Spectral Tuning of Rhodopsin and Visual Cone Pigments Xiuwen Zhou, † Dage Sundholm, ‡ Tomasz A. Wesolowski, † and Ville R. I. Kaila* ,§ † De ́ partement de Chimie Physique, Universite ́ de Gene ̀ ve, 30 quai Ernest-Ansermett, CH-1211 Gene ̀ ve 4, Switzerland ‡ Department of Chemistry, P.O. Box 55, A. I. Virtanens plats 1, University of Helsinki, FIN-00014 Helsinki, Finland § Department Chemie, Technische Universitä t Mü nchen, Lichtenbergstrasse 4, D-85747 Garching, Germany * S Supporting Information ABSTRACT: Retinal is the light-absorbing biochromo- phore responsible for the activation of vision pigments and light-driven ion pumps. Nature has evolved molecular tuning mechanisms that significantly shift the optical properties of the retinal pigments to enable their absorption of visible light. Using large-scale quantum chemical calculations at the density functional theory level combined with frozen density embedding theory, we show here how the protein environment of vision pigments tunes the absorption of retinal by electrostatically dominated interactions between the chromophore and the surrounding protein residues. The calculations accurately reproduce the experimental absorption maxima of rhodopsin and the red, green, and blue color pigments. We further identify key interactions responsible for the color-shifting effects by mutating the rhodopsin structure in silico, and we find that deprotonation of the retinyl is likely to be responsible for the blue-shifted absorption in the blue cone vision pigment. R etinal is a conjugated polyene that occurs in the light- capturing unit of several photobiological systems. In vision pigments 1 and bacterial light-driven proton pumps, 2 retinal is covalently linked to the protein by a lysine residue, forming a Schiff base (SB). The protein environment shifts the absorption maximum of retinal from 365-430 nm (2.80-3.40 eV) in aqueous solution to 420-560 nm (2.20-2.95 eV) in the vision proteins, 1 enabling their absorption of visible light. The exact molecular mechanism of the spectral shift has remained elusive for more than half a century. It has been suggested that the tuning may arise from an altered conjugation of the polyene, 3 by specific electrostatic interactions between protein residues and the retinal, 4 and by charge transfer and polarization effects. 5 The development of accurate electronic structure theory methods open up new ways of addressing the molecular mechanism of spectral tuning. In this study, we investigate the protein-induced spectral shifts of retinal in rhodopsin and its homologous color cone pigments using large-scale quantum chemical calculations. Rhodopsin is a protein in the rod cells of the vertebrate eye, responsible for dim vision. 1 Color vision takes place in the cone cells and is catalyzed by three color pigment proteins, responsible for the absorption of red, green, and blue photons, respectively. 1b Light absorption by these G-protein coupled receptors leads to an 11-cis to all-trans isomerization of the retinyl side chain, activating a G-protein- mediated signaling cascade that triggers the vision process. 1 Photobiological systems face unique computational challenges due to their complex chromophore-protein environment, which must be explicitly considered using large computational models. 6 Although ab initio methodologies can accurately predict optical transitions in molecules, most such methods are inapplicable to photobiology due to their high computational costs. Recent developments, such as the restricted virtual space approach in combination with low-order correlation methods, increase the possibility of treating large photobiological systems. 4c,7 However, due to the high computational scaling of such methods, extensive studies of the chromophore-protein interactions beyond the immediate chromophore vicinity are demanding. We use here a frozen-density embedding theory (FDET) 8 based method to compute the vertical excitation energies of retinal embedded in large protein surroundings, within the linear-response time-dependent density functional theory (TDDFT) 9 framework. In these calculations, we treat the chromophore region as an active system that is quantum chemically embedded in a frozen electron density of surrounding protein residues. Due to the large computational savings introduced by treating the surroundings as a frozen electron density, the FDET approach allows the modeling of the chromophore-protein interactions at full quantum mechanical level, using system sizes comprising ∼400 atoms, usually beyond the capabilities of conventional TDDFT methods, especially when a large number of calculations are necessary, as in this work. Molecular models of rhodopsin and of the red, green, and blue cone pigments were constructed on the basis of coordinates of the crystal structure from Bos taurus 11 and the homology models obtained from Brookhaven Protein Data Bank (PDB IDs: 1U19, 1KPX, 1KPN, 1KPW). 12 The models comprised 329-370 atoms, with the retinal surrounded by 25-30 residues nearest to the chromophore binding pocket (see SI Table 1, SI Figures 1 and 2). All amino acid residues were cut at the C β atoms, which were saturated by hydrogen atoms. The models were structure optimized using the BP86 functional with the RI-MARIJ approximation and def2-SVP basis sets. 13 The retinal side chain and hydrogen atoms in the surrounding residues were allowed to fully relax in the structure optimization. To study the saturation of these models, the CHARMM27 force field 14 was used to embed the quantum chemical models in the point charge surroundings of the protein residues beyond the QM model Received: November 21, 2013 Published: January 14, 2014 Communication pubs.acs.org/JACS © 2014 American Chemical Society 2723 dx.doi.org/10.1021/ja411864m | J. Am. Chem. Soc. 2014, 136, 2723-2726