Crystal Structure Of Rhodopsin Research Articles

Insights into the Protein Functions and Absorption Wavelengths of Microbial Rhodopsins.

Using a quantum mechanical/molecular mechanical approach, the absorption wavelength of the retinal Schiff base was calculated based on 13 microbial rhodopsin crystal structures. The results showed that the protein electrostatic environment decreases the absorption wavelength significantly in the cation-conducting rhodopsin but only slightly in the sensory rhodopsin. Among the microbial rhodopsins with different functions, the differences in the absorption wavelengths are caused by differences in the arrangement of the charged residues at the retinal Schiff base binding moiety, namely, one or two counterions at the three common positions. Among the microbial rhodopsins with similar functions, the differences in the polar residues at the retinal Schiff base binding site are responsible for the differences in the absorption wavelengths. Counterions contribute to an absorption wavelength shift of 50-120 nm, whereas polar groups contribute to a shift of up to ∼10 nm. It seems likely that protein function is directly associated with the absorption wavelength in microbial rhodopsins.

Phote-HrTH (Phormia terraenovae Hypertrehalosaemic Hormone), the Metabolic Hormone of the Fruit Fly: Solution Structure and Receptor Binding Model

Fruit flies are a widely distributed pest insect that pose a significant threat to food security. Flight is essential for the dispersal of the adult flies to find new food sources and ideal breeding spots. The supply of metabolic fuel to power the flight muscles of insects is regulated by adipokinetic hormones (AKHs). The fruit fly, Drosophila melanogaster, has the same AKH that is present in the blowfly, Phormia terraenovae; this AKH has the code-name Phote-HrTH. Binding of the AKH to the extra-cellular binding site of a G protein-coupled receptor causes its activation. In this paper, the structure of Phote-HrTH in sodium dodecyl sulfate (SDS) micelle solution was determined using NMR restrained molecular dynamics. The peptide was found to bind to the micelle and be fairly rigid, with an S2 order parameter of 0.96. The translated protein sequence of the AKH receptor from the fruit fly, D. melanogaster, Drome-AKHR, was used to construct two models of the receptor. It is proposed that these two models represent the active and inactive state of the receptor. The model based on the crystal structure of the β-2 adrenergic receptor was found to bind Phote-HrTH with a binding constant of −102kJmol−1, while the other model, based on the crystal structure of rhodopsin, did not bind the peptide. Under molecular dynamic simulation, in a palmitoyloleoylphosphatidylcholine (POPC) membrane, the receptor complex changed from an inactive to an active state. The identification and characterisation of the ligand binding site of Drome-AKHR provide novel information of ligand–receptor interaction, which could lead to the development of species-specific control substances to use discriminately against the fruit fly.

Crystal structure of rhodopsin in complex with a mini-Go sheds light on the principles of G protein selectivity.

Selective coupling of G protein (heterotrimeric guanine nucleotide-binding protein)-coupled receptors (GPCRs) to specific Gα-protein subtypes is critical to transform extracellular signals, carried by natural ligands and clinical drugs, into cellular responses. At the center of this transduction event lies the formation of a signaling complex between the receptor and G protein. We report the crystal structure of light-sensitive GPCR rhodopsin bound to an engineered mini-Go protein. The conformation of the receptor is identical to all previous structures of active rhodopsin, including the complex with arrestin. Thus, rhodopsin seems to adopt predominantly one thermodynamically stable active conformation, effectively acting like a "structural switch," allowing for maximum efficiency in the visual system. Furthermore, our analysis of the well-defined GPCR-G protein interface suggests that the precise position of the carboxyl-terminal "hook-like" element of the G protein (its four last residues) relative to the TM7/helix 8 (H8) joint of the receptor is a significant determinant in selective G protein activation.

Connecting PIE-FCCS Measurements to Dimerization Affinity to Resolve the Role of GPCR Dimerization in Live Cells

Since the rhodopsin crystal structure was reported over 15 years ago, the structure and dynamics of class A G-protein coupled receptors (GPCR) have been a growing area of investigation. A significant body of research has shown the existence of GPCR dimers and possibly higher order oligomers in native tissue. Although GPCR dimerization is still controversial, a critical question now is what role, if any, the oligomeric states play in function and signaling. In trying to connect the oligomerization state to the receptor activation kinetics, we need an intelligent assay that can fully define the oligomer equilibrium in live cells. Fluorescence techniques, like FRET, FRAP or FCS/FCCS, can be used to obtain dynamic in vivo information. Each one brings their own advantages and challenges. Our lab recently showed evidence for the density dependent dimerization of rhodopsin in live cells with PIE-FCCS. The equilibrium states cannot be resolved until the concentrations of the different species are quantified. Here we present a new approach to utilize the fluorescence data to decipher the complex state of the membrane. This approach will use calibration and statistical analysis to mathematically determine the equilibrium concentrations and dissociation constant for various GPCRs.

Structural and Functional Studies of a Newly Grouped Haloquadratum walsbyi Bacteriorhodopsin Reveal the Acid-resistant Light-driven Proton Pumping Activity

Retinal bound light-driven proton pumps are widespread in eukaryotic and prokaryotic organisms. Among these pumps, bacteriorhodopsin (BR) proteins cooperate with ATP synthase to convert captured solar energy into a biologically consumable form, ATP. In an acidic environment or when pumped-out protons accumulate in the extracellular region, the maximum absorbance of BR proteins shifts markedly to the longer wavelengths. These conditions affect the light-driven proton pumping functional exertion as well. In this study, wild-type crystal structure of a BR with optical stability under wide pH range from a square halophilic archaeon, Haloquadratum walsbyi (HwBR), was solved in two crystal forms. One crystal form, refined to 1.85 Å resolution, contains a trimer in the asymmetric unit, whereas another contains an antiparallel dimer was refined at 2.58 Å. HwBR could not be classified into any existing subgroup of archaeal BR proteins based on the protein sequence phylogenetic tree, and it showed unique absorption spectral stability when exposed to low pH values. All structures showed a unique hydrogen-bonding network between Arg(82) and Thr(201), linking the BC and FG loops to shield the retinal-binding pocket in the interior from the extracellular environment. This result was supported by R82E mutation that attenuated the optical stability. The negatively charged cytoplasmic side and the Arg(82)-Thr(201) hydrogen bond may play an important role in the proton translocation trend in HwBR under acidic conditions. Our findings have unveiled a strategy adopted by BR proteins to solidify their defenses against unfavorable environments and maintain their optical properties associated with proton pumping.

Model-Free Spectral Density Mapping Applied to Dynamics of Rhodopsin in Solid-State NMR Spectroscopy

Crystal structures of rhodopsin are available, yet details of the activation mechanism remain unknown [1,2]. We applied solid-state 2H NMR to investigate structural and dynamical changes occurring in the process of rhodopsin activation. From the 2H NMR spectra, molecular mobility can be obtained by calculating the segmental order parameters from the residual quadrupolar couplings (RQCs). Moreover 2H nuclear spin relaxation rates related to the dynamics can be measured together with the RQCs [2]. Site-specific 2H labels were introduced into different methyl groups of retinal, and relaxation rate measurements were performed as a function of temperature (−30 to −150°C) [3]. Model-free analysis employed an irreducible representation of the combined 2H NMR line shape and relaxation data. Fluctuations of the irreducible components with respect to the average values are characterized by the individual spectral densities of motion evaluated at characteristic frequencies: J0(0), J1(ω0), and J2(2ω0), where ω0 is the nuclear resonance frequency [4]. Differences in the spectral densities manifest details of the methyl group motions within the retinal binding pocket at low temperature. At the high temperature limit, J1(ω0) and J2(2ω0) are insensitive to details of motion and collapse to a universal curve, thus substantiating the validity of the model-free analysis. Further analysis of J1(ω0) and J2(2ω0) involved simultaneous temperature-dependent fitting in terms of both diffusion and jump models for the methyl group dynamics. We conclude that spectral density analysis in terms of fluctuations of nuclear spin Hamiltonian will help us understand the activation mechanism and molecular dynamics of rhodopsin and related G protein-coupled receptors.[1] A.V. Struts et al. (2011) PNAS 108, 8263-8268. [2] M.F. Brown et al. (2010) BBA 1798, 177-193. [3] A.V. Struts et al. (2011) NSMB 18, 392-394. [4] M.F. Brown (1982) JCP 77, 1576-1599.

Conopeptide ρ-TIA Defines a New Allosteric Site on the Extracellular Surface of the α1B-Adrenoceptor

The G protein-coupled receptor (GPCR) superfamily is an important drug target that includes over 1000 membrane receptors that functionally couple extracellular stimuli to intracellular effectors. Despite the potential of extracellular surface (ECS) residues in GPCRs to interact with subtype-specific allosteric modulators, few ECS pharmacophores for class A receptors have been identified. Using the turkey β(1)-adrenergic receptor crystal structure, we modeled the α(1B)-adrenoceptor (α(1B)-AR) to help identify the allosteric site for ρ-conopeptide TIA, an inverse agonist at this receptor. Combining mutational radioligand binding and inositol 1-phosphate signaling studies, together with molecular docking simulations using a refined NMR structure of ρ-TIA, we identified 14 residues on the ECS of the α(1B)-AR that influenced ρ-TIA binding. Double mutant cycle analysis and docking confirmed that ρ-TIA binding was dominated by a salt bridge and cation-π between Arg-4-ρ-TIA and Asp-327 and Phe-330, respectively, and a T-stacking-π interaction between Trp-3-ρ-TIA and Phe-330. Water-bridging hydrogen bonds between Asn-2-ρ-TIA and Val-197, Trp-3-ρ-TIA and Ser-318, and the positively charged N terminus and Glu-186, were also identified. These interactions reveal that peptide binding to the ECS on transmembrane helix 6 (TMH6) and TMH7 at the base of extracellular loop 3 (ECL3) is sufficient to allosterically inhibit agonist signaling at a GPCR. The ligand-accessible ECS residues identified provide the first view of an allosteric inhibitor pharmacophore for α(1)-adrenoceptors and mechanistic insight and a new set of structural constraints for the design of allosteric antagonists at related GPCRs.

Role of rhodopsin N-terminus in structure and function of rhodopsin-bitter taste receptor chimeras

The bitter taste receptors (T2Rs) belong to the G protein-coupled receptor (GPCR) superfamily. In humans, bitter taste sensation is mediated by 25 T2Rs. Structure–function studies on T2Rs are impeded by the low-level expression of these receptors. Different lengths of rhodopsin N-terminal sequence inserted at the N-terminal region of T2Rs are commonly used to express these receptors in heterologous systems. While the additional sequences were reported, to enhance the expression of the T2Rs, the local structural perturbations caused by these sequences and its effect on receptor function or allosteric ligand binding were not characterized. In this study, we elucidated how different lengths of rhodopsin N-terminal sequence effect the structure and function of the bitter taste receptor, T2R4. Guided by molecular models of T2R4 built using a rhodopsin crystal structure as template, we constructed chimeric T2R4 receptors containing the rhodopsin N-terminal 33 and 38 amino acids. The chimeras were functionally characterized using calcium imaging, and receptor expression was determined by flow cytometry. Our results show that rhodopsin N-terminal 33 amino acids enhance expression of T2R4 by 2.5-fold and do not cause perturbations in the receptor structure.

Structure and activation of rhodopsin

Rhodopsin is the first G-protein-coupled receptor (GPCR) with its three-dimensional structure solved by X-ray crystallography. The crystal structure of rhodopsin has revealed the molecular mechanism of photoreception and signal transduction in the visual system. Although several other GPCR crystal structures have been reported over the past few years, the rhodopsin structure remains an important model for understanding the structural and functional characteristics of other GPCRs. This review summarizes the structural features, the photoactivation, and the G protein signal transduction of rhodopsin.

Molecular Simulations Illuminate Rhodopsin Activation Based on New Crystal Structures

The rhodopsin proteolipid system was modeled through all-atom molecular dynamics (MD) simulations on the microsecond timescale and compared to experimental 2H NMR data. The post-isomerization behavior of the covalently bound ligand, retinal, was tested for two independent models: (i) the counterion-switch (neutral binding pocket) and (ii) complex-counterion (negative binding pocket) [1]. Each model leads to distinct geometrical rearrangements, with direct implications for interpretation of recent rhodopsin crystal structures [2,3]. The distinctive feature of the counterion-switch simulation entails fluctuations of the C11=C12-C13=C14 dihedral angle. These motions are correlated with changes in the C5-, C9-, and C13-methyl group orientations, and result in a long-axis flip of the polyene chain within the binding pocket of rhodopsin. In contrast, the complex-counterion simulation produced retinal fluctuations at the C7=C8-C9=C10 dihedral. This facilitates stabilization of the methyl group orientations (≈60° with respect to the membrane normal), consistent with 2H NMR results for the Meta I state [4]. Recently, a putative structure of the fully-activated Meta II state revealed a long-axis flip of the retinylidene chain relative to its orientation in the dark state [2]. Our simulations show that electrostatic changes to the rhodopsin binding pocket lead to alternate pathways of retinal conformational release. Agreement between simulation and spectroscopy indicates that the retinylidene flip may only occur in the Meta I ↔ Meta II transition. These simulations provide an essential framework for interpreting molecular snapshots (crystal structures) of membrane protein activation, illuminating how small-scale changes in a GPCR binding pocket can affect large-scale membrane protein-lipid bilayer dynamics.[1] K. Martinez-Mayorga et al. (2006) JACS 128:16502.[2] H.-W. Choe et al. (2011) Nature 471:651.[3] J. Standfuss et al. (2011) Nature 471:656.[4] G.F.J. Salgado et al. (2006) JACS 128:11067.

Comparative modeling of human kappa opioid receptor and docking analysis with the peptide YFa

The kappa opioid receptor belongs to the super family of G protein – coupled receptors that are of utmost significance in the development of potent analgesic drugs for the treatment of severe pain. An accurate evaluation of the ligand binding pathways into this receptor at molecular level may play a key role in the design of new molecules with more desirable properties and reduced side effects. In this study, homology model of the human kappa opioid receptor was developed by MODELLER using the X-ray crystal structure of bovine rhodopsin as template. Initial structure of the receptor was refined computationally with energy minimization and molecular dynamics simulation at 300 K in a pre-equilibrated phospholipid bilayer by GROMACS. The Met-enkaphalin-Arg-Phe based opioid peptide YFa (YGGFMKKKFMRF) designed and characterized by our laboratory was docked into the optimized model and the critical amino acids responsible for binding were identified. A number of low energy binding poses of YFa with the receptor were assessed after the molecular docking in which the peptide was observed to interact with the receptor's extracellular amino acids through hydrogen bonds. The human kappa opioid receptor model optimized in a phospholipid bilayer should provide a good starting point for further characterization of the binding modes of other opioid ligands. Furthermore, the biologically favorable molecular interactions between YFa and human kappa opioid receptor observed by our study might be able to justify the specificity of this peptide.

Homology modelling of metabotropic glutamate receptor 2

Many studies show involvement of metabotropic glutamate receptors (mGluRs) in synaptic excitation transudation. The mGluR family consists of eight proteins divided into three groups corresponding to sequence similarities, pharmacology and physiological role. These groups are: I (mGluR1, -5), II (mGluR2, -3) and III (mGluR4, -6, -7, -8). Group II lies in field of our interest due to its potential as therapeutic target for stroke and pain drugs. Primary goal of this research is to create viable virtual model of transmembrane domain of mGluR2 receptor capable of binding reference ligands. This model will be used for further research. Our approach is based on homology modeling. Rhodopsin crystal structure has been used as a template for creating mGluR2 models. Due to inconsistencies between sequence alignments found in literature our alignment has been prepared basing on experimental secondary structure prediction for mGluR1 and mGluR3 [1]. So created models were then tested against available mutational data [2,3] and by flexible docking of known active/inactive compounds.

Homology modeling of human CCR5 and analysis of its binding properties through molecular docking and molecular dynamics simulation

In this study, homology modeling, molecular docking and molecular dynamics simulation were performed to explore structural features and binding mechanism of some inhibitors of chemokine receptor type 5 (CCR5), and to construct a model for designing new CCR5 inhibitors for preventing HIV attachment to the host cell. A homology modeling procedure was employed to construct a 3D model of CCR5. For this procedure, the X-ray crystal structure of bovine rhodopsin (1F88A) at 2.80Å resolution was used as template. After inserting the constructed model into a hydrated lipid bilayer, a 20ns molecular dynamics (MD) simulation was performed on the whole system. After reaching the equilibrium, twenty-four CCR5 inhibitors were docked in the active site of the obtained model. The binding models of the investigated antagonists indicate the mechanism of binding of the studied compounds to the CCR5 obviously. Moreover, 3D pictures of inhibitor–protein complex provided precious data regarding the binding orientation of each antagonist into the active site of this protein. One additional 20ns MD simulation was performed on the initial structure of the CCR5–ligand 21 complex, resulted from the previous docking calculations, embedded in a hydrated POPE bilayer to explore the effects of the presence of lipid bilayer in the vicinity of CCR5–ligand complex. This article is part of a Special Issue entitled Protein translocation across or insertion into membranes

Recent Advances in Structure-Based Virtual Screening of G-Protein Coupled Receptors

In addition to the rhodopsin crystal structure, high-resolution crystal structures of ligand-mediated G-protein-coupled receptors (GPCRs) have recently become available, and these have become attractive templates for developing homology models of several GPCRs of therapeutic interest. These crystal structures and the homology models derived from them have provided significant insights into ligand-receptor interactions. Moreover, several studies have demonstrated that the structural models are indeed suitable for virtual screening of compound databases to identify new ligands for various GPCRs. Recent examples of such virtual screening against GPCRs are discussed in this review.

Characterization of species-related differences in the pharmacology of tachykinin NK receptors 1, 2 and 3

Tachykinin NK receptors (NKRs) differ to a large degree among species with respect to their affinities for small molecule antagonists. The aims of the present study were to clone NKRs from gerbil (NK2R and NK3R) and dog (NK1R, NK2R and NK3R) in which the sequence was previously unknown and to investigate the potency of several NKR antagonists at all known human, dog, gerbil and rat NKRs.The NKR protein coding sequences were cloned and expressed in CHO cells. The inhibitory concentrations of selective and non-selective NKR antagonists were determined by inhibition of agonist-induced mobilization of intracellular Ca2+. Receptor homology models were constructed based on the rhodopsin crystal structure to investigate and identify the antagonist binding sites and interaction points in the transmembrane (TM) regions of the NKRs.Data collected using the cloned dog NK1R confirmed that the dog NK1R displays similar pharmacology as the human and the gerbil NK1R, but differs greatly from the mouse and the rat NK1R. Despite species-related amino acid (AA) differences located close to the antagonist binding pocket of the NK2R, they did not affect the potency of the antagonists ZD6021 and saredutant. Two AA differences located close to the antagonist binding site of NK3R likely influence the NK3R antagonist potency, explaining the 3–10-fold decrease in potency observed for the rat NK3R. For the first time, detailed pharmacological experiments in vitro with cloned NKRs demonstrate that not only human, but also dog and gerbil NKR displays similar antagonist pharmacology while rat diverges significantly with respect to NK1R and NK3R.

The Green-absorbing Drosophila Rh6 Visual Pigment Contains a Blue-shifting Amino Acid Substitution That Is Conserved in Vertebrates

The molecular mechanisms that regulate invertebrate visual pigment absorption are poorly understood. Through sequence analysis and functional investigation of vertebrate visual pigments, numerous amino acid substitutions important for this adaptive process have been identified. Here we describe a serine/alanine (S/A) substitution in long wavelength-absorbing Drosophila visual pigments that occurs at a site corresponding to Ala-292 in bovine rhodopsin. This S/A substitution accounts for a 10-17-nm absorption shift in visual pigments of this class. Additionally, we demonstrate that substitution of a cysteine at the same site, as occurs in the blue-absorbing Rh5 pigment, accounts for a 4-nm shift. Substitutions at this site are the first spectrally significant amino acid changes to be identified for invertebrate pigments sensitive to visible light and are the first evidence of a conserved tuning mechanism in vertebrate and invertebrate pigments of this class.

Active Sites for Retinal Binding to Bovine Rhodopsin

Rhodopsin is a membrane protein and its retinal (RET) active binding sites are related to the process of vision and the pathology of some ophthalmic ailments. Based on the bovine rhodopsin crystal structure (PDB code: 1U19), computations were performed using density functional theory to explore the interaction and binding energies between the RET-Lys296 residue and each of the 30 amino acid residues arranged in a sphere with 0.6 nm radius around a RET molecule. Results show that Glu113, Glu181 and Glu122 residues are the active binding sites for the protonated RET-Lys296 residue and that their binding energies are -333.38, -205.67 and -194.56 kJ·mol -1, respectively. They each have one negative charge to interact with the protonated RET-Lys296 residue through a strong electrostatic interaction. Other residues Ala292, Cys187, Phe293, Pro291 and Trp265 have smaller binding energies with the protonated RET-Lys296 residue at the 1U19 protein. When the RET-Lys296 residue is deprotonated, the interactions mentioned above disappear therefore to promote the dissociation of retinal from rhodopsin. Our results demonstrate that two crystal H2O molecules that form hydrogen bonds to Glu113 and Glu181 residues also play an important role in stabilizing the RET-Lys296 residue.

Activation of the μ Opioid Receptor Involves Conformational Rearrangements of Multiple Transmembrane Domains

We previously demonstrated that D3.49(164)Y or T6.34(279)K mutation in the rat mu opioid receptor (MOPR) resulted in agonist-independent activation. Here, we identified the cysteine(s) within the transmembrane domains (TMs) of the D3.49(164)Y mutant that became accessible in the binding-site crevice by use of methanethiosulfonate ethylammonium (MTSEA) and inferred conformational changes associated with receptor activation. While the C7.38(321)S mutant was insensitive to MTSEA, the D3.49(164)Y/C7.38(321)S mutant showed similar sensitivity as the D3.49(164)Y, suggesting that, in the D3.49(164)Y mutant, C7.38(321) becomes inaccessible while other cysteines are accessible in the binding-site crevice. Each of the other seven cysteines in the TMs was mutated to serine on the background of D3.49(164)Y/C7.38(321)S, and the resulting triple mutants were evaluated for [3H]diprenorphine and [d-Ala2,NMe-Phe4,Gly5-ol]-enkephalin (DAMGO) binding and effect of MTSEA on [3H]diprenorphine binding. The D3.49(164)Y/C7.38(321)S mutant and the triple mutants, except the C6.47(292)S triple mutant, retained similar affinities for [3H]diprenorphine and DAMGO as the D3.49(164)Y mutant. The second-order rate constants for MTSEA reactions showed that C3.44(159)S, C4.48(190)S, C5.41(235)S, and C7.47(330)S significantly reduced sensitivity to MTSEA, compared with the D3.49(164)Y/C7.38(321)S. These results suggest that the four cysteines may be rotated and/or tilted to become accessible. While the D3.49(164)Y/C7.38(321)S was similarly sensitive to MTSEA as the D3.49(164)Y mutant, the T6.34(279)K/C7.38(321)S was much less sensitive to MTSEA than the T6.34(279)K mutant, suggesting that the two constitutively active mutants assume different conformations and/or possess different dynamic properties. Molecular models of the MOPR monomer and homodimer, using the crystal structures of rhodopsin, the beta2-adrenergic receptor, and the ligand-free opsin, which contains several features characteristic of the active state, were employed to analyze these experimental results in a structural context.

Heterologous GPCR Expression: A Bottleneck to Obtaining Crystal Structures

G protein-coupled receptors (GPCRs) are an important, medically relevant class of integral membrane proteins. Laboratories throughout all disciplines of science devote time and energy into developing practical methods for the discovery, isolation, and characterization of these proteins. Since the crystal structure of rhodopsin was solved 6 years ago, the race to determine high-resolution structures of more GPCRs has gained momentum. Since certain GPCRs are currently produced at sufficient levels for X-ray crystallography trials, it is speculated that heterologous expression of GPCRs may no longer be a bottleneck in obtaining crystal structures. This Review focuses on the current approaches in heterologous expression of GPCRs and explores the problems associated with obtaining crystal structures from GPCRs expressed in different systems. Although milligram amounts of certain GPCRs are attainable, the majority of GPCRs are still either produced at very low levels or not at all. Developing reliable expression techniques for GPCRs is still a major priority for the structural characterization of GPCRs.

Simulations of a G protein-coupled receptor homology model predict dynamic features and a ligand binding site

A computational approach to predict structures of rhodopsin-like G protein-coupled receptors (GPCRs) is presented and evaluated by comparison to the X-ray structural models. By combining sequence alignment, the rhodopsin crystal structure, and point mutation data on the β2 adrenoreceptor (b2ar), we predict a (−)-epinephrine-bound computational model of the β2 adrenoreceptor. The model is evaluated by molecular dynamics simulations and by comparison with the recent X-ray structures of b2ar. The overall correspondence between the predicted and the X-ray structural model is high. Especially the prediction of the ligand binding site is accurate. This shows that the proposed dynamic homology modelling approach can be used to create reasonable models for the understanding of structure and dynamics of other rhodopsin-like GPCRs.