CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes.

By Sunhwan Jo, Joseph B. Lim, Jeffery B. Klauda, Wonpil Im. Biophysical Journal, 2009

1,603 citations recorded by the source corpus.

The CHARMM-GUI Membrane Builder (http://www.charmm-gui.org/input/membrane), an intuitive, straightforward, web-based graphical user interface, was expanded to automate the building process of heterogeneous lipid bilayers, with or without a protein and with support for up to 32 different lipid types. The efficacy of these new features was tested by building and simulating lipid bilayers that resemble yeast membranes, composed of cholesterol, dipalmitoylphosphatidylcholine, dioleoylphosphatidylcholine, palmitoyloleoylphosphatidylethanolamine, palmitoyloleoylphosphatidylamine, and palmitoyloleoylphosphatidylserine. Four membranes with varying concentrations of cholesterol and phospholipids were simulated, for a total of 170 ns at 303.15 K. Unsaturated phospholipid chain concentration had the largest influence on membrane properties, such as average lipid surface area, density profiles, deuterium order parameters, and cholesterol tilt angle. Simulations with a high concentration of unsaturated chains (73%, membrane(unsat)) resulted in a significant increase in lipid surface area and a decrease in deuterium order parameters, compared with membranes with a high concentration of saturated chains (60-63%, membrane(sat)). The average tilt angle of cholesterol with respect to bilayer normal was largest, and the distribution was significantly broader for membrane(unsat). Moreover, short-lived cholesterol orientations parallel to the membrane surface existed only for membrane(unsat). The membrane(sat) simulations were in a liquid-ordered state, and agree with similar experimental cholesterol-containing membranes.

Subfields: Atomic and Molecular Physics, and Optics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c9ad08b57a4dc395a93b698801d4b250dda92a76

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Atomic and Molecular Physics, and Optics

1. Michael Feig
2. Jeffrey J. Gray
3. Andrei L. Lomize
4. Irina D. Pogozheva
5. Mikhail A. Lomize
6. Henry I. Mosberg

In Molecular Biology

1. Lim Heo
2. Wonpil Im
3. Sunhwan Jo
4. Michael Feig
5. Bercem Dutagaci
6. Rebecca F. Alford
7. Jeffrey J. Gray
8. Mikhail A. Lomize

Citations in the corpus

• Structure Refinement of Membrane Proteins via Molecular Dynamics Simulations (2018, methodology): “Minimization was followed by 400 ps equilibration as prescribed by the CHARMM-GUI server.(52,53) A 6-step equilibration procedure was applied with restraints for proteins, lipids, water molecules and ions.”
• OPM database and PPM web server: resources for positioning of proteins in membranes (2011, methodology): “Links to the OPM database are currently integrated in several widely used resources including PDBsum, OCA, Wikipedia, Membrane Builder (42), and Cell Microcismos Membrane Editor (43).”
• Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane. (2020, methodology): “CHARMM-GUI (40) was used to configure each bilayer system with 75 lipids in each leaflet, 22.5 Å of water on each side, and 0.1 MNaCl.”
• CHARMM-GUI Glycan Modeler for modeling and simulation of carbohydrates and glycoconjugates (2019, methodology): “This example illustrates how to build a complete CTB:GM1 pentameric complex using Glycan Reader & Modeler and to insert the ceramide lipid portions into a membrane bilayer using Membrane Builder (Jo et al. 2009; Wu et al. 2014) (Figure 4C); see Section 3 of Supplementary Data for the detailed steps.”