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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.
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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
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Radzin S, Wiśniewska-Becker A, Markiewicz M, Bętkowski S, Furso J, Waresiak J, Grolik J, Sarna T, Pawlak AM. Structural Impact of Selected Retinoids on Model Photoreceptor Membranes. MEMBRANES 2023; 13:575. [PMID: 37367779 DOI: 10.3390/membranes13060575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/07/2023] [Accepted: 05/27/2023] [Indexed: 06/28/2023]
Abstract
Photoreceptor membranes have a unique lipid composition. They contain a high level of polyunsaturated fatty acids including the most unsaturated fatty acid in nature, docosahexaenoic acid (22:6), and are enriched in phosphatidylethanolamines. The phospholipid composition and cholesterol content of the subcellular components of photoreceptor outer segments enables to divide photoreceptor membranes into three types: plasma membranes, young disc membranes, and old disc membranes. A high degree of lipid unsaturation, extended exposure to intensive irradiation, and high respiratory demands make these membranes sensitive to oxidative stress and lipid peroxidation. Moreover, all-trans retinal (AtRAL), which is a photoreactive product of visual pigment bleaching, accumulates transiently inside these membranes, where its concentration may reach a phototoxic level. An elevated concentration of AtRAL leads to accelerated formation and accumulation of bisretinoid condensation products such as A2E or AtRAL dimers. However, a possible structural impact of these retinoids on the photoreceptor-membrane properties has not yet been studied. In this work we focused just on this aspect. The changes induced by retinoids, although noticeable, seem not to be significant enough to be physiologically relevant. This is, however, an positive conclusion because it can be assumed that accumulation of AtRAL in photoreceptor membranes will not affect the transduction of visual signals and will not disturb the interaction of proteins engaged in this process.
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Affiliation(s)
- Szymon Radzin
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Anna Wiśniewska-Becker
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Michał Markiewicz
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics, Jagiellonian University, 30-387 Krakow, Poland
| | - Sebastian Bętkowski
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics, Jagiellonian University, 30-387 Krakow, Poland
| | - Justyna Furso
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Joanna Waresiak
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Jarosław Grolik
- Department of Organic Chemistry, Faculty of Chemistry, Jagiellonian University, 30-387 Krakow, Poland
| | - Tadeusz Sarna
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
| | - Anna M Pawlak
- Department of Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387 Krakow, Poland
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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.
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Opsins outside the eye and the skin: a more complex scenario than originally thought for a classical light sensor. Cell Tissue Res 2021; 385:519-538. [PMID: 34236517 DOI: 10.1007/s00441-021-03500-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/23/2021] [Indexed: 12/19/2022]
Abstract
Since the discovery of melanopsin as a retinal non-visual photopigment, opsins have been described in several organs and cells. This distribution is strikingly different from the classical localization of photopigments in light-exposed tissues such as the eyes and the skin. More than 10 years ago, a new paradigm in the field was created as opsins were shown, to detect not only light, but also thermal energy in Drosophila. In agreement with these findings, thermal detection by opsins was also reported in mammalian cells. Considering the presence of opsins in tissues not reached by light, an intriguing question has emerged: What is the role of a classical light-sensor, and more recently appreciated thermo-sensor, in these tissues? To tackle this question, we address in this review the most recent studies in the field, with emphasis in mammals. We provide the present view about the role of opsins in peripheral tissues, aiming to integrate the current knowledge of the presence and function of opsins in organs that are not directly affected by light.
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Barua A, Beygi A, Hatzikirou H. Close to Optimal Cell Sensing Ensures the Robustness of Tissue Differentiation Process: The Avian Photoreceptor Mosaic Case. ENTROPY 2021; 23:e23070867. [PMID: 34356408 PMCID: PMC8303396 DOI: 10.3390/e23070867] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 07/05/2021] [Accepted: 07/05/2021] [Indexed: 12/22/2022]
Abstract
The way that progenitor cell fate decisions and the associated environmental sensing are regulated to ensure the robustness of the spatial and temporal order in which cells are generated towards a fully differentiating tissue still remains elusive. Here, we investigate how cells regulate their sensing intensity and radius to guarantee the required thermodynamic robustness of a differentiated tissue. In particular, we are interested in finding the conditions where dedifferentiation at cell level is possible (microscopic reversibility), but tissue maintains its spatial order and differentiation integrity (macroscopic irreversibility). In order to tackle this, we exploit the recently postulated Least microEnvironmental Uncertainty Principle (LEUP) to develop a theory of stochastic thermodynamics for cell differentiation. To assess the predictive and explanatory power of our theory, we challenge it against the avian photoreceptor mosaic data. By calibrating a single parameter, the LEUP can predict the cone color spatial distribution in the avian retina and, at the same time, suggest that such a spatial pattern is associated with quasi-optimal cell sensing. By means of the stochastic thermodynamics formalism, we find out that thermodynamic robustness of differentiated tissues depends on cell metabolism and cell sensing properties. In turn, we calculate the limits of the cell sensing radius that ensure the robustness of differentiated tissue spatial order. Finally, we further constrain our model predictions to the avian photoreceptor mosaic.
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Affiliation(s)
- Arnab Barua
- Centre for Information Services and High Performance Computing, Technische Universität Dresden, Nöthnitzer Straße 46, 01062 Dresden, Germany; (A.B.); (A.B.)
| | - Alireza Beygi
- Centre for Information Services and High Performance Computing, Technische Universität Dresden, Nöthnitzer Straße 46, 01062 Dresden, Germany; (A.B.); (A.B.)
| | - Haralampos Hatzikirou
- Centre for Information Services and High Performance Computing, Technische Universität Dresden, Nöthnitzer Straße 46, 01062 Dresden, Germany; (A.B.); (A.B.)
- Mathematics Department, Khalifa University, Abu Dhabi P.O. Box 127788, United Arab Emirates
- Correspondence:
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Marazzi M, Gattuso H, Giussani A, Zhang H, Navarrete-Miguel M, Chipot C, Cai W, Roca-Sanjuán D, Dehez F, Monari A. Induced Night Vision by Singlet-Oxygen-Mediated Activation of Rhodopsin. J Phys Chem Lett 2019; 10:7133-7140. [PMID: 31652065 DOI: 10.1021/acs.jpclett.9b02911] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In humans, vision is limited to a small fraction of the whole electromagnetic spectrum. One possible strategy for enhancing vision in deep-red or poor-light conditions consists of recruiting chlorophyll derivatives in the rod photoreceptor cells of the eye, as suggested in the case of some deep-sea fish. Here, we employ all-atom molecular simulations and high-level quantum chemistry calculations to rationalize how chlorin e6 (Ce6), widely used in photodynamic therapy although accompanied by enhanced visual sensitivity, mediates vision in the dark, shining light on a fascinating but largely unknown molecular mechanism. First, we identify persistent interaction sites between Ce6 and the extracellular loops of rhodopsin, the transmembrane photoreceptor protein responsible for the first steps in vision. Triggered by Ce6 deep-red light absorption, the retinal within rhodopsin can be isomerized thus starting the visual phototransduction cascade. Our data largely exclude previously hypothesized energy-transfer mechanisms while clearly lending credence to a retinal isomerization indirectly triggered by singlet oxygen, proposing an alternative mechanism to rationalize photosensitizer-mediated night vision.
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Affiliation(s)
- Marco Marazzi
- LPCT , UMR 7019, Université de Lorraine and CNRS, F-54000 Vandoeuvre-lès-Nancy , France
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering , Universidad de Alcalá, Ctra , Madrid-Barcelona Km. 33,600 , E-28805 Alcalá de Henares ( Madrid ), Spain
- Chemical Research Institute "Andrés M. del Río" (IQAR) , Universidad de Alcalá , E-28871 Alcalá de Henares ( Madrid ), Spain
| | - Hugo Gattuso
- LPCT , UMR 7019, Université de Lorraine and CNRS, F-54000 Vandoeuvre-lès-Nancy , France
| | - Angelo Giussani
- Institut de Ciència Molecular , Universitat de València , P.O. Box 22085 València , Spain
| | - Hong Zhang
- LPCT , UMR 7019, Université de Lorraine and CNRS, F-54000 Vandoeuvre-lès-Nancy , France
- Research Center for Analytical Sciences, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Nankai University , Tianjin 300071 , China
| | | | - Christophe Chipot
- LPCT , UMR 7019, Université de Lorraine and CNRS, F-54000 Vandoeuvre-lès-Nancy , France
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign , F-54000 Vandoeuvre-lès-Nancy , France
- Department of Physics , University of Illinois at Urbana-Champaign , 1110 West Green Street , Urbana , Illinois 61801 , United States
| | - Wensheng Cai
- Research Center for Analytical Sciences, College of Chemistry, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Nankai University , Tianjin 300071 , China
| | - Daniel Roca-Sanjuán
- Institut de Ciència Molecular , Universitat de València , P.O. Box 22085 València , Spain
| | - François Dehez
- LPCT , UMR 7019, Université de Lorraine and CNRS, F-54000 Vandoeuvre-lès-Nancy , France
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign , F-54000 Vandoeuvre-lès-Nancy , France
| | - Antonio Monari
- LPCT , UMR 7019, Université de Lorraine and CNRS, F-54000 Vandoeuvre-lès-Nancy , France
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