A QM/MM study of the initial excited state dynamics of green-absorbing proteorhodopsin

Abstract

The primary photochemical reaction of the green-absorbing proteorhodopsin is studied by means of a hybrid quantum mechanics/molecular mechanics (QM/MM) approach. The simulations are based on a homology model derived from the blue-absorbing proteorhodopsin crystal structure. The geometry of retinal and the surrounding sidechains in the protein binding pocket were optimized using the QM/MM method. Starting from this geometry the isomerization was studied with a relaxed scan along the C13[double bond, length as m-dash]C14 dihedral. It revealed an "aborted bicycle pedal" mechanism of isomerization that was originally proposed by Warshel for bovine rhodopsin and bacteriorhodopsin. However, the isomerization involved the concerted rotation about C13[double bond, length as m-dash]C14 and C15[double bond, length as m-dash]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 200. In addition, we have simulated a nonadiabatic trajectory which showed the timing of the isomerization. In the first 20 fs upon excitation the order of the conjugated double and single bonds is inverted, consecutively the C13[double bond, length as m-dash]C14 rotation is activated for 200 fs until the S1-S0 transition is detected. However, the isomerization is reverted due to the specific interaction with the tyrosine as observed along the relaxed scan calculation. Our simulations indicate that the retinal - tyrosine 200 interaction plays an important role in the outcome of the photoisomerization.

Accurate Prediction of Absorption Spectral Shifts of Proteorhodopsin Using a Fragment-Based Quantum Mechanical Method

“…In this work, the structure of Blue-absorbing PR (BPR—PR105Q) was prepared by means of a hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) approach and MD simulation [ 25 ]. The initial structure was taken from the X-ray crystal structure of BPR (PR105Q) in the dark state (PDB id: 4JQ6, chain B), which we chose as the template of PR105Q (PR with GLN105).…”

“…Schapiro and co-workers studied the initial excited state dynamics of GPR, and their simulations indicated that the retinal-TYR200 interaction played an important role in the outcome of the photo isomerization [ 25 ]. In this study, during classical MD simulation, the fluctuation of TYR200 had a significant influence on the excitation energy of the chromophore LYR231.…”

Low‐temperature Raman spectroscopy reveals small chromophore distortion in primary photointermediate of proteorhodopsin

“…PR has multiple aromatic amino acid residues (Trp98, Trp197 and Tyr200) surrounding the chromophore, and these bulky residues can exert the effect of steric hindrance [13]. In that study, the authors used a fixed protein structure and proposed that the steric interaction between the chromophore and Tyr200 played an important role in the outcome of photoisomerization at about the C 13 =C 14 bond [45]. 4.…”

“…crystal structure of a blue-absorbing PR variant [44]. In that study, the authors used a fixed protein structure and proposed that the steric interaction between the chromophore and Tyr200 played an important role in the outcome of photoisomerization at about the C 13 =C 14 bond [45]. Therefore, the flexibility in the position of Tyr200 was suggested to decrease steric interaction in the formation of PR K .…”

Photosensitized Retinal Isomerization in Rhodopsin Mediated by a Triplet State

“…The 6‐31G(d) basis set was employed. This QM/MM strategy was demonstrated to successfully model the photochemistry of several rhodopsin types, reaching quantitative spectroscopic values, comparable with the experiment . In this case, a state average (SA) procedure was employed including 3 roots for both singlet and triplet manifold.…”