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Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly
dc.contributor.author | Park, Soohyung | |
dc.contributor.author | Im, Wonpil | |
dc.date.accessioned | 2017-05-17T15:40:27Z | |
dc.date.available | 2017-05-17T15:40:27Z | |
dc.date.issued | 2013 | |
dc.identifier.citation | Park, S., & Im, W. (2013). Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly. Journal of Chemical Theory and Computation, 9(1), 13–17. http://doi.org/10.1021/ct3008556 | en_US |
dc.identifier.uri | http://hdl.handle.net/1808/24233 | |
dc.description.abstract | The method of window exchange umbrella sampling molecular dynamics (WEUSMD) with a pre-optimized parameter set was recently used to obtain the most probable conformations and the energetics of transmembrane (TM) helix assembly of a generic TM sequence. When applied to glycophorin A TM domain (GpA-TM) using the restraint potentials along the helix-helix distance, however, tight interfacial packing of GpA-TM resulted in insufficient conformational sampling at short helix-helix separation. This sampling issue is addressed by extending the WEUSMD into two dimensions with the restraint potentials along the helix-helix distance and crossing angle. The two-dimensional WEUSMD results demonstrate that the incomplete sampling in the one-dimensional WEUSMD arises from high barriers along the crossing angle between the GpA-TM helices. Together with the faster convergence in both the assembled conformations and the potential of mean force, the 2D-WEUSMD can be a general and efficient approach in computational studies of TM helix assembly. | en_US |
dc.publisher | American Chemical Society | en_US |
dc.rights | This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of Chemical Theory and Computation, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://doi.org/10.1021/ct3008556. | en_US |
dc.subject | Glycophorin A | en_US |
dc.subject | Replica Exchange Methods | en_US |
dc.subject | First Passage Time Optimization | en_US |
dc.subject | Potential of Mean Force | en_US |
dc.title | Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly | en_US |
dc.type | Article | en_US |
kusw.kuauthor | Park, Soohyung | |
kusw.kuauthor | Im, Wonpil | |
kusw.kudepartment | Molecular Biosciences | en_US |
dc.identifier.doi | 10.1021/ct3008556 | en_US |
dc.identifier.orcid | https://orcid.org/0000-0002-4883-3031 | |
kusw.oaversion | Scholarly/refereed, author accepted manuscript | en_US |
kusw.oapolicy | This item meets KU Open Access policy criteria. | en_US |
dc.identifier.pmid | PMC3593060 | en_US |
dc.rights.accessrights | openAccess |