Membrane-associated proteins and peptides.
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.
Lensink
Marc F
MF
Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.
D008051:Lipid Bilayers / Q000737:chemistry / Q000378:metabolism; D008563:Membrane Lipids / Q000737:chemistry / Q000378:metabolism; D008565:Membrane Proteins / Q000737:chemistry*; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation
D008051:Lipid Bilayers; D008563:Membrane Lipids; D008565:Membrane Proteins; D010455:Peptides