Journal
BIOMED RESEARCH INTERNATIONAL
Volume 2013, Issue -, Pages -Publisher
HINDAWI LTD
DOI: 10.1155/2013/628536
Keywords
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Funding
- National Basic Research Program of China (973 Program) [2012CB517900]
- National Key Basic Research Program [30800210]
- National Natural Science Foundation of China [31200547, 90913009]
- Shanghai Pujiang Scholarship Program [10PJ1408000]
- Doctoral Program Foundation of Institutions of Higher Education of China [20110073120078]
- China Postdoctoral Science Foundation [2012M520949]
- SA-SIBS scholarship Program
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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.
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