The vibrational structure of the chromophore in the primary photoproduct of vision, bathorhodopsin, is examined to determine the cause of the anomalously decoupled and intense C 11 =C 12 hydrogenout-of-plane (HOOP) wagging modes and their relation to energy storage in the primary photoproduct. Low-temperature (77 K) resonance Raman spectra of Glu181 and Ser186 mutants of bovine rhodopsin reveal only mild mutagenic perturbations of the photoproduct spectrum suggesting that dipolar, electrostatic, or steric interactions with these residues do ded by NIHnot cause the HOOP mode frequencies and intensities. Density functional theory calculations are performed to investigate the effect of geometric distortion on the HOOP coupling. The decoupled HOOP modes can be simulated by imposing ∼40° twists in the same direction about the C 11 =C 12 and C 12 -C 13 bonds. Sequence comparison and examination of the binding site suggests that these distortions are caused by three constraints consisting of an electrostatic anchor between the protonated Schiff base and the Glu113 counterion, as well as steric interactions of the 9-and 13-methyl groups with surrounding residues. This distortion stores light energy that is used to drive the subsequent protein conformational changes that activate rhodopsin.Photoactive proteins play a vital role in a variety of light-energy and light-signaling processes that are characterized by pico-to femtosecond light-driven structural changes of a proteinbound chromophore followed by activated conformational changes of the protein. In systems such as rhodopsin (Rho) 1 (1), bacteriorhodopsin (2,3), halorhodopsin (4), photoactive yellow protein (5), and phytochrome (6,7), primary high-energy intermediates are produced with structurally perturbed chromophores. What is the nature of the protein-chromophore interactions that store the energy needed to drive subsequent protein conformational changes? To address this question, we have studied the photoactivation of rhodopsin, a dim-light photoreceptor, using a multidisciplinary approach that integrates Raman spectroscopy, mutagenesis, density functional theory (DFT) calculations, and bioinformatic analysis. † Funding was provided by NIH Grant EY02051 (to R.A.M. Rho is a paradigmatic G protein-coupled receptor, whose 7-transmembrane helical structure forms a binding pocket for 11-cis-retinal, which is covalently linked to Lys296 on helix 7. Within 200 fs after photoexcitation (8,9), the 11-cis-retinal protonated Schiff base (PSB) isomerizes to all-trans-retinal (ATR) with a quantum yield of 0.65 to form the primary photoproduct, Bathorhodopsin (10,11), which stores ∼30 kcal/mol or ∼60% of the incident photon energy (Figure 1) (12)(13)(14). Subsequently, the highly distorted chromophore relaxes, and the transduced energy is used to drive conformational changes in the opsin protein (15)(16)(17)(18). Recently, we found that this structural evolution includes a retinal counterion switch from Glu113 in the dark state to Glu181 in the metarhodopsin I (Met...