On the role of protein environment in the excited state dynamics of the green absorbing proteorhodopsin

The primary photochemical reaction of the green absorbing Proteorhodopsin is investigated by means of a hybrid quantum mechanics/molecular mechanics (QM/MM) approach. The homology model for the green absorbing Proteorhodopsin was derived from the crystal structure of blue‐absorbing variant.¹

The nonadiabatic molecular dynamics simulations were initiated from 100 initial conditions obtained in the ground state. We have analyzed the resulting nonadiabatic trajectories within 1 ps of simulation time. The photoisomerization of the GPR occurs through a highly specific path in which the S₁ to S₀ population transfer is achieved by the torsion around C₁₃=C₁₄ bond. The photoisomerization quantum yield from trans to cis isomer is found to be 0.59 which is in qualitative agreement with the experimental yield of 0.65 at the alkaline medium. The excited state population shows a time constant of 239 fs (for the trajectories that hopped to the S₀ state) compared to the experimental value of 300 fs.

All these calculations were carried out by keeping the binding pocket relaxed around 5 Å from the retinal chromophore. We have tested the effect of constrained protein environment by fixing the amino acids of the binding pocket in space. In this case the C13=C14 rotation leads the retinal out of the FC region until the S₁‐S₀ transition occurs within 200 fs.² An “aborted bicycle pedal” mechanism of isomerization was observed involving a concerted rotation about C13=C14 and C15=N, with the latter being highly twisted but not isomerized. Further, the simulation showed an increased steric interaction between the hydrogen at the C14 of the isomerizing bond and the hydroxyl group at the neighbouring tyrosine Y200. Our simulations indicate that the retinal‐Y200 interaction plays an important role in the overall outcome of the photoisomerization.

References

1. Ran, T.; Ozorowski, G.; Gao, Y.; Sineshchekov O. A.; Wang, W.; Spudich, J. L.; Luecke, H. Acta Cryst. 2013, D69, 1965–1980.
2. Borin, V. A.; Wiebeler, C.; Schapiro, I. Faraday Discuss. 2018, 207, 137–152.