Molecular dynamics simulation of dark-adapted rhodopsin in an explicit membrane bilayer: coupling between local retinal and larger scale conformational change

J Mol Biol. 2003 Oct 24;333(3):493-514. doi: 10.1016/j.jmb.2003.08.045.


The light-driven photocycle of rhodopsin begins the photoreceptor cascade that underlies visual response. In a sequence of events, the retinal covalently attached to the rhodopsin protein undergoes a conformational change that communicates local changes to a global conformational change throughout the whole protein. In turn, the large-scale protein change then activates G-proteins and signal amplification throughout the cell. The nature of this change, involving a coupling between a local process and larger changes throughout the protein, may be important for many membrane proteins. In addition, functional work has shown that this coupling occurs with different efficiency in different lipid settings. To begin to understand the nature of the efficiency of this coupling in different lipid settings, we present a molecular dynamics study of rhodopsin in an explicit dioleoyl-phosphatidylcholine bilayer. Our system was simulated for 40 ns and provides insights into the very early events of the visual cascade, before the full transition and activation have occurred. In particular, we see an event near 10 ns that begins with a change in hydrogen bonding near the retinal and that leads through a series of coupled changes to a shift in helical tilt. This type of event, though rare on the molecular dynamics time-scale, could be an important clue to the types of coupling that occur between local and large-scale conformational change in many membrane proteins.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Animals
  • Binding Sites
  • Cattle
  • Computer Simulation
  • Crystallography, X-Ray
  • Dark Adaptation*
  • Hydrogen Bonding
  • Hydrophobic and Hydrophilic Interactions
  • Lipid Bilayers / chemistry*
  • Lipids / chemistry
  • Models, Molecular
  • Protein Binding
  • Protein Structure, Secondary
  • Retina / metabolism*
  • Rhodopsin / chemistry*
  • Rhodopsin / metabolism*
  • Solvents / chemistry
  • Thermodynamics
  • Time Factors
  • Water / chemistry


  • Lipid Bilayers
  • Lipids
  • Solvents
  • Water
  • Rhodopsin