The conformation of retinal bound to the G protein-coupled receptor rhodopsin is intimately linked to its photochemistry, which initiates the visual process. Site-directed deuterium ((2)H) NMR spectroscopy was used to investigate the structure of retinal within the binding pocket of bovine rhodopsin. Aligned recombinant membranes were studied containing rhodopsin that was regenerated with retinal (2)H-labeled at the C(5), C(9), or C(13) methyl groups by total synthesis. Studies were conducted at temperatures below the gel to liquid-crystalline phase transition of the membrane lipid bilayer, where rotational and translational diffusion of rhodopsin is effectively quenched. The experimental tilt series of (2)H NMR spectra were fit to a theoretical line shape analysis [Nevzorov, A. A., Moltke, S., Heyn, M. P., and Brown, M. F. (1999) J. Am. Chem. Soc. 121, 7636-7643] giving the retinylidene bond orientations with respect to the membrane normal in the dark state. Moreover, the relative orientations of pairs of methyl groups were used to calculate effective torsional angles between different planes of unsaturation of the retinal chromophore. Our results are consistent with significant conformational distortion of retinal, and they have important implications for quantum mechanical calculations of its electronic spectral properties. In particular, we find that the beta-ionone ring has a twisted 6-s-cis conformation, whereas the polyene chain is twisted 12-s-trans. The conformational strain of retinal as revealed by solid-state (2)H NMR is significant for explaining the quantum yields and mechanism of its ultrafast photoisomerization in visual pigments. This work provides a consensus view of the retinal conformation in rhodopsin as seen by X-ray diffraction, solid-state NMR spectroscopy, and quantum chemical calculations.

SummaryRhodopsin is a prototype for G protein-coupled receptors (GPCRs) that are implicated in many biological responses in humans. A site-directed 2 H NMR approach was used for structural analysis of retinal within its binding cavity in the dark and pre-activated meta I states. Retinal was labeled with 2 H at the C5, C9, or C13 methyl groups by total synthesis, and was used to regenerate the opsin apoprotein. Solid-state 2 H NMR spectra were acquired for aligned membranes in the lowtemperature lipid gel phase versus the tilt angle to the magnetic field. Data reduction assumed a static uniaxial distribution, and gave the retinylidene methyl bond orientations together with the alignment disorder (mosaic spread). The 2 H NMR structure of 11-cis-retinal in the dark state revealed torsional twisting of the polyene chain and the β-ionone ring. The distorted retinylidene ligand undergoes restricted motion, as evinced by order parameters of ≈ 0.9 for the rapidly spinning C-C 2 H 3 groups, with off-axial fluctuations of ≈ 15°. Retinal is accommodated within the rhodopsin binding pocket with a negative pre-twist about the C11=C12 double bond, which explains its rapid photochemistry and indicates the trajectory of the 11-cis to trans isomerization.For the cryotrapped meta I state, the 2 H NMR structure showed a reduction of the polyene strain, whereas the β-ionone ring maintained its torsional twisting. Strain energy and dynamics of retinal are interpreted with regard to substituent control of receptor activation. Steric hindrance between trans retinal and Trp 265 can trigger formation of the subsequent activated meta II state. Our results are pertinent to quantum and classical molecular mechanics simulations, and show how 2 H NMR can be applied to ligands bound to GPCRs in relation to their characteristic mechanisms of action.

In seeking to understand G protein-coupled receptor (GPCR)-mediated signaling, X-ray and magnetic resonance approaches have played important roles—yet neither the protein dynamics nor the plasticity of GPCRs are amenable to study. Here we show that solid-state 2H NMR relaxation elucidates picosecond-nanosecond timescale motions of the retinal ligand that impact upon larger-scale functional dynamics of rhodopsin in membranes. A multiscale activation mechanism is put forward, whereby retinal initiates collective helix fluctuations in the Meta I–Meta II equilibrium on the microsecond-millisecond timescale.

Rhodopsin is a canonical member of the family of G proteincoupled receptors, which transmit signals across cellular membranes and are linked to many drug interventions in humans. Here we show that solid-state 2 H NMR relaxation allows investigation of light-induced changes in local ps-ns time scale motions of retinal bound to rhodopsin. Site-specific 2 H labels were introduced into methyl groups of the retinal ligand that are essential to the activation process. We conducted solid-state 2 H NMR relaxation (spinlattice, T 1Z , and quadrupolar-order, T 1Q ) experiments in the dark, Meta I, and Meta II states of the photoreceptor. Surprisingly, we find the retinylidene methyl groups exhibit site-specific differences in dynamics that change upon light excitation-even more striking, the C9-methyl group is a dynamical hotspot that corresponds to a crucial functional hotspot of rhodopsin. Following 11-cis to trans isomerization, the 2 H NMR data suggest the β-ionone ring remains in its hydrophobic binding pocket in all three states of the protein.We propose a multiscale activation mechanism with a complex energy landscape, whereby the photonic energy is directed against the E2 loop by the C13-methyl group, and toward helices H3 and H5 by the C5-methyl of the β-ionone ring. Changes in retinal structure and dynamics initiate activating fluctuations of transmembrane helices H5 and H6 in the Meta I-Meta II equilibrium of rhodopsin. Our proposals challenge the Standard Model whereby a single light-activated receptor conformation yields the visual response -rather an ensemble of substates is present, due to the entropy gain produced by photolysis of the inhibitory retinal lock.GPCR | solid-state NMR | generalized model-free analysis G protein-coupled receptors (GPCRs) (1-3) are the largest family of integral membrane proteins in the human genome, and they are the targets of about 30% of all human pharmaceuticals. At present the 3D structures of several GPCRs-including rhodopsin (4-8), the β 1 -and β 2 -adrenergic receptors (9, 10), and the adenosine A 2A receptor (11)-have been established in various functional states (2). Yet the mechanisms of GPCR activation remain elusive, as they are membrane-embedded molecules that are often recalcitrant to crystallization, and push the size limits of solution NMR spectroscopy. Rhodopsin is the quintessential prototype for Family A GPCRs, because previous X-ray (5,6) and electron diffraction (12) studies have yielded crystal structures of its dark state (4-6) and several photointermediates (13,14). Notably, the retinal ligand is buried deeply within a 7-transmembrane (TM) helical bundle, where it locks the receptor in the inactive state, with negligible basal (constitutive) activity (4). Upon light absorption, rhodopsin catalyzes the rapid and highly selective 11-cis to trans isomerization of retinal (15, 16) switching it from an inverse agonist to an agonist. In the Metarhodopsin I-Metarhodopsin II equilibrium, recognition sites are exposed for a heterotrimeric G protein (transducin or...

The structural and photochemical changes in rhodopsin due to absorption of light are crucial for understanding the process of visual signaling. We investigated the structure of trans-retinal in the metarhodopsin I photointermediate (MI), where the retinylidene cofactor functions as an antagonist. Rhodopsin was regenerated using retinal that was (2)H-labeled at the C5, C9, or C13 methyl groups and was reconstituted with 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine. Membranes were aligned by isopotential centrifugation, and rhodopsin in the supported bilayers was then bleached and cryotrapped in the MI state. Solid-state (2)H NMR spectra of oriented rhodopsin in the low-temperature lipid gel state were analyzed in terms of a static uniaxial distribution (Nevzorov, A. A.; Moltke, S.; Heyn, M. P.; Brown, M. F. J. Am. Chem. Soc. 1999, 121, 7636-7643). The line shape analysis allowed us to obtain the methyl bond orientations relative to the membrane normal in the presence of substantial alignment disorder (mosaic spread). Relative orientations of the methyl groups were used to calculate effective torsional angles between the three different planes that represent the polyene chain and the beta-ionone ring of retinal. Assuming a three-plane model, a less distorted structure was found for retinal in MI compared to the dark state. Our results are pertinent to how photonic energy is channeled within the protein to allow the strained retinal conformation to relax, thereby forming the activated state of the receptor.

Visual rhodopsin is an important archetype for G‐protein‐coupled receptors, which are membrane proteins implicated in cellular signal transduction. Herein, we show experimentally that approximately 80 water molecules flood rhodopsin upon light absorption to form a solvent‐swollen active state. An influx of mobile water is necessary for activating the photoreceptor, and this finding is supported by molecular dynamics (MD) simulations. Combined force‐based measurements involving osmotic and hydrostatic pressure indicate the expansion occurs by changes in cavity volumes, together with greater hydration in the active metarhodopsin‐II state. Moreover, we discovered that binding and release of the C‐terminal helix of transducin is coupled to hydration changes as may occur in visual signal amplification. Hydration–dehydration explains signaling by a dynamic allosteric mechanism, in which the soft membrane matter (lipids and water) has a pivotal role in the catalytic G‐protein cycle.

Solid-state 2H NMR spectroscopy gives a powerful avenue to investigating the structures of ligands and cofactors bound to integral membrane proteins. For bacteriorhodopsin (bR) and rhodopsin, retinal was site-specifically labeled by deuteration of the methyl groups followed by regeneration of the apoprotein. 2H NMR studies of aligned membrane samples were conducted under conditions where rotational and translational diffusion of the protein were absent on the NMR time scale. The theoretical lineshape treatment involved a static axial distribution of rotating C-C2H3 groups about the local membrane frame, together with the static axial distribution of the local normal relative to the average normal. Simulation of solid-state 2H NMR lineshapes gave both the methyl group orientations and the alignment disorder (mosaic spread) of the membrane stack. The methyl bond orientations provided the angular restraints for structural analysis. In the case of bR the retinal chromophore is nearly planar in the dark- and all-trans light-adapted states, as well upon isomerization to 13-cis in the M state. The C13-methyl group at the "business end" of the chromophore changes its orientation to the membrane upon photon absorption, moving towards W182 and thus driving the proton pump in energy conservation. Moreover, rhodopsin was studied as a prototype for G protein-coupled receptors (GPCRs) implicated in many biological responses in humans. In contrast to bR, the retinal chromophore of rhodopsin has an 11-cis conformation and is highly twisted in the dark state. Three sites of interaction affect the torsional deformation of retinal, viz. the protonated Schiff base with its carboxylate counterion; the C9-methyl group of the polyene; and the beta-ionone ring within its hydrophobic pocket. For rhodopsin, the strain energy and dynamics of retinal as established by 2H NMR are implicated in substituent control of activation. Retinal is locked in a conformation that is twisted in the direction of the photoisomerization, which explains the dark stability of rhodopsin and allows for ultra-fast isomerization upon absorption of a photon. Torsional strain is relaxed in the meta I state that precedes subsequent receptor activation. Comparison of the two retinal proteins using solid-state 2H NMR is thus illuminating in terms of their different biological functions.

Solid-state NMR spectroscopy gives a powerful avenue for investigating G protein-coupled receptors and other integral membrane proteins in a native-like environment. This article reviews the use of solid-state 2 H NMR to study the retinal cofactor of rhodopsin in the dark state as well as the meta I and meta II photointermediates. Site-specific 2 H NMR labels have been introduced into three regions (methyl groups) of retinal that are crucially important for the photochemical function of rhodopsin. Despite its phenomenal stability 2 H NMR spectroscopy indicates retinal undergoes rapid fluctuations within the protein binding cavity. The spectral lineshapes reveal the methyl groups spin rapidly about their three-fold (C 3 ) axes with an order parameter for the off-axial motion of S C3 % 0:9: For the dark state, the 2 H NMR structure of 11-cis-retinal manifests torsional twisting of both the polyene chain and the b-ionone ring due to steric interactions of the ligand and the protein. Retinal is accommodated within the rhodopsin binding pocket with a negative pretwist about the C11=C12 double bond. Conformational distortion explains its rapid photochemistry and reveals the trajectory of the 11-cis to trans isomerization. In addition, 2 H NMR has been applied to study the retinylidene dynamics in the dark and light-activated states. Upon isomerization there are drastic changes in the mobility of all three methyl groups. The relaxation data support an activation mechanism whereby the b-ionone ring of retinal stays in nearly the same environment, without a large displacement of the ligand. Interactions of the b-ionone ring and the retinylidene Schiff base with the protein transmit the force of the retinal isomerization. Solid-state 2 H NMR thus provides information about the flow of energy that triggers changes in hydrogen-bonding networks and helix movements in the activation mechanism of the photoreceptor.