONAL TRANSITION ; CRYSTAL-STRUCTURES ; MOTIONS ; LANDSCAPE ; COMPLEX ; SIMULATIONS ; ACTIVATION ; RESOLUTION
资助项目National Natural Science Foundation of China[21573205] ; National Natural Science Foundation of China[21807095] ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences[XDPB10]
WOS研究方向Biochemistry & Molecular Biology ; Biophysics
语种英语
WOS记录号WOS:000460650500008
出版者WILEY
资助机构National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; National Natural Science Foundation of China ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences ; Strategic Priority Research Program (Pilot study): Biological basis of aging and therapeutic strategies of the Chinese Academy of Sciences
源URL[http://ir.hfcas.ac.cn:8080/handle/334002/42196]  
专题合肥物质科学研究院_中科院强磁场科学中心
通讯作者Zhang, Zhiyong
作者单位1.Univ Sci & Technol China, Hefei Natl Lab Phys Sci Microscale, Hefei, Anhui, Peoples R China
2.Chinese Acad Sci, High Magnet Field Lab, Hefei, Anhui, Peoples R China
3.Univ Sci & Technol China, Sch Life Sci, 443 Huangshan Rd, Hefei 230027, Anhui, Peoples R China
推荐引用方式
GB/T 7714		 Ye, Chun,Ding, Chengtao,Ma, Rongsheng,et al. Electrostatic interactions determine entrance/release order of substrates in the catalytic cycle of adenylate kinase[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,2019,87(4):337-347.
APA Ye, Chun,Ding, Chengtao,Ma, Rongsheng,Wang, Junfeng,&Zhang, Zhiyong.(2019).Electrostatic interactions determine entrance/release order of substrates in the catalytic cycle of adenylate kinase.PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,87(4),337-347.
MLA Ye, Chun,et al."Electrostatic interactions determine entrance/release order of substrates in the catalytic cycle of adenylate kinase".PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 87.4(2019):337-347.

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来源：合肥物质科学研究院

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