Summary
This chapter discusses the practical aspects of setting up molecular dynamics simulations for membrane-associated proteins and peptides. Special emphasis lies on the analysis of such systems. The main focus is the association between a cationic peptide and an anionic lipid bilayer—a peptide/lipid—bilayer system—but the extension onto more complicated systems is discussed. Topology files for selected lipids and several new analysis tools relevant for protein—membrane simulations are presented, the most important ones of which are: g_helixaxis, to calculate the axis of a helix and its angle with the bilayer; g_arom, to calculate aromatic order parameters; and g_under, to calculate which lipids interact with the protein. A procedure is explained to calculate properties involving peptide-interacting lipids only, as opposed to all lipids.
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Acknowledgments
I thank Prof. D.P. Tieleman (University of Calgary) and his coworkers for making lipid topologies and bilayer structures available, and the GROMACS development team for sharing their simulation program and analysis routines with the open-source community.
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Lensink, M.F. (2008). Membrane-Associated Proteins and Peptides. In: Kukol, A. (eds) Molecular Modeling of Proteins. Methods Molecular Biology™, vol 443. Humana Press. https://doi.org/10.1007/978-1-59745-177-2_9
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DOI: https://doi.org/10.1007/978-1-59745-177-2_9
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