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. 2014 Oct 15;35(27):1997-2004.
doi: 10.1002/jcc.23702. Epub 2014 Aug 7.

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations

Emilia L Wu  1 , Xi Cheng, Sunhwan Jo, Huan Rui, Kevin C Song, Eder M Dávila-Contreras, Yifei Qi, Jumin Lee, Viviana Monje-Galvan, Richard M Venable, Jeffery B Klauda, Wonpil Im
Affiliations

CHARMM-GUI Membrane Builder toward realistic biological membrane simulations

Emilia L Wu et al. J Comput Chem. .

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 simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), 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: CL 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.

Keywords: cardiolipin; lipid penetration detection; phosphoinositides; sphingolipids.

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Figures

Figure 1
Figure 1
E. coli membrane system. (A) Snapshots of the polar and septal E. coli membrane, and (B) the chemical structures of lipids in the polar and septal E. coli membrane model. CL and PE are colored in yellow and green, respectively. Phosphate atoms (orange) and K+ ions (purple) are shown in spheres and water molecules are shown in surface.
Figure 2
Figure 2
The chemical structures of SAPI, PIP head groups (PI13, PI14, and PI15), PIP2 (PI24 and PI25), and PIP3 (PI33, PI34 and PI35). In PIP, the different phosphorylation sites lead to PI13, PI14, and PI15, respectively. In PIP2 and PIP3, the different protonation sites lead to PI24, PI25, PI33, PI34, and PI35, respectively.
Figure 3
Figure 3
The chemical structures of three sphingolipids: PSM, OSM, and CER240.
Figure 4
Figure 4
Snapshots for lipid tail (pink) penetration across (A) chemical rings (blue) and (B) protein surface (green).
Figure 5
Figure 5
Protein surface penetration detection algorithm.
Figure 6
Figure 6
Average 2H order parameters and standard errors over 3 replicas of DPPE, PMPE, PMCL2, DXPE, and TXCL2 for the polar and septal E. coli membrane model at 310.15K. Note that the standard errors are smaller than the symbol size.
Figure 7
Figure 7
Radial distribution functions between C10 to C14 of PMPE (sn-2) and PMCL2 (sn-4) and saturated acyl chains in the E. coli lipid bilayer with the standard error over three replicas.
See this image and copyright information in PMC

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