title: A Parameterization of Cholesterol for Mixed Lipid Bilayer Simulation within the Amber Lipid14 Force Field.
abstract: The Amber Lipid14 force field is expanded to include cholesterol parameters for all-atom cholesterol and lipid bilayer molecular dynamics simulations. The General Amber and Lipid14 force fields are used as a basis for assigning atom types and basic parameters. A new RESP charge derivation for cholesterol is presented, and tail parameters are adapted from Lipid14 alkane tails. 1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers are simulated at a range of cholesterol contents. Experimental bilayer structural properties are compared with bilayer simulations and are found to be in good agreement. With this parameterization, another component of complex membranes is available for molecular dynamics with the Amber Lipid14 force field.
authors.affiliation: Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Dr. MC 0505, La Jolla, California 92093-0505, United States.|San Diego Supercomputer Center , 9500 Gilman Dr. MC 0505, La Jolla, California 92093-0505, United States.
authors.forename: Benjamin D
authors.initials: BD
authors.lastname: Madej
authors.affiliation: Department of Chemistry and Institute of Chemical Biology, Imperial College London , South Kensington SW7 2AZ, United Kingdom.
authors.forename: Ian R
authors.initials: IR
authors.lastname: Gould
authors.affiliation: Department of Chemistry and Biochemistry, University of California San Diego , 9500 Gilman Dr. MC 0505, La Jolla, California 92093-0505, United States.|San Diego Supercomputer Center , 9500 Gilman Dr. MC 0505, La Jolla, California 92093-0505, United States.
authors.forename: Ross C
authors.initials: RC
authors.lastname: Walker
mesh_terms: D000473:Alkanes / Q000737:chemistry; D002784:Cholesterol / Q000737:chemistry*; D004134:Dimyristoylphosphatidylcholine / Q000737:chemistry; D005997:Glycerylphosphorylcholine / Q000031:analogs & derivatives / Q000737:chemistry; D008051:Lipid Bilayers / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009281:Naphthalenes / Q000737:chemistry; D033363:Neutron Diffraction; D010713:Phosphatidylcholines / Q000737:chemistry; D013696:Temperature; D014961:X-Ray Diffraction
chemical_list: D000473:Alkanes; D008051:Lipid Bilayers; D009281:Naphthalenes; D010713:Phosphatidylcholines; D005997:Glycerylphosphorylcholine; C007229:decalin; D002784:Cholesterol; C017251:1,2-oleoylphosphatidylcholine; C007932:n-hexadecane; C028694:1-palmitoyl-2-oleoylphosphatidylcholine; D004134:Dimyristoylphosphatidylcholine