Molecular Dynamics Studies on the Conformational Transitions of Adenylate Kinase: A Computational Evidence for the Conformational Selection Mechanism
Joint Authors
Li, Yixue
Ping, Jie
Wang, Jing-Fang
Hao, Pei
Source
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-7, 7 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-06-26
Country of Publication
Egypt
No. of Pages
7
Main Subjects
Abstract EN
Escherichia coli adenylate kinase (ADK) is a monomeric phosphotransferase enzyme that catalyzes reversible transfer of phosphoryl group from ATP to AMP with a large-scale domain motion.
The detailed mechanism for this conformational transition remains unknown.
In the current study, we performed long time-scale molecular dynamics simulations on both open and closed states of ADK.
Based on the structural analyses of the simulation trajectories, we detected over 20 times conformational transitions between the open and closed states of ADK and identified two novel conformations as intermediate states in the catalytic processes.
With these findings, we proposed a possible mechanism for the large-scale domain motion of Escherichia coli ADK and its catalytic process: (1) the substrate free ADK adopted an open conformation; (2) ATP bound with LID domain closure; (3) AMP bound with NMP domain closure; (4) phosphoryl transfer occurred with ATP, and AMP converted into two ADPs, and no conformational transition was detected in the enzyme; (5) LID domain opened with one ADP released; (6) another ADP released with NMP domain open.
As both open and closed states sampled a wide range of conformation transitions, our simulation strongly supported the conformational selection mechanism for Escherichia coli ADK.
American Psychological Association (APA)
Ping, Jie& Hao, Pei& Li, Yixue& Wang, Jing-Fang. 2013. Molecular Dynamics Studies on the Conformational Transitions of Adenylate Kinase: A Computational Evidence for the Conformational Selection Mechanism. BioMed Research International،Vol. 2013, no. 2013, pp.1-7.
https://search.emarefa.net/detail/BIM-1004760
Modern Language Association (MLA)
Ping, Jie…[et al.]. Molecular Dynamics Studies on the Conformational Transitions of Adenylate Kinase: A Computational Evidence for the Conformational Selection Mechanism. BioMed Research International No. 2013 (2013), pp.1-7.
https://search.emarefa.net/detail/BIM-1004760
American Medical Association (AMA)
Ping, Jie& Hao, Pei& Li, Yixue& Wang, Jing-Fang. Molecular Dynamics Studies on the Conformational Transitions of Adenylate Kinase: A Computational Evidence for the Conformational Selection Mechanism. BioMed Research International. 2013. Vol. 2013, no. 2013, pp.1-7.
https://search.emarefa.net/detail/BIM-1004760
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1004760