Abstract
Previous work in our laboratory has identified lipid-protein interactions that appear unique to the class of lipids having polyunsaturated fatty acids (PUFA). In this work we extend these studies to examine the effect of PUFA on lipid mediated protein-protein interactions. Specifically, we have used molecular dynamics (MD) computer simulation methods to compute the potential of mean force (PMF) between a pair of alpha helical peptides, i.e. the free energy as a function of separation. Constant pressure, constant temperature simulations of the identical peptides in phosphidylcholine bilayers with saturated chains (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) and those containing PUFA (1-palmitoyl-2-docosahexaenoyl-sn-glycero-3-phosphocholine) have been carried out using the techniques of umbrella sampling and the weighted histogram analysis method. These lipids were carefully chosen for their near identical hydrophobic thicknesses so that the effect of unsaturation could be uniquely examined.
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