Pulling single bacteriorhodopsin out of a membrane: Comparison of simulation and experiment

Biochim Biophys Acta. 2006 Apr;1758(4):537-44. doi: 10.1016/j.bbamem.2006.03.028. Epub 2006 Apr 19.


Mechanical unfolding of single bacteriorhodopsins from a membrane bilayer is studied using molecular dynamics simulations. The initial conformation of the lipid membrane is determined through all-atom simulations and then its coarse-grained representation is used in the studies of stretching. A Go-like model with a realistic contact map and with Lennard-Jones contact interactions is applied to model the protein-membrane system. The model qualitatively reproduces the experimentally observed differences between force-extension patterns obtained on bacteriorhodopsin at different temperatures and predicts a lack of symmetry in the choice of the terminus to pull by. It also illustrates the decisive role of the interactions of the protein with the membrane in determining the force pattern and thus the stability of transmembrane proteins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Proteins / chemistry
  • Bacterial Proteins / isolation & purification
  • Bacteriorhodopsins / chemistry*
  • Bacteriorhodopsins / isolation & purification*
  • Cell Membrane / ultrastructure
  • Computer Simulation
  • Halobacterium salinarum
  • Lipid Bilayers
  • Models, Molecular
  • Protein Conformation
  • Protein Denaturation
  • Protein Structure, Secondary


  • Bacterial Proteins
  • Lipid Bilayers
  • Bacteriorhodopsins