STRUCTURE OF BACTERIORHODOPSIN and in situ ISOMERIZATION OF RETINAL: A MOLECULAR DYNAMICS STUDY*

Abstract

Abstract– Henderson's model of the structure of bacteriorhodopsin has been completed by adding the missing loop regions and by subsequent energy minimization and equilibration (for about 100 ps) at 300 K. Analysis of the structure during a later 20 ps molecular dynamics run showed no significant deviations from the Henderson model. In situ isomerization reactions of the retinal chromophore in bacteriorhodopsin have then been simulated to investigate the chromophore protein interaction for the three isomerization reactions: (i) all‐trans→ 13‐cis; (ii)all‐trans→ 13,14‐dicis; and (iii) all‐trans→ 13,15‐dicis. We find that reaction (iii) which accompanies dark‐adaptation of bacteriorhodopsin can proceed in the binding site without any sterical hinderance and involves negligible motions of the covalently bound Lys‐216 and other side groups. Reaction (ii) exhibits a somewhat larger but still small energy barrier and involves little rearrangement of Lys‐216 and the protein backbone. Reaction (i) experiences a sterical impediment amounting to more than 10 kT at physiological temperatures and also induces significant structural changes at the binding site. Our simulations also reveal that reaction (ii) as a photo‐isomerization process can be completed within about 400 fs, whereas reaction (i) requires longer times for completion. Reaction (i) is also accompanied by a co‐rotation of the 14–15 bond by 150° (even when a torsional barrier of 20 kcal/mol is imposed to impede rotation of the 14–15 bond) such that photoreactions (i) and (ii), in effect, lead to very similar final geometries. Isomerization (ii) can readily explain the pump mechanism of bacteriorhodopsin: the sequential, thermal back‐reaction 13,14‐dicis→ 13‐cisall‐trans can be acid‐base catalyzed, i.e., coupled to deprotonation and reprotonation of retinal's Schiff base nitrogen. The orientation of retinal is such that Asp‐85 can act as the acceptor and Asp‐96 as the (indirect) donor. The thermal back‐reaction 13,14‐dicis→ all‐trans can be coupled to vectorial Cl− ion transport as well.