title: Membrane-associated proteins and peptides.
abstract: This chapter discusses the practical aspects of setting up molecular dynamics simulations of membrane-associated proteins and peptides, and the analysis thereof. Topology files for selected lipids are provided and selected analysis tools presented. These include tools for the creation of lipid bilayers of mixed lipid content (DOPE) and easy extraction of lipid coordinates (g_zcoor, g_xycoor), the calculation of helical axes (g_helixaxis) and aromatic order parameters (g_arom), the determination of peptide- or protein-interacting lipids (g_under), and the investigation of lipid-specific interactions through the calculation of lipid-bridged residue-residue contacts (g_prolip).
authors.affiliation: Interdisciplinary Research Institute, CNRS USR3078, University Lille1, Parc de la Haute Borne, 50 avenue de Halley, 59658, Villeneuve d'Ascq cedex, France, marc.lensink@iri.univ-lille1.fr.
authors.forename: Marc F
authors.initials: MF
authors.lastname: Lensink
mesh_terms: D015060:1,2-Dipalmitoylphosphatidylcholine / Q000737:chemistry; D003903:Deuterium; D008051:Lipid Bilayers / Q000737:chemistry; D008055:Lipids / Q000737:chemistry; D008565:Membrane Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D010714:Phosphatidylethanolamines / Q000737:chemistry; D017433:Protein Structure, Secondary; D012492:Salts / Q000737:chemistry; D012997:Solvents / Q000737:chemistry
chemical_list: D008051:Lipid Bilayers; D008055:Lipids; D008565:Membrane Proteins; D010455:Peptides; D010714:Phosphatidylethanolamines; D012492:Salts; D012997:Solvents; C057561:1-palmitoyl-2-oleoylphosphatidylethanolamine; D015060:1,2-Dipalmitoylphosphatidylcholine; D003903:Deuterium