Journal
JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume 38, Issue 16, Pages 1472-1478Publisher
WILEY
DOI: 10.1002/jcc.24742
Keywords
ion channels; voltage gating; potassium channel; targeted molecular dynamics; umbrella sampling
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Funding
- Swiss Foundation for Excellence and Talent in Biomedical Research
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We used targeted molecular dynamics, informed by experimentally determined inter-atomic distances defining the pore region of open and closed states of the KvAP voltage-gated potassium channel, to generate a gating pathway of the pore domain in the absence of the voltage-sensing domains. We then performed umbrella sampling simulations along this pathway to calculate a potential of mean force that describes the free energy landscape connecting the closed and open conformations of the pore domain. The resulting energetic landscape displays three minima, corresponding to stable open, closed, and intermediate conformations with roughly similar stabilities. We found that the extent of hydration of the interior of the pore domain could influence the free energy landscape for pore opening/closing. (c) 2017 Wiley Periodicals, Inc.
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