title: MD Simulations of P-Type ATPases in a Lipid Bilayer System.
abstract: Molecular dynamics (MD) simulation is a computational method which provides insight on protein dynamics with high resolution in both space and time, in contrast to many experimental techniques. MD simulations can be used as a stand-alone method to study P-type ATPases as well as a complementary method aiding experimental studies. In particular, MD simulations have proved valuable in generating and confirming hypotheses relating to the structure and function of P-type ATPases. In the following, we describe a detailed practical procedure on how to set up and run a MD simulation of a P-type ATPase embedded in a lipid bilayer using software free of use for academics. We emphasize general considerations and problems typically encountered when setting up simulations. While full coverage of all possible procedures is beyond the scope of this chapter, we have chosen to illustrate the MD procedure with the Nanoscale Molecular Dynamics (NAMD) and the Visual Molecular Dynamics (VMD) software suites.
authors.affiliation: Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark. henriette@mbg.au.dk.|Centre for Membrane Pumps in Cells and Disease-PUMPkin, Danish National Research Foundation, Aarhus C, Denmark. henriette@mbg.au.dk.
authors.forename: Henriette Elisabeth
authors.initials: HE
authors.lastname: Autzen
authors.affiliation: Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK. maria.musgaard@bioch.ox.ac.uk.
authors.forename: Maria
authors.initials: M
authors.lastname: Musgaard
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry*; D030562:Databases, Protein; D008051:Lipid Bilayers; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D012995:Solubility
chemical_list: D008051:Lipid Bilayers; D000251:Adenosine Triphosphatases
keywords: MD simulation s; Membrane proteins; Molecular dynamics simulation s; P-type ATPases; Protein dynamics; Protein –lipid interactions; SERCA; Sarco(endo)plasmic reticulum Ca2+-ATPase