Loading...
Two Dimensional Window Exchange Umbrella Sampling for Transmembrane Helix Assembly
Park, Soohyung Im, Wonpil
Park, Soohyung
Im, Wonpil
Citations
Altmetric:
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.
Description
Date
2013
Journal Title
Journal ISSN
Volume Title
Publisher
American Chemical Society
Collections
Files
Loading...
Park_2014.pdf
Adobe PDF, 1.1 MB
Research Projects
Organizational Units
Journal Issue
Keywords
Glycophorin A, Replica Exchange Methods, First Passage Time Optimization, Potential of Mean Force
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