Lateral clustering of lipids in hydrated bilayers composed of dioleoylphosphatidylcholine and dipalmitoylphosphatidylcholine
Investigation of lateral heterogeneities (clusters) in cell membranes is an important step toward understanding the physical processes that lead to the formation of lipid domains and rafts. Computer modeling methods represent a powerful tool to solve the problem, since they can detect clusters containing only a few lipid molecules—the situation that still resists characterization with modern experimental techniques. Parameters of clustering depend on lipid composition of a membrane. In this work, we propose a computational method to detect and analyze parts of membrane with different packing densities. Series of one- and two-component fluid systems containing lipids with the same polar heads and different acyl chains, dioleoylphosphatidylcholine (18 : 1) and dipalmitoylphosphatidylcholine (16 : 0), were chosen as the objects under study. The developed algorithm is based on molecular dynamics simulation of hydrated lipid bilayers in all-atom mode. The method is universal and could be applied to any other membrane system with arbitrary lipid composition. Here, we demonstrated that the studied lipid bilayers reveal small lateral dynamic clusters composed of just several (most often, three) lipid molecules. This seems to be one of the most important reasons determining the “mosaic” nature of the membrane-water interface.
Keywordslipid membranes two-component lipid bilayers molecular dynamics lateral membrane heterogeneities lipid-lipid interactions structural organization of lipid bilayer
- 11.Nicolini C., Kraineva J., Khurana M., Periasamy N., Funari S.S., Winter R. 2006. Temperature and pressure effects on structural and conformational properties of POPC/SM/cholesterol model raft mixtures — a FT-IR, SAXS, DSC, PPC and Laurdan fluorescence spectroscopy study. Biochim. Biophys. Acta. 1758, 248–258.PubMedCrossRefGoogle Scholar
- 26.Pasenkiewicz-Gierula M., Takaoka Y., Miyagawa H., Kitamura K., Kusumi A. 1997. Hydrogen bonding of water to phosphatidylcholine in the membrane as studied by a molecular dynamics simulation: Location, geometry, and lipid-lipid bridging via hydrogen bonded water. J. Phys. Chem. A. 101, 3677–3691.CrossRefGoogle Scholar
- 32.Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., Hermans J. 1981. Interaction Models for Water in Relation to Protein Hydration. Dordrecht: Pullman, p. 331–342.Google Scholar
- 33.Lindahl E., Hess B., van der Spole D. 2001. Gromacs 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Mod. 7, 306–317.Google Scholar
- 38.Efremov R.G., Gulyaev D.I., Vergoten G., Modyanov N.N. 1992. Application of 3D molecular hydrophobicity potential to the analysis of spatial organization of membrane domains in proteins. I. Hydrophobic properties of transmembrane segments of Na,K-ATPase. J. Protein Chemistry. 11, 665–675.CrossRefGoogle Scholar