Automated Builder and Database of Protein/Membrane Complexes for Molecular Dynamics Simulations
By Sunhwan Jo, Taehoon Kim, Wonpil Im. PLoS ONE, 2007
1,150 citations recorded by the source corpus.
Molecular dynamics simulations of membrane proteins have provided deeper insights into their functions and interactions with surrounding environments at the atomic level. However, compared to solvation of globular proteins, building a realistic protein/membrane complex is still challenging and requires considerable experience with simulation software. Membrane Builder in the CHARMM-GUI website (http://www.charmm-gui.org) helps users to build such a complex system using a web browser with a graphical user interface. Through a generalized and automated building process including system size determination as well as generation of lipid bilayer, pore water, bulk water, and ions, a realistic membrane system with virtually any kinds and shapes of membrane proteins can be generated in 5 minutes to 2 hours depending on the system size. Default values that were elaborated and tested extensively are given in each step to provide reasonable options and starting points for both non-expert and expert users. The efficacy of Membrane Builder is illustrated by its applications to 12 transmembrane and 3 interfacial membrane proteins, whose fully equilibrated systems with three different types of lipid molecules (DMPC, DPPC, and POPC) and two types of system shapes (rectangular and hexagonal) are freely available on the CHARMM-GUI website. One of the most significant advantages of using the web environment is that, if a problem is found, users can go back and re-generate the whole system again before quitting the browser. Therefore, Membrane Builder provides the intuitive and easy way to build and simulate the biologically important membrane system.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/4ca3f4d354f7f0a3e8cfe528cae4526825f3fe3f
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In Molecular Biology
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.”
- CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans. (2018, background): “Its first implementation allowed users to build a protein-membrane complex system with three lipid types 28 .”
- Lipid-Dependent Alternating Access Mechanism of a Bacterial Multidrug ABC Exporter (2019, neutral): “Prior to equilibration, each system was energy minimized for 10 000 steps using conjugate gradient algorithm 76 and further relaxed using a multistep restraining procedure explained elsewhere 67 for ∼ 1 ns.”
- CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes. (2009, methodology): “Because the overall building process of a protein/membrane system remains the same as described previously (16), we briefly describe the step-by-step building procedure and emphasize its new features.”