Molecular modeling of charged membrane systems
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Doctoral thesis (monograph)
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Date
2006-11-11
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Mcode
Degree programme
Language
en
Pages
149
Series
Helsinki University of Technology Laboratory of Computational Engineering publications. Report B, 58
Abstract
We have performed molecular modeling of membrane systems by employing the classical molecular dynamics method and force field parameterizations. In this thesis, our main interest is on the structural and dynamic properties of charged model membrane systems. This thesis consists of four related projects. The first project focuses on cationic DMPC (dimyristoylphosphatidylcholine) / DOTAP (dimyristoyltrimethylammonium propane) lipid bilayers in the presence of chloride ions. We study the electrostatic interactions involving the dipolar headgroups of DMPC, the cationic headgroups of DOTAP, anionic counterions, and water molecules in the hydration zone of the membranes. We also investigate the effects of longer and unsaturated hydrocarbon chains of DOTAP on the structural properties of the mixed DMPC/DOTAP bilayers. In the second project, we consider an anionic POPG (palmitoyloleolyphosphatidylglycerol) lipid bilayer in the presence of sodium ions as counterions. We study the electrostatic interactions between the sodium ions and different groups in POPG molecules. We find that the sodium ions tend to bind strongly to the carbonyl oxygens instead of the phosphodiester oxygens. This kind of binding results in the formation of extensive lipid clusters, in which the lipids are bridged via sodium ions. The hydrogen bonds are also investigated as well as other properties such as the ordering of water molecules near the lipid bilayer. Then, using the POPG model developed in the previous study, we have investigated a bacterial model membrane consisting of 75% zwitterionic POPE (palmitoyloleolyphosphatidylethanolamine) and 25% anionic POPG. The intraand inter-molecular hydrogen bonds between the POPE and POPG molecules are analyzed and compared to separate simulations of pure POPE and pure POPG bilayers. We find that the hydrogen bonds contribute considerably to the interfacial properties of the mixed POPE/POPG bilayer. Another important observation is the formation of ion-lipid bridges and lipid clusters, which have not been found in other studies. We propose that as possible mechanism how bacteria may be able to control their permeability against solvents. In the fourth project we study the dynamic behavior of water molecules in the vicinity of different lipid bilayer surfaces. In this work, we have analyzed the interface effects of three different lipid bilayers – POPC, POPE, and POPG on water dynamics.Description
Keywords
computer simulation, molecular dynamics, electrostatics, soft matter