1
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Hofmann KP, Lamb TD. Rhodopsin, light-sensor of vision. Prog Retin Eye Res 2023; 93:101116. [PMID: 36273969 DOI: 10.1016/j.preteyeres.2022.101116] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/20/2022] [Accepted: 08/22/2022] [Indexed: 11/06/2022]
Abstract
The light sensor of vertebrate scotopic (low-light) vision, rhodopsin, is a G-protein-coupled receptor comprising a polypeptide chain with bound chromophore, 11-cis-retinal, that exhibits remarkable physicochemical properties. This photopigment is extremely stable in the dark, yet its chromophore isomerises upon photon absorption with 70% efficiency, enabling the activation of its G-protein, transducin, with high efficiency. Rhodopsin's photochemical and biochemical activities occur over very different time-scales: the energy of retinaldehyde's excited state is stored in <1 ps in retinal-protein interactions, but it takes milliseconds for the catalytically active state to form, and many tens of minutes for the resting state to be restored. In this review, we describe the properties of rhodopsin and its role in rod phototransduction. We first introduce rhodopsin's gross structural features, its evolution, and the basic mechanisms of its activation. We then discuss light absorption and spectral sensitivity, photoreceptor electrical responses that result from the activity of individual rhodopsin molecules, and recovery of rhodopsin and the visual system from intense bleaching exposures. We then provide a detailed examination of rhodopsin's molecular structure and function, first in its dark state, and then in the active Meta states that govern its interactions with transducin, rhodopsin kinase and arrestin. While it is clear that rhodopsin's molecular properties are exquisitely honed for phototransduction, from starlight to dawn/dusk intensity levels, our understanding of how its molecular interactions determine the properties of scotopic vision remains incomplete. We describe potential future directions of research, and outline several major problems that remain to be solved.
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Affiliation(s)
- Klaus Peter Hofmann
- Institut für Medizinische Physik und Biophysik (CC2), Charité, and, Zentrum für Biophysik und Bioinformatik, Humboldt-Unversität zu Berlin, Berlin, 10117, Germany.
| | - Trevor D Lamb
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia.
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2
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Ancient whale rhodopsin reconstructs dim-light vision over a major evolutionary transition: Implications for ancestral diving behavior. Proc Natl Acad Sci U S A 2022; 119:e2118145119. [PMID: 35759662 PMCID: PMC9271160 DOI: 10.1073/pnas.2118145119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Cetaceans are fully aquatic mammals that descended from terrestrial ancestors, an iconic evolutionary transition characterized by adaptations for underwater foraging via breath-hold diving. Although the evolutionary history of this specialized behavior is challenging to reconstruct, coevolving sensory systems may offer valuable clues. The dim-light visual pigment, rhodopsin, which initiates phototransduction in the rod photoreceptors of the eye, has provided insight into the visual ecology of depth in several aquatic vertebrate lineages. Here, we use ancestral sequence reconstruction and protein resurrection experiments to quantify light-activation metrics in rhodopsin pigments from ancestors bracketing the cetacean terrestrial-to-aquatic transition. By comparing multiple reconstruction methods on a broadly sampled cetartiodactyl species tree, we generated highly robust ancestral sequence estimates. Our experimental results provide direct support for a blue-shift in spectral sensitivity along the branch separating cetaceans from terrestrial relatives. This blue-shift was 14 nm, resulting in a deep-sea signature (λmax = 486 nm) similar to many mesopelagic-dwelling fish. We also discovered that the decay rates of light-activated rhodopsin increased in ancestral cetaceans, which may indicate an accelerated dark adaptation response typical of deeper-diving mammals. Because slow decay rates are thought to help sequester cytotoxic photoproducts, this surprising result could reflect an ecological trade-off between rod photoprotection and dark adaptation. Taken together, these ancestral shifts in rhodopsin function suggest that some of the first fully aquatic cetaceans could dive into the mesopelagic zone (>200 m). Moreover, our reconstructions indicate that this behavior arose before the divergence of toothed and baleen whales.
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3
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Guérin DMA, Digilio A, Branda MM. Dimeric Rhodopsin R135L Mutant-Transducin-like Complex Sheds Light on Retinitis Pigmentosa Misfunctions. J Phys Chem B 2021; 125:12958-12971. [PMID: 34793169 DOI: 10.1021/acs.jpcb.1c06348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhodopsin (RHO) is a light-sensitive pigment in the retina and the main prototypical protein of the G-protein-coupled receptor (GCPR) family. After receiving a light stimulus, RHO and its cofactor retinylidene undergo a series of structural changes that initiate an intricate transduction mechanism. Along with RHO, other partner proteins play key roles in the signaling pathway. These include transducin, a GTPase, kinases that phosphorylate RHO, and arrestin (Arr), which ultimately stops the signaling process and promotes RHO regeneration. A large number of RHO genetic mutations may lead to very severe retinal dysfunction and eventually to impaired dark adaptation disease called autosomal dominant retinitis pigmentosa (adRP). In this study, we used molecular dynamics (MD) simulations to evaluate the different behaviors of the dimeric form of wild-type RHO (WT dRHO) and its mutant at position 135 of arginine to leucine (dR135L), both in the free (noncomplexed) and in complex with the transducin-like protein (Gtl). Gtl is a heterotrimeric model composed of a mixture of human and bovine G proteins. Our calculations allow us to explain how the mutation causes structural changes in the RHO dimer and how this can affect the signal that transducin generates when it is bound to RHO. Moreover, the structural modifications induced by the R135L mutation can also account for other misfunctions observed in the up- and downstream signaling pathways. The mechanism of these dysfunctions, together with the transducin activity reduction, provides structure-based explanations of the impairment of some key processes that lead to adRP.
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Affiliation(s)
- Diego M A Guérin
- Department of Biochemistry and Molecular Biology, University of the Basque Country (EHU) and Instituto Biofisika (CSIC, UPV/EHU), Barrio Sarriena S/N, 48940 Leioa, Vizcaya, Spain
| | - Ayelen Digilio
- Department of Physics, National University of San Luis (UNSL), Av. Ejército de los Andes 950, 5700 San Luis, Argentina
| | - María Marta Branda
- Institute of Applied Physics (CONICET-UNSL), Av. Ejercito de los Andes 950, 5700 San Luis, Argentina
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4
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Katayama K, Takeyama Y, Enomoto A, Imai H, Kandori H. Disruption of Hydrogen-Bond Network in Rhodopsin Mutations Cause Night Blindness. J Mol Biol 2020; 432:5378-5389. [PMID: 32795534 DOI: 10.1016/j.jmb.2020.08.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/14/2020] [Accepted: 08/04/2020] [Indexed: 01/09/2023]
Abstract
Rhodopsin is the photosensitive protein, which binds to 11-cis-retinal as its chromophore. In the dark, rhodopsin exists as a stable complex between the opsin moiety and 11-cis-retinal. The absorption of a light photon converts 11-cis-retinal to all-trans-retinal and initiates our vision. As a result, the increase in the rate of dark activation of rhodopsin reduces its photosensitivity resulting in night blindness. The mutations, G90D and T94I are night blindness-causing mutations that exhibit completely different physicochemical characteristics associated with the dark activation of rhodopsin, such as a high rate of thermal isomerization of 11-cis-retinal and a slow pigment regeneration. To elucidate the molecular mechanism by which G90D and T94I mutations affect rhodopsin dark activation and regeneration, we performed light-induced difference FTIR spectroscopy on dark and primary photo-intermediate states of G90D and T94I mutants. The FTIR spectra clearly show that both charged G90D and hydrophobic T94I mutants alter the H-bond network at the Schiff base region of the chromophore, which weakens the electrostatic interaction with Glu113 counterion. Our results further show an altered water-mediated H-bond network around the central transmembrane region of mutant rhodopsin, which is reminiscent of the active Meta-II state. This altered water-mediated H-bond network may cause thermal isomerization of the chromophore and facilitate rhodopsin dark activation.
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Affiliation(s)
- Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - Yuri Takeyama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Akiko Enomoto
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hiroo Imai
- Primate Research Institute, Kyoto University, Inuyama 484-8506, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
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5
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Ciancetta A, Rubio P, Lieberman DI, Jacobson KA. A 3 adenosine receptor activation mechanisms: molecular dynamics analysis of inactive, active, and fully active states. J Comput Aided Mol Des 2019; 33:983-996. [PMID: 31758354 DOI: 10.1007/s10822-019-00246-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 11/02/2019] [Indexed: 12/12/2022]
Abstract
We investigated the Gi-coupled A3 adenosine receptor (A3AR) activation mechanism by running 7.2 µs of molecular dynamics (MD) simulations. Based on homology to G protein-coupled receptor (GPCR) structures, three constitutively active mutant (CAM) and the wild-type (WT) A3ARs in the apo form were modeled. Conformational signatures associated with three different receptor states (inactive R, active R*, and bound to Gi protein mimic) were predicted by analyzing and comparing the CAMs with WT receptor and by considering site-directed mutagenesis data. Detected signatures that were correlated with receptor state included: Persistent salt-bridges involving key charged residues for activation (including a novel, putative ionic lock), rotameric state of conserved W6.48, and Na+ ions and water molecules present. Active-coupled state signatures similar to the X-ray structures of β2 adrenergic receptor-Gs protein and A2AAR-mini-Gs and the recently solved cryo-EM A1AR-Gi complexes were found. Our MD analysis suggests that constitutive activation might arise from the D1073.49-R1083.50 ionic lock destabilization in R and the D1073.49-R1113.53 ionic lock stabilization in R* that presumably lowers the energy barrier associated with an R to R* transition. This study provides new opportunities to understand the underlying interactions of different receptor states of other Gi protein-coupled GPCRs.
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Affiliation(s)
- Antonella Ciancetta
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
- Sygnature Discovery, Nottingham, UK.
| | - Priscila Rubio
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David I Lieberman
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
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6
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Sahu B, Shah S, Prabhudesai K, Contini A, Idicula-Thomas S. Discovery of small molecule binders of human FSHR(TMD) with novel structural scaffolds by integrating structural bioinformatics and machine learning algorithms. J Mol Graph Model 2019; 89:156-166. [DOI: 10.1016/j.jmgm.2019.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 01/30/2019] [Accepted: 02/01/2019] [Indexed: 02/08/2023]
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7
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Katayama K, Gulati S, Ortega JT, Alexander NS, Sun W, Shenouda MM, Palczewski K, Jastrzebska B. Specificity of the chromophore-binding site in human cone opsins. J Biol Chem 2019; 294:6082-6093. [PMID: 30770468 DOI: 10.1074/jbc.ra119.007587] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/13/2019] [Indexed: 01/21/2023] Open
Abstract
The variable composition of the chromophore-binding pocket in visual receptors is essential for vision. The visual phototransduction starts with the cis-trans isomerization of the retinal chromophore upon absorption of photons. Despite sharing the common 11-cis-retinal chromophore, rod and cone photoreceptors possess distinct photochemical properties. Thus, a detailed molecular characterization of the chromophore-binding pocket of these receptors is critical to understanding the differences in the photochemistry of vision between rods and cones. Unlike for rhodopsin (Rh), the crystal structures of cone opsins remain to be determined. To obtain insights into the specific chromophore-protein interactions that govern spectral tuning in human visual pigments, here we harnessed the unique binding properties of 11-cis-6-membered-ring-retinal (11-cis-6mr-retinal) with human blue, green, and red cone opsins. To unravel the specificity of the chromophore-binding pocket of cone opsins, we applied 11-cis-6mr-retinal analog-binding analyses to human blue, green, and red cone opsins. Our results revealed that among the three cone opsins, only blue cone opsin can accommodate the 11-cis-6mr-retinal in its chromophore-binding pocket, resulting in the formation of a synthetic blue pigment (B6mr) that absorbs visible light. A combination of primary sequence alignment, molecular modeling, and mutagenesis experiments revealed the specific amino acid residue 6.48 (Tyr-262 in blue cone opsins and Trp-281 in green and red cone opsins) as a selectivity filter in human cone opsins. Altogether, the results of our study uncover the molecular basis underlying the binding selectivity of 11-cis-6mr-retinal to the cone opsins.
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Affiliation(s)
- Kota Katayama
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106; Department of Life Science and Applied Chemistry, Showa-ku, Nagoya 466-8555, Japan; OptoBio Technology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Sahil Gulati
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697
| | - Joseph T Ortega
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Nathan S Alexander
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Wenyu Sun
- Polgenix Inc., Cleveland, Ohio 44106
| | - Marina M Shenouda
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Krzysztof Palczewski
- Gavin Herbert Eye Institute and the Department of Ophthalmology, University of California, Irvine, California 92697; Polgenix Inc., Cleveland, Ohio 44106.
| | - Beata Jastrzebska
- From the Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106.
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8
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Dungan SZ, Chang BSW. Epistatic interactions influence terrestrial-marine functional shifts in cetacean rhodopsin. Proc Biol Sci 2018; 284:rspb.2016.2743. [PMID: 28250185 DOI: 10.1098/rspb.2016.2743] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 02/03/2017] [Indexed: 12/12/2022] Open
Abstract
Like many aquatic vertebrates, whales have blue-shifting spectral tuning substitutions in the dim-light visual pigment, rhodopsin, that are thought to increase photosensitivity in underwater environments. We have discovered that known spectral tuning substitutions also have surprising epistatic effects on another function of rhodopsin, the kinetic rates associated with light-activated intermediates. By using absorbance spectroscopy and fluorescence-based retinal release assays on heterologously expressed rhodopsin, we assessed both spectral and kinetic differences between cetaceans (killer whale) and terrestrial outgroups (hippo, bovine). Mutation experiments revealed that killer whale rhodopsin is unusually resilient to pleiotropic effects on retinal release from key blue-shifting substitutions (D83N and A292S), largely due to a surprisingly specific epistatic interaction between D83N and the background residue, S299. Ancestral sequence reconstruction indicated that S299 is an ancestral residue that predates the evolution of blue-shifting substitutions at the origins of Cetacea. Based on these results, we hypothesize that intramolecular epistasis helped to conserve rhodopsin's kinetic properties while enabling blue-shifting spectral tuning substitutions as cetaceans adapted to aquatic environments. Trade-offs between different aspects of molecular function are rarely considered in protein evolution, but in cetacean and other vertebrate rhodopsins, may underlie multiple evolutionary scenarios for the selection of specific amino acid substitutions.
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Affiliation(s)
- Sarah Z Dungan
- Department Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
| | - Belinda S W Chang
- Department Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2 .,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, ON, Canada M5S 3B2.,Department Cell and Systems Biology, University of Toronto, Toronto, ON, Canada M5S 3G5
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9
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Salas-Estrada LA, Leioatts N, Romo TD, Grossfield A. Lipids Alter Rhodopsin Function via Ligand-like and Solvent-like Interactions. Biophys J 2018; 114:355-367. [PMID: 29401433 PMCID: PMC5984976 DOI: 10.1016/j.bpj.2017.11.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 09/20/2017] [Accepted: 11/09/2017] [Indexed: 10/18/2022] Open
Abstract
Rhodopsin, a prototypical G protein-coupled receptor, is a membrane protein that can sense dim light. This highly effective photoreceptor is known to be sensitive to the composition of its lipidic environment, but the molecular mechanisms underlying this fine-tuned modulation of the receptor's function and structural stability are not fully understood. There are two competing hypotheses to explain how this occurs: 1) lipid modulation occurs via solvent-like interactions, where lipid composition controls membrane properties like hydrophobic thickness, which in turn modulate the protein's conformational equilibrium; or 2) protein-lipid interactions are ligand-like, with specific hot spots and long-lived binding events. By analyzing an ensemble of all-atom molecular dynamics simulations of five different states of rhodopsin, we show that a local ordering effect takes place in the membrane upon receptor activation. Likewise, docosahexaenoic acid acyl tails and phosphatidylethanolamine headgroups behave like weak ligands, preferentially binding to the receptor in inactive-like conformations and inducing subtle but significant structural changes.
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Affiliation(s)
- Leslie A Salas-Estrada
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York
| | - Nicholas Leioatts
- Department of Theoretical and Computational Biophysics, Max Plank Institute for Biophysical Chemistry, Göttingen, Germany
| | - Tod D Romo
- Center for Integrated Research Computing, University of Rochester, Rochester, New York
| | - Alan Grossfield
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
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10
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Szundi I, Funatogawa C, Guo Y, Yan ECY, Kliger DS. Protein Sequence and Membrane Lipid Roles in the Activation Kinetics of Bovine and Human Rhodopsins. Biophys J 2017; 113:1934-1944. [PMID: 29117518 DOI: 10.1016/j.bpj.2017.08.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/26/2017] [Accepted: 08/28/2017] [Indexed: 12/17/2022] Open
Abstract
Rhodopsin is a G protein-coupled receptor found in the rod outer segments in the retina, which triggers a visual response under dim light conditions. Recently, a study of the late, microsecond-to-millisecond kinetics of photointermediates of the human and bovine rhodopsins in their native membranes revealed a complex, double-square mechanism of rhodopsin activation. In this kinetic scheme, the human rhodopsin exhibited more Schiff base deprotonation than bovine rhodopsin, which could arise from the ∼7% sequence difference between the two proteins, or from the difference between their membrane lipid environments. To differentiate between the effects of membrane and protein structure on the kinetics, the human and bovine rhodopsins were inserted into 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine lipid nanodiscs and the kinetics of activation at 15°C and pH 8.7 was investigated by time-resolved absorption spectroscopy and global kinetic analysis. For both proteins, the kinetics in nanodiscs shows the characteristics observed in the native membranes, and is described by a multisquare model with Schiff base deprotonation at the lumirhodopsin I intermediate stage. The results indicate that the protein sequence controls the extent of Schiff base deprotonation and accumulation of intermediates, and thus plays the main role in the different activation kinetics observed between human and bovine rhodopsins. The membrane lipid does have a minor role by modulating the timing of the kinetics, with the nanodisc environment leading to an earlier Schiff base deprotonation.
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Affiliation(s)
- Istvan Szundi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Chie Funatogawa
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Ying Guo
- Department of Chemistry, Yale University, New Haven, Connecticut
| | - Elsa C Y Yan
- Department of Chemistry, Yale University, New Haven, Connecticut
| | - David S Kliger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California.
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11
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Krumm BE, Lee S, Bhattacharya S, Botos I, White CF, Du H, Vaidehi N, Grisshammer R. Structure and dynamics of a constitutively active neurotensin receptor. Sci Rep 2016; 6:38564. [PMID: 27924846 PMCID: PMC5141500 DOI: 10.1038/srep38564] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/03/2016] [Indexed: 11/09/2022] Open
Abstract
Many G protein-coupled receptors show constitutive activity, resulting in the production of a second messenger in the absence of an agonist; and naturally occurring constitutively active mutations in receptors have been implicated in diseases. To gain insight into mechanistic aspects of constitutive activity, we report here the 3.3 Å crystal structure of a constitutively active, agonist-bound neurotensin receptor (NTSR1) and molecular dynamics simulations of agonist-occupied and ligand-free receptor. Comparison with the structure of a NTSR1 variant that has little constitutive activity reveals uncoupling of the ligand-binding domain from conserved connector residues, that effect conformational changes during GPCR activation. Furthermore, molecular dynamics simulations show strong contacts between connector residue side chains and increased flexibility at the intracellular receptor face as features that coincide with robust signalling in cells. The loss of correlation between the binding pocket and conserved connector residues, combined with altered receptor dynamics, possibly explains the reduced neurotensin efficacy in the constitutively active NTSR1 and a facilitated initial engagement with G protein in the absence of agonist.
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Affiliation(s)
- Brian E Krumm
- Membrane Protein Structure Function Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland 20852, United States
| | - Sangbae Lee
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, California 91010, United States
| | - Supriyo Bhattacharya
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, California 91010, United States
| | - Istvan Botos
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, United States
| | - Courtney F White
- Membrane Protein Structure Function Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland 20852, United States
| | - Haijuan Du
- Membrane Protein Structure Function Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland 20852, United States
| | - Nagarajan Vaidehi
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, California 91010, United States
| | - Reinhard Grisshammer
- Membrane Protein Structure Function Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland 20852, United States
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12
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Szundi I, Funatogawa C, Kliger DS. Complexity of Bovine Rhodopsin Activation Revealed at Low Temperature and Alkaline pH. Biochemistry 2016; 55:5095-105. [DOI: 10.1021/acs.biochem.6b00687] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Istvan Szundi
- Department
of Chemistry and
Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Chie Funatogawa
- Department
of Chemistry and
Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - David S. Kliger
- Department
of Chemistry and
Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, United States
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13
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van Hazel I, Dungan SZ, Hauser FE, Morrow JM, Endler JA, Chang BSW. A comparative study of rhodopsin function in the great bowerbird (Ptilonorhynchus nuchalis): Spectral tuning and light-activated kinetics. Protein Sci 2016; 25:1308-18. [PMID: 26889650 DOI: 10.1002/pro.2902] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 02/16/2016] [Accepted: 02/16/2016] [Indexed: 12/18/2022]
Abstract
Rhodopsin is the visual pigment responsible for initiating the phototransduction cascade in vertebrate rod photoreceptors. Although well-characterized in a few model systems, comparative studies of rhodopsin function, particularly for nonmammalian vertebrates are comparatively lacking. Bowerbirds are rare among passerines in possessing a key substitution, D83N, at a site that is otherwise highly conserved among G protein-coupled receptors. While this substitution is present in some dim-light adapted vertebrates, often accompanying another unusual substitution, A292S, its functional relevance in birds is uncertain. To investigate functional effects associated with these two substitutions, we use the rhodopsin gene from the great bowerbird (Ptilonorhynchus nuchalis) as a background for site-directed mutagenesis, in vitro expression and functional characterization. We also mutated these sites in two additional rhodopsins that do not naturally possess N83, chicken and bovine, for comparison. Both sites were found to contribute to spectral blue-shifts, but had opposing effects on kinetic rates. Substitutions at site 83 were found to primarily affect the kinetics of light-activated rhodopsin, while substitutions at site 292 had a larger impact on spectral tuning. The contribution of substitutions at site 83 to spectral tuning in particular depended on genetic background, but overall, the effects of substitutions were otherwise surprisingly additive, and the magnitudes of functional shifts were roughly similar across all three genetic backgrounds. By employing a comparative approach with multiple species, our study provides new insight into the joint impact of sites 83 and 292 on rhodopsin structure-function as well as their evolutionary significance for dim-light vision across vertebrates.
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Affiliation(s)
- Ilke van Hazel
- Department of Ecology and Evolutionary Biology, University of Toronto, Canada
| | - Sarah Z Dungan
- Department of Ecology and Evolutionary Biology, University of Toronto, Canada
| | - Frances E Hauser
- Department of Ecology and Evolutionary Biology, University of Toronto, Canada
| | - James M Morrow
- Department of Cell and Systems Biology, University of Toronto, Canada
| | - John A Endler
- Centre for Integrative Ecology, Deakin University, Australia
| | - Belinda S W Chang
- Department of Ecology and Evolutionary Biology, University of Toronto, Canada.,Department of Cell and Systems Biology, University of Toronto, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, Canada
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14
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Comparative sequence analyses of rhodopsin and RPE65 reveal patterns of selective constraint across hereditary retinal disease mutations. Vis Neurosci 2016; 33:e002. [DOI: 10.1017/s0952523815000322] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
AbstractRetinitis pigmentosa (RP) comprises several heritable diseases that involve photoreceptor, and ultimately retinal, degeneration. Currently, mutations in over 50 genes have known links to RP. Despite advances in clinical characterization, molecular characterization of RP remains challenging due to the heterogeneous nature of causal genes, mutations, and clinical phenotypes. In this study, we compiled large datasets of two important visual genes associated with RP: rhodopsin, which initiates the phototransduction cascade, and the retinoid isomerase RPE65, which regenerates the visual cycle. We used a comparative evolutionary approach to investigate the relationship between interspecific sequence variation and pathogenic mutations that lead to degenerative retinal disease. Using codon-based likelihood methods, we estimated evolutionary rates (dN/dS) across both genes in a phylogenetic context to investigate differences between pathogenic and nonpathogenic amino acid sites. In both genes, disease-associated sites showed significantly lower evolutionary rates compared to nondisease sites, and were more likely to occur in functionally critical areas of the proteins. The nature of the dataset (e.g., vertebrate or mammalian sequences), as well as selection of pathogenic sites, affected the differences observed between pathogenic and nonpathogenic sites. Our results illustrate that these methods can serve as an intermediate step in understanding protein structure and function in a clinical context, particularly in predicting the relative pathogenicity (i.e., functional impact) of point mutations and their downstream phenotypic effects. Extensions of this approach may also contribute to current methods for predicting the deleterious effects of candidate mutations and to the identification of protein regions under strong constraint where we expect pathogenic mutations to occur.
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15
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Abstract
We previously determined the structure of neurotensin receptor NTSR1 in an active-like conformation with six thermostabilizing mutations bound to the peptide agonist neurotensin. This receptor was unable to activate G proteins, indicating that the mutations restricted NTSR1 to relate agonist binding to G-protein activation. Here we analyse the effect of three of those mutations (E166A3.49, L310A6.37, F358A7.42) and present two structures of NTSR1 able to catalyse nucleotide exchange at Gα. The presence of F3587.42 causes the conserved W3216.48 to adopt a side chain orientation parallel to the lipid bilayer sealing the collapsed Na+ ion pocket and linking the agonist with residues in the lower receptor part implicated in GPCR activation. In the intracellular receptor half, the bulkier L3106.37 side chain dictates the position of R1673.50 of the highly conserved D/ERY motif. These residues, together with the presence of E1663.49 provide determinants for G-protein activation by NTSR1. The structural basis of how G-protein coupled receptors respond to unique stimuli remains poorly understood. Here, Krumm et al. present new structures of the neurotensin receptor and reveal insights into how ligand binding is linked to structural rearrangements associated with receptor activation.
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16
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Soriano-Ursúa MA, Trujillo-Ferrara JG, Arias-Montaño JA, Villalobos-Molina R. Insights into a defined secondary binding region on β-adrenoceptors and putative roles in ligand binding and drug design. MEDCHEMCOMM 2015. [DOI: 10.1039/c5md00011d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Putative roles of a secondary binding region shared among beta-adrenoceptors.
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Affiliation(s)
- M. A. Soriano-Ursúa
- Posgraduate and Research Section
- Escuela Superior de Medicina
- Instituto Politécnico Nacional
- Mexico City
- Mexico
| | - J. G. Trujillo-Ferrara
- Posgraduate and Research Section
- Escuela Superior de Medicina
- Instituto Politécnico Nacional
- Mexico City
- Mexico
| | - J. A. Arias-Montaño
- Departamento de Fisiología
- Biofísica y Neurociencias. Centro de Investigación y de Estudios Avanzados del IPN
- Mexico City
- Mexico
| | - R. Villalobos-Molina
- Unidad de Investigación en Biomedicina
- Facultad de Estudios Superiores Iztacala
- Universidad Nacional Autónoma de México
- Tlalnepantla
- Mexico
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