Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations

Biophys J. 1997 Dec;73(6):2972-9. doi: 10.1016/S0006-3495(97)78326-7.

Abstract

Formation of bacteriorhodopsin (bR) from apoprotein and retinal has been studied experimentally, but the actual pathway, including the point of entry, is little understood. Molecular dynamics simulations provide a surprisingly clear prediction. A window between bR helices E and F in the transmembrane part of the protein can be identified as an entry point for retinal. Steered molecular dynamics, performed by applying a series of external forces in the range of 200-1000 pN over a period of 0.2 ns to retinal, allows one to extract this chromophore from bR once the Schiff base bond to Lys216 is cleaved. Extraction proceeds until the retinal tail forms a hydrogen bond network with Ala144, Met145, and Ser183 side groups lining the exit/entry window. The manipulation induces a distortion with a fitted root mean square deviation of coordinates (ignoring retinal, water, and hydrogen atoms) of less than 1.9 A by the time the retinal carbonyl reaches the protein surface. The forces needed to extract retinal are due to friction and do not indicate significant potential barriers. The simulations therefore suggest a pathway for the binding of retinal. Water molecules are found to play a crucial role in the binding process.

Publication types

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

MeSH terms

  • Bacteriorhodopsins / chemistry*
  • Bacteriorhodopsins / metabolism*
  • Binding Sites
  • Biophysical Phenomena
  • Biophysics
  • Computer Simulation
  • Models, Molecular
  • Protein Binding
  • Protein Conformation
  • Retinaldehyde / chemistry*
  • Retinaldehyde / metabolism*
  • Thermodynamics

Substances

  • Bacteriorhodopsins
  • bacterio-opsin
  • Retinaldehyde