Preferences help
enabled [disable] Abstract
Number of results
2000 | 47 | 3 | 601-611
Article title

Molecular dynamics simulation studies of lipid bilayer systems.

Title variants
Languages of publication
The main structural element of biological membranes is a liquid-crystalline lipid bilayer. Other constituents, i.e. proteins, sterols and peptides, either intercalate into or loosely attach to the bilayer. We applied a molecular dynamics simulation method to study membrane systems at various levels of compositional complexity. The studies were started from simple lipid bilayers containing a single type phosphatidylcholine (PC) and water molecules (PC bilayers). As a next step, cholesterol (Chol) molecules were introduced to the PC bilayers (PC-Chol bilayers). These studies provided detailed information about the structure and dynamics of the membrane/water interface and the hydrocarbon chain region in bilayers built of various types of PCs and Chol. This enabled studies of membrane systems of higher complexity. They included the investigation of an integral membrane protein in its natural environment of a PC bilayer, and the antibacterial activity of magainin-2. The latter study required the construction of a model bacterial membrane which consisted of two types of phospholipids and counter ions. Whenever published experimental data were available, the results of the simulations were compared with them.
Physical description
  • Institute of Molecular Biology, Jagiellonian University, Al. A. Mickiewicza 3, 31-120 Kraków, Poland
  • Institute of Molecular Biology, Jagiellonian University, Al. A. Mickiewicza 3, 31-120 Kraków, Poland
  • Institute of Molecular Biology, Jagiellonian University, Al. A. Mickiewicza 3, 31-120 Kraków, Poland
  • Faculty of Chemistry, University of Gdańsk, J. Sobieskiego 18, 80-952 Gdańsk, Poland
  • Bloom, M. & Mouritsen, O.G. (1995) The evolution of membranes; in Structure and Dynamics of Membranes (Lipowsky, R. & Sackmann, E., eds.) pp. 65-95, Elsevier, Amsterdam.
  • Borle, F. & Seelig, J. (1983) Hydration of Escherichia coli lipids. Deuterium T1 relaxation time studies of phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. Biochim. Biophys. Acta 735, 131-136.
  • Czaplewski, C., Kazmierkiewicz, R. & Ciarkowski, J. (1998) Molecular modeling of the human vasopressin V2 receptor/agonist complex. J. Comput. Aided Mol. Design 12, 275-287.
  • Czaplewski, C., Pasenkiewicz-Gierula, M. & Ciarkowski, J. (1999a) Molecular dynamics of a vasopressin V2 receptor in a phospholipid bilayer membrane. J. Rec. Signal Tranduction Res. 19, 355-367.
  • Czaplewski, C., Pasenkiewicz-Gierula, M. & Ciarkowski, J. (1999b) G protein-coupled receptor-bioligand interaction modeled in a phospholipid bilayer. Int. J. Quantum Chem. 73, 61-70.
  • Gorter, E. & Grendel, F. (1925) On bimolecular layers of lipoids on the chromocytes of the blood. J. Exp. Med. 41, 439-443.
  • Hyslop, P., Morel, B. & Sauerneber, R. (1990) Organization and interaction of cholesterol and phosphatidylcholine in model bilayer membrane. Biochemistry 29, 1025-1038.
  • Kraulis, P. (1991) MolScript: A program to produce both detailed and schematic plots of proteins. J. Appl. Cryst. 24, 946-950.
  • Kusumi, A., Tsuda, M., Akino, T., Ohnishi, S. & Terayama, Y. (1983) Protein-phospholipid- cholesterol interaction in the photolysis of invertebrate rhodopsin. Biochemistry 22, 1165- 1170.
  • Meraldi, J.P. & Schlitter, J. (1981) A statistical mechanical treatment of fatty acyl chain order in phospholipid bilayers and correlation with experimental data. Biochim. Biophys. Acta 645, 193-210.
  • Merritt, E.A. & Bacon, D.J. (1997) Raster3D: Photorealistic molecular graphics. Methods Enzymol. 277, 505-524.
  • Murzyn, K. & Pasenkiewicz-Gierula, M. (1999) Construction and optimisation of a computer model for a bacterial membrane. Acta Biochim. Polon. 46, 631-639.
  • Nagle, J. (1993) Area/lipid of bilayers from NMR. Biophys. J. 64, 1476-1481.
  • 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. 101, 3677-3691.
  • Pasenkiewicz-Gierula, M., Takaoka, Y., Miyagawa, H., Kitamura, K. & Kusumi, A. (1999) Charge pairing of headgroups in phosphatidylcholine membranes. A molecular dynamics simulation study. Biophys. J. 76, 1228-1240.
  • Pasenkiewicz-Gierula, M., Rog, T., Kitamura, K. & Kusumi, A. (2000) Cholesterol effects on the phosphatidylcholine bilayer polar region: A molecular simulation study. Biophys. J. 78, 1376-1389.
  • Rand, R. & Parsegian, V. (1989) Hydration forces between phospholipid bilayers. Biochim. Biophys. Acta 988, 351-376.
  • RógKrakówT. (2000) Cholesterol effects on the structure and the dynamics of phospholipid bilayers molecular dynamics simulation studies. PhD Dissertation, Jagiellonian University, Kraków, Poland (in Polish).
  • Sackmann, E. (1995) Biological membranes architecture and function; in Structure and Dynamics of Membranes (Lipowsky, R. & Sackmann, E., eds.) pp. 1-64, Elsevier, Amsterdam.
  • Saberwal, G. & Nagaraj, R. (1994) Cell-lytic and antibacterial peptides that act by perturbing the barrier function of membranes: Facets of their conformational features, structure-function correlation and membrane-perturbing abilities. Biochim. Biophys. Acta 1197, 109- 131.
  • Smaby, J.M., Momsen, M., Brockman, H. & Brown, R. (1997) Phosphatidylcholine acyl unsaturation modulates the decrease in the interfacial elasticity induced by cholesterol. Biophys. J. 73, 1492-1505.
  • Subczynski, W.K., Wisniewska, A., Yin, J.-J., Hyde, J.S. & Kusumi, A. (1994) Hydrophobic barriers of lipid bilayer membranes formed by reduction of water penetration by alkyl chain unsaturation and cholesterol. Biochemistry 33, 7670-7681.
  • Tuchtenhagen, J., Ziegler, W. & Blume, A. (1994) Acyl chain conformational ordering in liquid-crystalline bilayers: Comparative FT-IR and 2H-NMR studies of phospholipids differing in headgroup structure and chain length. Eur. Biophys. J. 23, 323-335.
  • Unger, V.M. & Schertler, G.F.X. (1995) Low resolution structure of bovine rhodopsin determined by electron cryo-microscopy. Biophys. J. 68, 1776-1786.
  • Volke, F., Eisenbältter, S., Galle, J. & Klose, G. (1994) Dynamic properties of water at phosphatidylcholine lipid-bilayer surface as seen by deuterium and pules field gradient proton NMR. Chem. Phys. Lipids 70, 121-131.
  • Wenk, M.R. & Seelig, J. (1998) Magainin 2 amide interaction with lipid membrane: Calorimetric detection of peptide binding and pore formation. Biochemistry 37, 3909-3916.
  • Wieprecht, T., Beyermann, M. & Seelig, J. (1999) Binding of antibacterial magainin peptide to electrically neutral membranes: Thermodynamics and structure. Biochemistry 38, 10377-10387.
Document Type
Publication order reference
YADDA identifier
JavaScript is turned off in your web browser. Turn it on to take full advantage of this site, then refresh the page.