FREE-ENERGY SIMULATIONS OF THE RETINAL CIS-]TRANS ISOMERIZATION IN BACTERIORHODOPSIN

Free-energy profiles for ground-state cis --> trans isomerization of r etinal in vacuum, in solution, and in the protein bacteriorhodopsin ar e calculated using free-energy simulations. The free-energy barriers i n the protein were 9 kcal/mol for ionized Asp85 and 14 kcal/mol for ne utral Asp85, significantly lower than those found in solution (18 kcal /mol) or vacuum (19 kcal/mol). Therefore, bacteriorhodopsin can be sai d to act as a catalyst in the isomerization. The barrier in the protei n is due mainly to stabilization of the transition state through favor able nonbonded interactions with the protein part of the system, with internal strain and interactions with solvent playing minor roles. The protonated Asp85 simulation models the behavior of the system in the N --> O transition. Our calculated 14 kcal/mol barrier and 4-ms relaxa tion time for this process are in excellent agreement with experimenta lly measured values of 12 kcal/mol and 5 ms, respectively. The ionized Asp85 simulation models two hypothetical processes: the N --> O trans ition with a proton removed from Asp85 and the initial BR568 --> L tra nsition on the ground-state energy surface. The cis-trans isomerizatio n barrier in this system is 9 kcal/mol, the lowest of all the studied cases. The presence of the charged carboxylate group in the ionized As p85 system leads to strong stabilization of the transition state by in teractions with the surroundings and changes the distance between Asp8 5 and the Schiff base proton compared to the corresponding distance in the neutral Asp85 system. This suggests that the protonation of Asp85 plays an important role in regulating access to the Schiff base proto n. For both Asp85 ionization states the calculated cis-trans free-ener gy difference was close to O, indicating that the protein can accommod ate both retinal isomers equally well. The computed negligible differe nce between the N and O free-energy levels is in accord with experimen tal data.