Modelling of photointermediates suggests a mechanism of the flip of the beta-ionone moiety of the retinylidene chromophore in the rhodopsin photocascade

Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes

As one of the best studied members of the pharmaceutically relevant family of G-protein-coupled receptors, rhodopsin serves as a prototype for understanding the mechanism of G-protein-coupled receptor activation. Here, we aim at exploring functionally relevant conformational changes and signal transmission mechanisms involved in its photoactivation brought about through a cis-trans photoisomerization of retinal. For this exploration, we propose a molecular dynamics simulation protocol that utilizes normal modes derived from the anisotropic network model for proteins. Deformations along multiple low-frequency modes of motion are used to efficiently sample collective conformational changes in the presence of explicit membrane and water environment, consistent with interresidue interactions. We identify two highly stable regions in rhodopsin, one clustered near the chromophore, the other near the cytoplasmic ends of transmembrane helices H1, H2, and H7. Due to redistribution of interactions in the neighborhood of retinal upon stabilization of the trans form, local structural rearrangements in the adjoining H3-H6 residues are efficiently propagated to the cytoplasmic end of these particular helices. In the structures obtained by our simulations, all-trans retinal interacts with Cys(167) on H4 and Phe(203) on H5, which were not accessible in the dark state, and exhibits stronger interactions with H5, while some of the contacts made (in the cis form) with H6 are lost.

Predisposition of the dark state of rhodopsin to functional changes in structure

As the only member of the family of G-protein-coupled receptors for which atomic coordinates are available, rhodopsin is widely studied for insight into the molecular mechanism of G-protein-coupled receptor activation. The currently available structures refer to the inactive, dark state, of rhodopsin, rather than the light-activated metarhodopsin II (Meta II) state. A model for the Meta II state is proposed here by analyzing elastic network normal modes in conjunction with experimental data. Key mechanical features and interactions broken/formed in the proposed model are found to be consistent with the experimental data. The model is further tested by using a set of Meta II fluorescence decay rates measured to empirically characterize the deactivation of rhodopsin mutants. The model is found to correctly predict 93% of the experimentally observed effects in 119 rhodopsin mutants for which the decay rates and misfolding data have been measured, including a systematic analysis of Cys-->Ser replacements reported here. Based on the detailed comparison between model and experiments, a cooperative activation mechanism is deduced that couples retinal isomerization to concerted changes in conformation, facilitated by the intrinsic dynamics of rhodopsin. A global hinge site is identified near the retinal-binding pocket that ensures the efficient propagation of signals from the central transmembrane region to both cytoplasmic and extracellular ends. The predicted activation mechanism opens the transmembrane helices at the critical G-protein binding cytoplasmic domain. This model provides a detailed, mechanistic description of the activation process, extending experimental observations and yielding new insights for further tests.

Possible role of the 11-cis-retinyl conformation in controlling the dual decay processes of excited rhodopsin

In this work, we examine how the reported dual decay processes of rhodopsin and binding site stereospecificity can be accounted for by the recently available crystal structure of rhodopsin. Arguments are presented for possible presence of two rhodopsin "rotamers" that fit within the binding cavity. Directed pathways of decay could account for the observed excited decay processes. We summarize evidence for the possible existence of two different ground-state configurations that give rise to two different excited species.

Resonance Raman analysis of the mechanism of energy storage and chromophore distortion in the primary visual photoproduct

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) hydrogen-out-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 not 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 approximately 40 degrees 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.

Conformation Analysis of Glu181 and Ser186 in the Metarhodopsin I State

Photoactivation of rhodopsin yields a photointermediate, metarhodopsin I, during the formation of the fully activated photointermediate, metarhodopsin II. It is proposed that Glu181 and Ser186, in the second extracellular loop, play important roles in the stabilization of the protonated Schiff base of metarhodopsin I. Glu181 and Ser186 form a network of hydrogen bonds mediated by a water molecule in the dark-state crystal structure of rhodopsin. On the other hand, the counter-ion of the protonated Schiff base, Glu113, is not involved in the hydrogen-bond network, as it is located further than hydrogen-bond distance from Ser186. Herein, the conformations and proton arrangements of the protonated form of Glu181 and Ser186 in the hydrogen-bond network have been investigated by molecular-dynamics calculations of the rhodopsin crystal structure as well as in the structural model of metarhodopsin I. In the metarhodopsin I model, Ser186 mediated the hydrogen-bond network between Glu113 and Glu181, changing the protein's conformation and creating a space by the outward motion of transmembrane segment 3, while the hydroxyl group of Glu181 was favored in the hydrogen-bond network. The hydrogen bond between Glu113 and Ser186 is thought to reduce the basicity of the carboxylate of Glu113, maintaining the protonated state of the Schiff base in the metarhodopsin I state. In the Glu181Gln mutant, the hydroxyl group of Ser186 favored the water molecule as a proton donor in the metarhodopsin I state, since the carbonyl group of the Gln residue was favored in the hydrogen-bond network. These results indicate that the Gln181 residue interferes with the hydrogen-bond between Glu113 and Ser186 in the metarhodopsin I state, facilitating the neutralization of the protonated Schiff base.

Structural Models of the Photointermediates in the Rhodopsin Photocascade, Lumirhodopsin, Metarhodopsin I, and Metarhodopsin II

Model building of the two photointermediates, lumirhodopsin and metarhodopsin I, and the activated form of rhodopsin, metarhodopsin II, is described. An outward swing of the C-terminal portion of transmembrane segment 3, pivoting on Cys110 at the N-terminal end of transmembrane segment 3, led to structural models of lumirhodopsin and metarhodopsin I. The conformation of the chromophore in the lumirhodopsin and metarhodopsin I models is controlled by the motion of transmembrane segment 3 and agreed closely with the hydrogen-bonding states of the protonated Schiff base in lumirhodopsin and metarhodopsin I as deduced from their FTIR and resonance Raman spectra and with the negative and positive CD bands of lumirhodopsin and metarhodopsin I, respectively. The structure of metarhodopsin II was constructed by an outward swing of transmembrane segment 3 and the rigid-body motion of transmembrane segment 6. The arrangement of the entire transmembrane segment of the metarhodopsin II model closely agreed with the electron paramagnetic resonance spectra of spin-labeled rhodopsin mutants and provided a structural basis for the protonation of Glu134, which is a key process in transducin activation.

Primary events in dim light vision: a chemical and spectroscopic approach toward understanding protein/chromophore interactions in rhodopsin

The visual pigment rhodopsin (bovine) is a 40 kDa protein consisting of 348 amino acids, and is a prototypical member of the subfamily A of G protein-coupled receptors (GPCRs). This remarkably efficient light-activated protein (quantum yield = 0.67) binds the chromophore 11-cis-retinal covalently by attachment to Lys296 through a protonated Schiff base. The 11-cis geometry of the retinylidene chromophore keeps the partially active opsin protein locked in its inactive state (inverse agonist). Several retinal analogs with defined configurations and stereochemistry have been incorporated into the apoprotein to give rhodopsin analogs. These incorporation results along with the spectroscopic properties of the rhodopsin analogs clarify the mode of entry of the chromophore into the apoprotein and the biologically relevant conformation of the chromophore in the rhodopsin binding site. In addition, difference UV, CD, and photoaffinity labeling studies with a 3-diazo-4-oxo analog of 11-cis-retinal have been used to chart the movement of the retinylidene chromophore through the various intermediate stages of visual transduction.

The molecular basis for the high photosensitivity of rhodopsin

Based on structural information derived from the F NMR data of labeled rhodopsins, rhodopsin crystal structure, and excited-state properties of model polyenes, we propose a molecular mechanism that accounts specifically for the causes of the well-known enhanced photoreactivity of rhodopsin (increased rates and quantum yield of isomerization). It involves the key features of close proximity of C-187 to H-12 and chromophore bond lengthening upon light absorption. The resultant "sudden punch" to H-12 triggers dual processes of decay of the Franck-Condon-excited rhodopsin, a productive directed photoisomerization and a nonproductive decay returning to the ground state as two separate molecular pathways [based on real-time fluorescence results of Chosrowjan, H., Mataga, N., Shibata, Y., Tachibanaki, S., Kandori, H., Shichida, Y., Okada, T. & Kouyama, T. (1998) J. Am. Chem. Soc. 120, 9706-9707]. The two processes are controlled by the local protein structure: an empty space provided by the intradiscal loop connecting transmembrane helices 4 and 5 and a protein wall composed of amino acid units in transmembrane 3. Suggestions, involving retinal analogs and rhodopsin mutants, to improve the unusually high photosensitivity of rhodopsin are proposed.

Molecular Dynamics Simulation of Dark-adapted Rhodopsin in an Explicit Membrane Bilayer: Coupling between Local Retinal and Larger Scale Conformational Change

The light-driven photocycle of rhodopsin begins the photoreceptor cascade that underlies visual response. In a sequence of events, the retinal covalently attached to the rhodopsin protein undergoes a conformational change that communicates local changes to a global conformational change throughout the whole protein. In turn, the large-scale protein change then activates G-proteins and signal amplification throughout the cell. The nature of this change, involving a coupling between a local process and larger changes throughout the protein, may be important for many membrane proteins. In addition, functional work has shown that this coupling occurs with different efficiency in different lipid settings. To begin to understand the nature of the efficiency of this coupling in different lipid settings, we present a molecular dynamics study of rhodopsin in an explicit dioleoyl-phosphatidylcholine bilayer. Our system was simulated for 40 ns and provides insights into the very early events of the visual cascade, before the full transition and activation have occurred. In particular, we see an event near 10 ns that begins with a change in hydrogen bonding near the retinal and that leads through a series of coupled changes to a shift in helical tilt. This type of event, though rare on the molecular dynamics time-scale, could be an important clue to the types of coupling that occur between local and large-scale conformational change in many membrane proteins.