Molecular dynamics simulations of rhodopsin in different one-component lipid bilayers

J Phys Chem B. 2007 Jun 28;111(25):7052-63. doi: 10.1021/jp0707788. Epub 2007 May 27.

Abstract

Four 20 ns molecular dynamic simulations of rhodopsin embedded in different one-component lipid bilayers have been carried out to ascertain the importance of membrane lipids on the protein structure. Specifically, dimyristoyl phosphatidylcholine (DMPC), dipalmitoyl phosphatidylcholine (DPPC), palmitoyl oleoyl phosphatidylcholine (POPC), and palmitoyl linoleyl phosphatidylcholine (PLPC) lipid bilayers have been considered for the present work. The results reported here provide information on the hydrophobic matching between the protein and the bilayer and about the differential effects of the protein on the thickness of the different membranes. Furthermore, a careful analysis of the individual protein-lipid interactions permits the identification of residues that exhibit permanent interactions with atoms of the lipid environment that may putatively act as hooks of the protein to the membrane. The analysis of the trajectories also provides information about the effect of the bilayer on the protein structure, including secondary structural elements, salt bridges, and rigid-body motions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computer Simulation
  • Crystallography, X-Ray
  • Hydrogen Bonding
  • Hydrophobic and Hydrophilic Interactions
  • Lipid Bilayers / chemistry*
  • Models, Molecular
  • Molecular Sequence Data
  • Molecular Structure
  • Oxygen / chemistry
  • Phosphatidylcholines / chemistry*
  • Rhodopsin / chemistry*
  • Sodium Chloride
  • Static Electricity

Substances

  • Lipid Bilayers
  • Phosphatidylcholines
  • Sodium Chloride
  • Rhodopsin
  • Oxygen