| In lipid bilayer structure research, modern structural efforts are directed to reducing the uncertainty in experimentally determined structural parameters and to providing, in collaboration with computer simulations, a quantitative basis for understanding biophysical interactions in bilayers and membranes. The present thesis work is an attempt to understand certain structural and functional aspects of lipid bilayer models of the cell membrane using molecular dynamics (MD) computer simulation techniques. The primary motivation of this work was to model lipid components of the biological membrane that have not been considered in computational studies, in particular negatively charged 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-L-serine (POPS) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG) lipid bilayers. The results help in explaining the effect of head group functionality on the lipid bilayer structure, in particular the difference in the distribution and interactions of Na+ ions in POPS and POPG bilayers. As an additional application of the MD simulation method, the distribution of an environmental pollutant, pentachlorophenol (PCP), in phospholipid bilayers was also studied. The results help in explaining the physical basis of cytoplasmic membrane modification, one of the adaptive mechanisms of bacteria in the presence of xenobiotic compounds. The results are also of physical chemistry interest to understand the partitioning of small molecule in inhomogeneous environments such as the lipid bilayer, which cannot be explained by regular bulk solution theories. |
