Origin of the Spectral Shifts among the Early Intermediates of the Rhodopsin Photocycle Pablo Campomanes, † Marilisa Neri, † Bruno A. C. Horta, † Ute F. Rö hrig, ‡ Stefano Vanni, † Ivano Tavernelli, † and Ursula Rothlisberger* ,† † Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fe ́ de ́ rale Lausanne, CH-1015 Lausanne, Switzerland ‡ Molecular Modeling Group, Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland * S Supporting Information ABSTRACT: A combined strategy based on the computation of absorption energies, using the ZINDO/S semiempirical method, for a statistically relevant number of thermally sampled configurations extracted from QM/MM trajectories is used to establish a one-to-one correspondence between the structures of the different early intermediates (dark, batho, BSI, lumi) involved in the initial steps of the rhodopsin photoactivation mechanism and their optical spectra. A systematic analysis of the results based on a correlation-based feature selection algorithm shows that the origin of the color shifts among these intermediates can be mainly ascribed to alterations in intrinsic properties of the chromophore structure, which are tuned by several residues located in the protein binding pocket. In addition to the expected electrostatic and dipolar effects caused by the charged residues (Glu113, Glu181) and to strong hydrogen bonding with Glu113, other interactions such as π-stacking with Ala117 and Thr118 backbone atoms, van der Waals contacts with Gly114 and Ala292, and CH/π weak interactions with Tyr268, Ala117, Thr118, and Ser186 side chains are found to make non-negligible contributions to the modulation of the color tuning among the different rhodopsin photointermediates. 1. INTRODUCTION G protein-coupled receptors (GPCRs) constitute a large family of transmembrane proteins, whose primary function consists in mediating cellular responses to a wide range of extracellular stimuli, thus being key components of a broad variety of biological signal transduction pathways. These receptors share a highly homologous fold characterized by a common seven transmembrane helix architecture, and present a conformational equilibrium between inactive and active conformations that is modulated by the selective binding of different ligands. 1 The visual pigment rhodopsin is a highly specialized member of the GPCR family found in vertebrate rod cells. Rhodopsin is able to capture and convert light into a chemical signal, in what constitutes the first step of vision. 2 In the dark-state, its natural ligand (11-cis-retinal) acts as a strong inverse agonist and is covalently linked to residue Lys296 of transmembrane helix 7 (TM7) of the opsin protein via a protonated Schiff base (PSB). 3,4 The ultrafast and efficient photoinduced isomer- ization of the retinal chromophore, from 11-cis- to all-trans (Scheme 1), inside the binding pocket initiates a cascade of conformational changes that ultimately leads to receptor activation and subsequent downstream signaling. 5 Several spectroscopically distinguishable intermediates in- volved in the rhodopsin photoactivation mechanism have first been detected using UV/visible spectroscopy. Although the sequences of spectroscopically distinct species that have been identified either employing time-resolved techniques at physiological temperature 6,7 or steady-state experiments at low temperature 8,9 are not completely identical, a mechanism involving a sequential decay between the experimentally detected intermediates is the most commonly accepted model (Figure 1). 10 Light absorption by the chromophore triggers the transition from dark state rhodopsin to a first photo- intermediate, photorhodopsin, whose formation is character- ized by a very fast rate (within 200 fs) 11 and a very high quantum yield (0.65). 12 Subsequently, photorhodopsin ther- mally relaxes within a few picoseconds to a new short-lived intermediate, bathorhodopsin, which in turn, on a nanosecond time scale, gives rise to the so-called blue-shifted intermediate, BSI, before it decays to form lumirhodopsin. Lumirhodopsin’s structural relaxation takes place on a longer time scale (microseconds) to give rise to another intermediate, meta- rhodopsin I, which is the precursor of the active conformation, Received: November 5, 2013 Published: February 10, 2014 Scheme 1. 11-cis- to all-trans-Isomerization of the Retinal Chromophore with the Atom Numbering for the Conjugated Chain Article pubs.acs.org/JACS © 2014 American Chemical Society 3842 dx.doi.org/10.1021/ja411303v | J. Am. Chem. Soc. 2014, 136, 3842-3851 Downloaded via ECOLE POLYTECHNIC FED LAUSANNE on February 7, 2019 at 09:15:28 (UTC). See https://pubs.acs.org/sharingguidelines for options on how to legitimately share published articles.