Productive proton pumping by bacteriorhodopsin requires that, after the all-trans to 13-cis photoisomerization of the retinal chromophore, the photocycle proceeds with proton transfer and not with thermal back isomerization. The question of how the protein controls these events in the active site was addressed using Quantum Mechanical/Molecular Mechanical and reaction path calculations with  CPR. The results indicate that while retinal twisting significantly contributes to lowering the barrier for the thermal cis-trans back isomerization, the rate-limiting barrier for this isomerization is still ~5 kcal/mol larger than for the first proton transfer step. In this way, the retinal twisting is finely tuned so as to store energy to drive the subsequent photocycle while preventing wasteful backisomerization.
 
 

Fig. 1.  The absorption of one photon by the all-trans retinal chromophore leads to rotation of the C13-C14 bond into the 13-cis conformation. This triggers a photocycle, the net effect of which is the transfer of one proton from the cytoplasmic to the extracellular side of the membrane.

Fig. 2.   Photoabsorption and electronic relaxation leave the protein in the K-state (13-cis retinal).  From there, unproductive cis-trans back isomerization competes with the productive first first proton transfer step.  The schematic energy profile is based on QM/MM-optimized energies (values in kcal/mol). The movies below show the retinal back-isomerization, first from L to K, then from K to BR.

Retinal back-isomerization from L to K.
Rate-limiting barrrier 9kcal/mol.  Download the movie , 1Mb

Retinal back-isomerization from K to BR.
It is a very small motion, yet it has a high rate-limiting barrrier of 11kcal/mol. Download the movie , 0.5Mb

Conclusions
See paper.

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