Barry Isralewitz, Sergei Izrailev, and Klaus Schulten.
Binding pathway of retinal to bacterio-opsin: A prediction by
molecular dynamics simulations.
Biophysical Journal, 73:2972-2979, 1997.
(PMC: 1181203)
ISRA97
Formation of bacteriorhodopsin (bR) from the 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 trans-membrane 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 RMS deviation of coordinates (ignoring retinal, water, and hydrogen atoms) of less than 1.9 Å 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.
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