Loading...
CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations
Wu, Emilia L. Cheng, Xi Jo, Sunhwan Rui, Huan Song, Kevin C. Dávila- Contreras, Eder M. Qi, Yifei Lee, Jumin Monje-Galvan, Viviana Venable, Richard M.
Wu, Emilia L.
Cheng, Xi
Jo, Sunhwan
Rui, Huan
Song, Kevin C.
Dávila- Contreras, Eder M.
Qi, Yifei
Lee, Jumin
Monje-Galvan, Viviana
Venable, Richard M.
Citations
Altmetric:
Abstract
CHARMM-GUI Membrane Builder, http://www.charmm-gui.org/input/membrane, is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems for molecular dynamics simulation through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builderthat allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types such as phosphoinositides, cardiolipin, sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance-based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: cardiolipin lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM-GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments.
Description
This is the peer reviewed version of the following article: Wu, E. L., Cheng, X., Jo, S., Rui, H., Song, K. C., Dávila-Contreras, E. M., … Im, W. (2014). CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations. Journal of Computational Chemistry, 35(27), 1997–2004. http://doi.org/10.1002/jcc.23702, which has been published in final form at http://doi.org/10.1002/jcc.23702. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.
Date
2014-10-15
Journal Title
Journal ISSN
Volume Title
Publisher
Wiley
Collections
Research Projects
Organizational Units
Journal Issue
Keywords
Cardiolipin, Phosphoinositides, Sphingolipids, Lipid penetration detection
Citation
Wu, E. L., Cheng, X., Jo, S., Rui, H., Song, K. C., Dávila-Contreras, E. M., … Im, W. (2014). CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations. Journal of Computational Chemistry, 35(27), 1997–2004. http://doi.org/10.1002/jcc.23702