Molecular Dynamics of Pf1 Coat Protein in a Phospholipid Bilayer
The anchoring, stabilization, and function of membrane proteins is of central importance for understanding numerous fundamental biological processes occurring at the surface of the cell. In recent years, extensive efforts have been devoted to develop such powerful tools as X-ray crystallography (Deisenhofer and Michel, 1989; Cowan et al, 1992; Weiss and Schulz, 1992; Picot et al, 1994), electron microscopy (Henderson et al, 1990) and nuclear magnetic resonance (Cross and Opella, 1994) to determine the three-dimensional structure of membrane proteins. Despite this progress, many of the factors responsible for the function of biomembranes are still poorly understood. This is due, in large part, to the extreme difficulties in applying experimental methods to obtain detailed information about the phospholipid bilayer environment and its influence on the structure, dynamics, and function of membrane proteins. In a simplified view, the membrane-solution interface is often pictured as a relatively sharp demarcation between the hydrophilic and hydrophobic regions (Edholm and Jahnig, 1988; Milik and Skolnick, 1993). Its dominant effect is usually represented as that of a thermodynamic driving force partitioning the amino acids according to their solubility (Eisenberg et al, 1982; Engelman et al, 1986; Wesson and Eisenberg, 1992); hydrophobic amino acids are more likely to be found within the hydrocarbon core of the membrane, whereas charged and polar amino acids are more likely to be found in the bulk solvent.
KeywordsMolecular Dynamic Simulation Coat Protein Phospholipid Bilayer Amphipathic Helix DPPC Bilayer
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- Chiu SW, Clarck M, Subramaniam S, Scott HL, Jakobsson E (1995): Incorporation of surface tension into molecular dynamics simulation of an interface: A fluid phase lipid bilayer membrane, to appear Biophys J Google Scholar
- Epand RM, Gawish A, Iqbal M, Gupta KB, Chen CH, Segrest JP, Anantharamaiah GM (1987): Studies of synthetic peptide analogs of the amphipathic helix. Effect of charge distribution, hydrophobicity, and secondary structure on lipid association and lecithimcholesterol acyltransferase activation.J Biol Chem 262:9389–9396PubMedGoogle Scholar
- Gennis RB (1989): Biomembranes Molecular Structure and Function. New York: Springer-VerlagGoogle Scholar
- Huang P, Loew GH (1995): Interaction of an amphiphilic peptide with a phospholipid bilayer surface by molecular dynamics simulation study. J Biomol Struct & Dyn 12:937–955Google Scholar
- Mackerell AD Jr, Bashford D, Bellot M, Dunbrack RL, Field MJ, Fischer S, Gao J, Guo H, Joseph D, Ha S, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Nguyen DT, Ngo T, Prodhom B, Roux B, Schlenkrich B, Smith J, Stote R, Straub J, Wiorkiewicz-Kuczera J, Karplus M (1992): Self-consistent parametrization of biomolecules for molecular modeling and condensed phase simulations. Biophys J 61:A143Google Scholar
- Pastor RW (1995): unpublishedGoogle Scholar
- Ryckaert JP, Ciccotti G, Berendsen HJC (1977): Numerical integration of the cartesian equation of motions of a system with constraints: Molecular dynamics of n-alkanes.J Comp Chem 23:327–341Google Scholar
- White J (1992): Membrane fusion. Nature 258:917–924Google Scholar
- Woolf TB, Roux B (1993): Molecular dynamics simulations of proteins in lipid membranes: the first steps. Biophys J A354Google Scholar
- Woolf TB, Desharnais J, Roux B (1994): Structure and dynamics of the side chains of gramicidin in a DMPC bilayer. In: NATO ASI Series: Computational Approaches in Supramolecular Chemistry, Vol. 426, Wipff G, ed. Dordrecht, The Netherlands: L Kluwer Academic PublishersGoogle Scholar