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Coarse-Grained Free-Energy Simulations of Conformational State Transitions in an ABC Exporter
liaojl
Author NameAffiliationE-mail
liaojl Department of Chemical Physics, University of Science and Technology of China,96 Jinzhai Rd, Hefei, Anhui Province, P. R. China, 230026 liaojl@ustc.edu.cn 
Abstract:
ATP-binding cassette (ABC) exporters transport many substrates out of cellular membranes via alternating between inward-facing (IF) and outward-facing (OF) conformations. Despite extensive research efforts over the past decades, understanding of the molecular mechanism remains elusive. As these large-scale conformational movements are global and collective, we have previously performed extensive coarse-grained molecular dynamics (CG-MD) simulations of the potential of mean force (PMF) along the conformational transition pathway [Z. Wang et. al JPCB, 119, 1295?1301 (2015)]. However, the occluded (OC) conformational state, in which both the internal and external gate are closed, was not determined in the calculated free energy profile. In this paper, we extend the above methods to the calculation of the free energy profile along the reaction coordinate, d1- d2, which are the COM distances between the two sides of the internal (d1) and the external gate (d2). The PMF is thus obtained to identify the transition pathway, along which several OF-, IF- and OC- state structures are predicted in good agreement with structural experiments. Our CG-MD free-energy simulations demonstrate that the internal gate is closed before the external gate is open during the IF to OF transition and vice versa during the IF to OF transition. Our results capture the unidirectional feature of substrate translocation via the exporter, which is functionally important in biology. This finding is different from the results, in which both the internal and external gates are open reported in an X-ray experiment [Ward A. et al, PNAS, 104, 19005?19010 (2007)]. Our study sheds light on the molecular mechanism of the state transitions in the ABC exporter.
Key words:  ATP-binding cassette (ABC) exporter, conformational state transition, coarse-grained molecular dynamics (CG-MD), potential of mean force (PMF)
FundProject:
Coarse-Grained Free-Energy Simulations of Conformational State Transitions in an ABC Exporter
liaojl
摘要:
ATP-binding cassette (ABC) exporters transport many substrates out of cellular membranes via alternating between inward-facing (IF) and outward-facing (OF) conformations. Despite extensive research efforts over the past decades, understanding of the molecular mechanism remains elusive. As these large-scale conformational movements are global and collective, we have previously performed extensive coarse-grained molecular dynamics (CG-MD) simulations of the potential of mean force (PMF) along the conformational transition pathway [Z. Wang et. al JPCB, 119, 1295?1301 (2015)]. However, the occluded (OC) conformational state, in which both the internal and external gate are closed, was not determined in the calculated free energy profile. In this paper, we extend the above methods to the calculation of the free energy profile along the reaction coordinate, d1- d2, which are the COM distances between the two sides of the internal (d1) and the external gate (d2). The PMF is thus obtained to identify the transition pathway, along which several OF-, IF- and OC- state structures are predicted in good agreement with structural experiments. Our CG-MD free-energy simulations demonstrate that the internal gate is closed before the external gate is open during the IF to OF transition and vice versa during the IF to OF transition. Our results capture the unidirectional feature of substrate translocation via the exporter, which is functionally important in biology. This finding is different from the results, in which both the internal and external gates are open reported in an X-ray experiment [Ward A. et al, PNAS, 104, 19005?19010 (2007)]. Our study sheds light on the molecular mechanism of the state transitions in the ABC exporter.
关键词:  ATP-binding cassette (ABC) exporter, conformational state transition, coarse-grained molecular dynamics (CG-MD), potential of mean force (PMF)
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