Spectral tuning in visual pigments: an ONIOM(QM:MM) study on bovine rhodopsin and its mutants

Abstract

We have investigated geometries and excitation energies of bovine rhodopsin and some of its mutants by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations in ONIOM scheme, employing B3LYP and BLYP density functionals as well as DFTB method for the QM part and AMBER force field for the MM part. QM/MM geometries of the protonated Schiff-base 11- cis-retinal with B3LYP and DFTB are very similar to each other. TD-B3LYP/MM excitation energy calculations reproduce the experimental absorption maximum of 500 nm in the presence of native rhodopsin environment and predict spectral shifts due to mutations within 10 nm, whereas TD-BLYP/MM excitation energies have red-shift error of at least 50 nm. In the wild-type rhodopsin, Glu113 shifts the first excitation energy to blue and accounts for most of the shift found. Other amino acids individually contribute to the first excitation energy but their net effect is small. The electronic polarization effect is essential for reproducing experimental bond length alternation along the polyene chain in protonated Schiff-base retinal, which correlates with the computed first excitation energy. It also corrects the excitation energies and spectral shifts in mutants, more effectively for deprotonated Schiff-base retinal than for the protonated form. The protonation state and conformation of mutated residues affect electronic spectrum significantly. The present QM/MM calculations estimate not only the experimental excitation energies but also the source of spectral shifts in mutants.

Figure 1

Backbone atom positions in the X-ray structure of Rh (pdb code: 1U19, in blue) and its AMBER-optimized geometry (in red). The 11-cis-retinal is shown with the ball and stick model.

Figure 2

The model part of the ONIOM calculations with hydrogen link atom H_L. H_PSB is not present for deprotonated SBR.

Figure 3

Environment of the 11-cis-retinal in Rh. The 11-cis-retinal and the attached Lys296 are shown in brown.

Figure 4

Changes in the side chains of amino acids with mutations and experimental absorption maxima.

Figure 5

Bond length alternation along the polyene chain of the PSB 11-cis-retinal chromophore of Rh. Comparison of (a) the MM-fitted values in the X-ray structures (pdb codes: 1U19, 1L9H, 1F88, and 1HZX; chain A), an NMR structure with pdb code of 1JFP, and the high resolution double-quantum solid-state NMR data for the C¹⁰–C¹⁵ moiety including vibrational correction that have confidence level of ± 0.025 Å, (b) the results of present ONIOM calculations, and (c) NMR experiments and DFT-EE results.

Figure 6

Bond angles along the polyene chain of the PSB 11-cis-retinal chromophore of Rh. Comparison of (a) the MM-fitted values in the X-ray structures and the NMR values and (b) the NMR experiment and the results of present ONIOM calculations.

Figure 7

Bond length alternation along the polyene chain of the 11-cis-retinal chromophore of Rh after transferring the Schiff-base hydrogen to Glu113 (deprotonated SBR and protonated Glu113).

Figure 8

The most important resonance structures of the PSB 11-cis-retinal in Rh

Figure 9

Correlation between the calculated average BLA (B3LYP-EE geometry) and the first excitation energy (B3LYP-EE//B3LYP-EE) for Rh and its mutants.