1
|
Wang F, Fernandez-Gonzalez P, Ramon E, Gomez-Gutierrez P, Morillo M, Garriga P. Effect of Trace Metal Ions on the Conformational Stability of the Visual Photoreceptor Rhodopsin. Int J Mol Sci 2023; 24:11231. [PMID: 37446409 DOI: 10.3390/ijms241311231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/15/2023] Open
Abstract
Trace metals are essential elements that play key roles in a number of biochemical processes governing human visual physiology in health and disease. Several trace metals, such as zinc, have been shown to play important roles in the visual phototransduction process. In spite of this, there has been little research conducted on the direct effect of trace metal elements on the visual photoreceptor rhodopsin. In the current study, we have determined the effect of several metal ions, such as iron, copper, chromium, manganese, and nickel, on the conformational stability of rhodopsin. To this aim, we analyzed, by means of UV-visible and fluorescence spectroscopic methods, the effects of these trace elements on the thermal stability of dark rhodopsin, the stability of its active Metarhodopsin II conformation, and its chromophore regeneration. Our results show that copper prevented rhodopsin regeneration and slowed down the retinal release process after illumination. In turn, Fe3+, but not Fe2+, increased the thermal stability of the dark inactive conformation of rhodopsin, whereas copper ions markedly decreased it. These findings stress the important role of trace metals in retinal physiology at the photoreceptor level and may be useful for the development of novel therapeutic strategies to treat retinal disease.
Collapse
Affiliation(s)
- Feifei Wang
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Pol Fernandez-Gonzalez
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Eva Ramon
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Patricia Gomez-Gutierrez
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Edifici ETSEIB, Av. Diagonal 647, 08028 Barcelona, Catalonia, Spain
| | - Margarita Morillo
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Pere Garriga
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| |
Collapse
|
2
|
What Makes GPCRs from Different Families Bind to the Same Ligand? Biomolecules 2022; 12:biom12070863. [PMID: 35883418 PMCID: PMC9313020 DOI: 10.3390/biom12070863] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 06/09/2022] [Accepted: 06/19/2022] [Indexed: 12/10/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of cell-surface receptor proteins with important functions in signal transduction and often serve as therapeutic drug targets. With the rapidly growing public data on three dimensional (3D) structures of GPCRs and GPCR-ligand interactions, computational prediction of GPCR ligand binding becomes a convincing option to high throughput screening and other experimental approaches during the beginning phases of ligand discovery. In this work, we set out to computationally uncover and understand the binding of a single ligand to GPCRs from several different families. Three-dimensional structural comparisons of the GPCRs that bind to the same ligand revealed local 3D structural similarities and often these regions overlap with locations of binding pockets. These pockets were found to be similar (based on backbone geometry and side-chain orientation using APoc), and they correlate positively with electrostatic properties of the pockets. Moreover, the more similar the pockets, the more likely a ligand binding to the pockets will interact with similar residues, have similar conformations, and produce similar binding affinities across the pockets. These findings can be exploited to improve protein function inference, drug repurposing and drug toxicity prediction, and accelerate the development of new drugs.
Collapse
|
3
|
Nonaka Y, Hanai S, Katayama K, Imai H, Kandori H. Unique Retinal Binding Pocket of Primate Blue-Sensitive Visual Pigment. Biochemistry 2020; 59:2602-2607. [PMID: 32567852 DOI: 10.1021/acs.biochem.0c00394] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The visual pigments of humans contain 11-cis retinal as the chromophore of light perception, and its photoisomerization to the all-trans form initiates visual excitation in our eyes. It is well-known that three isomeric states of retinal (11-cis, all-trans, and 9-cis) are in photoequilibrium at very low temperatures such as 77 K. Here we report the lack of formation of the 9-cis form in monkey blue (MB) at 77 K, as revealed by light-induced difference Fourier transform infrared spectroscopy. This indicates that the chromophore binding pocket of MB does not accommodate the 9-cis form, even though it accommodates the all-trans form by twisting the chromophore. Mutation of the blue-specific tyrosine at position 265 to tryptophan, which is highly conserved in other animal rhodopsins, led to formation of the 9-cis form in MB, suggesting that Y265 is one of the determinants of the unique photochemistry in blue pigments. We also found that 9-cis retinal does not bind to MB opsin, implying that the chromophore binding pocket does not accommodate the 9-cis form at physiological temperature. The unique property of MB is discussed on the basis of the results presented here.
Collapse
Affiliation(s)
- Yuki Nonaka
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Shunpei Hanai
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - 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
| | - 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
| |
Collapse
|
4
|
Srinivasan S, Guixà-González R, Cordomí A, Garriga P. Ligand Binding Mechanisms in Human Cone Visual Pigments. Trends Biochem Sci 2019; 44:629-639. [PMID: 30853245 DOI: 10.1016/j.tibs.2019.02.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/04/2019] [Accepted: 02/07/2019] [Indexed: 12/13/2022]
Abstract
Vertebrate vision starts with light absorption by visual pigments in rod and cone photoreceptor cells of the retina. Rhodopsin, in rod cells, responds to dim light, whereas three types of cone opsins (red, green, and blue) function under bright light and mediate color vision. Cone opsins regenerate with retinal much faster than rhodopsin, but the molecular mechanism of regeneration is still unclear. Recent advances in the area pinpoint transient intermediate opsin conformations, and a possible secondary retinal-binding site, as determinant factors for regeneration. In this Review, we compile previous and recent findings to discuss possible mechanisms of ligand entry in cone opsins, involving a secondary binding site, which may have relevant functional and evolutionary implications.
Collapse
Affiliation(s)
- Sundaramoorthy Srinivasan
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Rambla de Sant Nebridi 22, 08222 Terrassa, Spain
| | - Ramon Guixà-González
- Laboratori de Medicina Computational, Universitat Autonòma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Arnau Cordomí
- Laboratori de Medicina Computational, Universitat Autonòma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Pere Garriga
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya-Barcelona Tech, Rambla de Sant Nebridi 22, 08222 Terrassa, Spain.
| |
Collapse
|
5
|
Srinivasan S, Fernández-Sampedro MA, Morillo M, Ramon E, Jiménez-Rosés M, Cordomí A, Garriga P. Human Blue Cone Opsin Regeneration Involves Secondary Retinal Binding with Analog Specificity. Biophys J 2018; 114:1285-1294. [PMID: 29590586 PMCID: PMC5883618 DOI: 10.1016/j.bpj.2018.01.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Revised: 01/22/2018] [Accepted: 01/29/2018] [Indexed: 12/16/2022] Open
Abstract
Human color vision is mediated by the red, green, and blue cone visual pigments. Cone opsins are G-protein-coupled receptors consisting of an opsin apoprotein covalently linked to the 11-cis-retinal chromophore. All visual pigments share a common evolutionary origin, and red and green cone opsins exhibit a higher homology, whereas blue cone opsin shows more resemblance to the dim light receptor rhodopsin. Here we show that chromophore regeneration in photoactivated blue cone opsin exhibits intermediate transient conformations and a secondary retinoid binding event with slower binding kinetics. We also detected a fine-tuning of the conformational change in the photoactivated blue cone opsin binding site that alters the retinal isomer binding specificity. Furthermore, the molecular models of active and inactive blue cone opsins show specific molecular interactions in the retinal binding site that are not present in other opsins. These findings highlight the differential conformational versatility of human cone opsin pigments in the chromophore regeneration process, particularly compared to rhodopsin, and point to relevant functional, unexpected roles other than spectral tuning for the cone visual pigments.
Collapse
Affiliation(s)
| | | | | | - Eva Ramon
- Universitat Politècnica de Catalunya, Terrassa, Spain
| | - Mireia Jiménez-Rosés
- Unitat de Bioestadística Bellaterra, Laboratori de Medicina Computacional, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Arnau Cordomí
- Unitat de Bioestadística Bellaterra, Laboratori de Medicina Computacional, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Pere Garriga
- Universitat Politècnica de Catalunya, Terrassa, Spain.
| |
Collapse
|
6
|
Alexander NS, Katayama K, Sun W, Salom D, Gulati S, Zhang J, Mogi M, Palczewski K, Jastrzebska B. Complex binding pathways determine the regeneration of mammalian green cone opsin with a locked retinal analogue. J Biol Chem 2017; 292:10983-10997. [PMID: 28487362 DOI: 10.1074/jbc.m117.780478] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 05/04/2017] [Indexed: 01/09/2023] Open
Abstract
Phototransduction is initiated when the absorption of light converts the 11-cis-retinal chromophore to its all-trans configuration in both rod and cone vertebrate photoreceptors. To sustain vision, 11-cis-retinal is continuously regenerated from its all-trans conformation through a series of enzymatic steps comprising the "visual or retinoid" cycle. Abnormalities in this cycle can compromise vision because of the diminished supply of 11-cis-retinal and the accumulation of toxic, constitutively active opsin. As shown previously for rod cells, attenuation of constitutively active opsin can be achieved with the unbleachable analogue, 11-cis-6-membered ring (11-cis-6mr)-retinal, which has therapeutic effects against certain degenerative retinal diseases. However, to discern the molecular mechanisms responsible for this action, pigment regeneration with this locked retinal analogue requires delineation also in cone cells. Here, we compared the regenerative properties of rod and green cone opsins with 11-cis-6mr-retinal and demonstrated that this retinal analogue could regenerate rod pigment but not green cone pigment. Based on structural modeling suggesting that Pro-205 in green cone opsin could prevent entry and binding of 11-cis-6mr-retinal, we initially mutated this residue to Ile, the corresponding residue in rhodopsin. However, this substitution did not enable green cone opsin to regenerate with 11-cis-6mr-retinal. Interestingly, deletion of 16 N-terminal amino acids in green cone opsin partially restored the binding of 11-cis-6mr-retinal. These results and our structural modeling indicate that a more complex binding pathway determines the regeneration of mammalian green cone opsin with chromophore analogues such as 11-cis-6mr-retinal.
Collapse
Affiliation(s)
| | - Kota Katayama
- From the Department of Pharmacology, School of Medicine and
| | - Wenyu Sun
- Polgenix Inc., Cleveland, Ohio 44106, and
| | - David Salom
- From the Department of Pharmacology, School of Medicine and
| | - Sahil Gulati
- From the Department of Pharmacology, School of Medicine and
| | - Jianye Zhang
- From the Department of Pharmacology, School of Medicine and
| | - Muneto Mogi
- the Novartis Institutes for BioMedical Research, Inc., Cambridge, Massachusetts 02139
| | - Krzysztof Palczewski
- From the Department of Pharmacology, School of Medicine and .,Polgenix Inc., Cleveland, Ohio 44106, and.,the Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, Ohio 44106
| | - Beata Jastrzebska
- From the Department of Pharmacology, School of Medicine and .,the Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, Ohio 44106
| |
Collapse
|
7
|
Jastrzebska B, Comar WD, Kaliszewski MJ, Skinner KC, Torcasio MH, Esway AS, Jin H, Palczewski K, Smith AW. A G Protein-Coupled Receptor Dimerization Interface in Human Cone Opsins. Biochemistry 2017; 56:61-72. [PMID: 28045251 PMCID: PMC5274527 DOI: 10.1021/acs.biochem.6b00877] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
G protein-coupled receptors (GPCRs) detect a wide variety of physical and chemical signals and transmit that information across the cellular plasma membrane. Dimerization is a proposed modulator of GPCR signaling, but the structure and stability of class A GPCR dimerization have been difficult to establish. Here we investigated the dimerization affinity and binding interface of human cone opsins, which initiate and sustain daytime color vision. Using a time-resolved fluorescence approach, we found that human red cone opsin exhibits a strong propensity for dimerization, whereas the green and blue cone opsins do not. Through mutagenesis experiments, we identified a dimerization interface in the fifth transmembrane helix of human red cone opsin involving amino acids I230, A233, and M236. Insights into this dimerization interface of red cone opsin should aid ongoing investigations of the structure and function of GPCR quaternary interactions in cell signaling. Finally, we demonstrated that the same residues needed for dimerization are also partially responsible for the spectral tuning of red cone opsin. This last observation has the potential to open up new lines of inquiry regarding the functional role of dimerization for red cone opsin.
Collapse
Affiliation(s)
- Beata Jastrzebska
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 2109 Adelbert Road, Cleveland, Ohio 44106, United States
| | - William D. Comar
- Department of Chemistry, University of Akron, 190 Buchtel Common, Akron, Ohio 44325, United States
| | - Megan J. Kaliszewski
- Department of Chemistry, University of Akron, 190 Buchtel Common, Akron, Ohio 44325, United States
| | - Kevin C. Skinner
- Department of Chemistry, University of Akron, 190 Buchtel Common, Akron, Ohio 44325, United States
| | - Morgan H. Torcasio
- Department of Chemistry, University of Akron, 190 Buchtel Common, Akron, Ohio 44325, United States
| | - Anthony S. Esway
- Department of Chemistry, University of Akron, 190 Buchtel Common, Akron, Ohio 44325, United States
| | - Hui Jin
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 2109 Adelbert Road, Cleveland, Ohio 44106, United States
| | - Krzysztof Palczewski
- Department of Pharmacology, Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 2109 Adelbert Road, Cleveland, Ohio 44106, United States
| | - Adam W. Smith
- Department of Chemistry, University of Akron, 190 Buchtel Common, Akron, Ohio 44325, United States
| |
Collapse
|
8
|
Fernández-Sampedro MA, Invergo BM, Ramon E, Bertranpetit J, Garriga P. Functional role of positively selected amino acid substitutions in mammalian rhodopsin evolution. Sci Rep 2016; 6:21570. [PMID: 26865329 PMCID: PMC4749998 DOI: 10.1038/srep21570] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/27/2016] [Indexed: 12/22/2022] Open
Abstract
Visual rhodopsins are membrane proteins that function as light photoreceptors in the vertebrate retina. Specific amino acids have been positively selected in visual pigments during mammal evolution, which, as products of adaptive selection, would be at the base of important functional innovations. We have analyzed the top candidates for positive selection at the specific amino acids and the corresponding reverse changes (F13M, Q225R and A346S) in order to unravel the structural and functional consequences of these important sites in rhodopsin evolution. We have constructed, expressed and immunopurified the corresponding mutated pigments and analyzed their molecular phenotypes. We find that position 13 is very important for the folding of the receptor and also for proper protein glycosylation. Position 225 appears to be important for the function of the protein affecting the G-protein activation process, and position 346 would also regulate functionality of the receptor by enhancing G-protein activation and presumably affecting protein phosphorylation by rhodopsin kinase. Our results represent a link between the evolutionary analysis, which pinpoints the specific amino acid positions in the adaptive process, and the structural and functional analysis, closer to the phenotype, making biochemical sense of specific selected genetic sequences in rhodopsin evolution.
Collapse
Affiliation(s)
- Miguel A Fernández-Sampedro
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Brandon M Invergo
- IBE - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Eva Ramon
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| | - Jaume Bertranpetit
- IBE - Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), CEXS-UPF-PRBB, Barcelona, Catalonia, Spain
| | - Pere Garriga
- Grup de Biotecnologia Molecular i Industrial, Centre de Biotecnologia Molecular, Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Edifici Gaia, Rambla de Sant Nebridi 22, 08222 Terrassa, Catalonia, Spain
| |
Collapse
|