Abstract
The present research is a part of a collaborative effort to improve the CHARMMi force field (FF) parameters, referred to as C36p, for accurate prediction of the properties of polyunsaturated fatty acid (PUFA) chains in lipid membranes. The focus of our study was to test the accuracy of C36p FF. Molecular dynamics (MD) simulations were used to study the behavior of 1,2-diarachidonyl-phosphatidylcholine (DAPC), a PUFA with two hydrophobic tails with identical degree of unsaturation. CHARMM and NAMDii software packages were used to equilibrate and analyze the bilayer systems. The system consisted of a DAPC bilayer formed by 72 fully hydrated lipids with periodic boundary conditions. The simulations were performed in the NPT (constant particle number, pressure, and temperature) ensemble at 1 bar and 323.15 K for 100 ns. Simulations with the C36p FF resulted in more accurate membrane properties such as surface area per lipid, deuterium order parameters, electron density profiles, and C-H spin-lattice relaxation times.iii Efforts continue to improve the FF for accurate prediction on the rigidity of PUFA lipid membranes and orientation of cholesterol within these bilayers.EndnotesiCHARMM(Chemistry ar HARvard Macromolecular Mechanics). http://www.charmm.orgiiNAMD, Scalable Molecular Dynamics. http://www.ks.uiuc.edu/Research/namd/iiiKlauda, J.B.; Monje, V; Kim, T; Im, W. Improving the CHARMM Force Field for Polyunsaturated Fatty Acid Chains. J. Phys. Chem, 2012, 116, 9424−9431.
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