Combined QM/MM study of the opsin shift in bacteriorhodopsin

Abstract

Combined quantum mechanical and molecular mechanical (QM/MM) calculations and molecular dynamics simulations of bacteriorhodopsin (bR) in the membrane matrix have been carried out to determine the factors that make significant contributions to the opsin shift. We found that both solvation and interactions with the protein significantly shifts the absorption maximum of the retinal protonated Schiff base, but the effects are much more pronounced in polar solvents such as methanol, acetonitrile, and water than in the protein environment. The differential solvatochromic shifts of PSB in methanol and in bR leads to a bathochromic shift of about 1800 cm(-1). Because the combined QM/MM configuration interaction calculation is essentially a point charge model, this contribution is attributed to the extended point-charge model of Honig and Nakanishi. The incorporation of retinal in bR is accompanied by a change in retinal conformation from the 6-s-cis form in solution to the 6-s-trans configuration in bR. The extension of the pi-conjugated system further increases the red-shift by 2400 cm(-1). The remaining factors are due to the change in dispersion interactions. Using an estimate of about 1000 cm(-1) in the dispersion contribution by Houjou et al., we obtained a theoretical opsin shift of 5200 cm(-1) in bR, which is in excellent agreement with the experimental value of 5100 cm(-1). Structural analysis of the PSB binding site revealed the specific interactions that make contributions to the observed opsin shift. The combined QM/MM method used in the present study provides an opportunity to accurately model the photoisomerization and proton transfer reactions in bR.

Structure, initial excited-state relaxation, and energy storage of rhodopsin resolved at the multiconfigurational perturbation theory level

“…Although a number of QM͞MM studies have been reported (9) for Rh proteins only a few used ab initio QM. Yamada et al (10) …”

Assessment of a composite CC2/DFT procedure for calculating 0–0 excitation energies of organic molecules

“…In a similar vein, the use of reference data from experimental spectra measured in solution calls for a treatment of solvent effects, which makes it less straightforward to directly assess the intrinsic quality of the quantum chemical description of an excited state. In this regard, gas-phase data are preferable for benchmarking purposes, despite the many methodological possibilities [8][9][10] to model solvatochromic shifts [11][12][13][14].…”

The retinal chromophore/chloride ion pair: Structure of the photoisomerization path and interplay of charge transfer and covalent states

“…In the present work, the isolated (i.e., gas-phase) models 1 and 2 (Scheme 1) are taken as qualitative (first order) models for contact ion pairs of PSB11 and PSBT. In fact, both computational (23)(24)(25)(26) and experimental (27,28) results indicate an Ϸ60°twisted (i.e., quasi-deconjugated) 6-s-cis ␤-ionone ring for retinal chromophores, supporting the use of five conjugated double bond models. ‡ ‡ Furthermore, the small difference between the absorption maxima of PSBT and PSB11 in This paper was submitted directly (Track II) to the PNAS office.…”