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Hanai S, Nagata T, Katayama K, Inukai S, Koyanagi M, Inoue K, Terakita A, Kandori H. Difference FTIR Spectroscopy of Jumping Spider Rhodopsin-1 at 77 K. Biochemistry 2023; 62:1347-1359. [PMID: 37001008 DOI: 10.1021/acs.biochem.3c00022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Animal visual rhodopsins can be classified into monostable and bistable rhodopsins, which are typically found in vertebrates and invertebrates, respectively. The former example is bovine rhodopsin (BovRh), whose structures and functions have been extensively studied. On the other hand, those of bistable rhodopsins are less known, despite their importance in optogenetics. Here, low-temperature Fourier-transform infrared (FTIR) spectroscopy was applied to jumping spider rhodopsin-1 (SpiRh1) at 77 K, and the obtained light-induced spectral changes were compared with those of squid rhodopsin (SquRh) and BovRh. Although chromophore distortion of the resting state monitored by HOOP vibrations is not distinctive between invertebrate and vertebrate rhodopsins, distortion of the all-trans chromophore after photoisomerization is unique for BovRh, and the distortion was localized at the center of the chromophore in SpiRh1 and SquRh. Highly conserved aspartate (D83 in BovRh) does not change the hydrogen-bonding environment in invertebrate rhodopsins. Thus, present FTIR analysis provides specific structural changes, leading to activation of invertebrate and vertebrate rhodopsins. On the other hand, the analysis of O-D stretching vibrations in D2O revealed unique features of protein-bound water molecules. Numbers of water bands in SpiRh1 and SquRh were less and more than those in BovRh. The X-ray crystal structure of SpiRh1 observed a bridged water molecule between the protonated Schiff base and its counterion (E194), but strongly hydrogen-bonded water molecules were never detected in SpiRh1, as well as SquRh and BovRh. Thus, absence of strongly hydrogen-bonded water molecules is substantial for animal rhodopsins, which is distinctive from microbial rhodopsins.
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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Bertalan É, Lesca E, Schertler GFX, Bondar AN. C-Graphs Tool with Graphical User Interface to Dissect Conserved Hydrogen-Bond Networks: Applications to Visual Rhodopsins. J Chem Inf Model 2021; 61:5692-5707. [PMID: 34670076 DOI: 10.1021/acs.jcim.1c00827] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Dynamic hydrogen-bond networks provide proteins with structural plasticity required to translate signals such as ligand binding into a cellular response or to transport ions and larger solutes across membranes and, thus, are of central interest to understand protein reaction mechanisms. Here, we present C-Graphs, an efficient tool with graphical user interface that analyzes data sets of static protein structures or of independent numerical simulations to identify conserved, vs unique, hydrogen bonds and hydrogen-bond networks. For static structures, which may belong to the same protein or to proteins with different sequences, C-Graphs uses a clustering algorithm to identify sites of the hydrogen-bond network where waters are conserved among the structures. Using C-Graphs, we identify an internal protein-water hydrogen-bond network common to static structures of visual rhodopsins and adenosine A2A G protein-coupled receptors (GPCRs). Molecular dynamics simulations of a visual rhodopsin indicate that the conserved hydrogen-bond network from static structure can recruit dynamic hydrogen bonds and extend throughout most of the receptor. We release with this work the code for C-Graphs and its graphical user interface.
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Affiliation(s)
- Éva Bertalan
- Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Elena Lesca
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, ETH Zürich, 5303 Villigen-PSI, Switzerland.,Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Gebhard F X Schertler
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, ETH Zürich, 5303 Villigen-PSI, Switzerland.,Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany.,Faculty of Physics, University of Bucharest, Strada Atomiştilor Nr. 405, Măgurele 077125, Romania.,Computational Biomedicine, IAS-5/INM-9, Institute for Neuroscience and Medicine and Institute for Advanced Simulations, Forschungszentrum Jülich, 52425 Jülich, Germany
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Hanai S, Katayama K, Imai H, Kandori H. Light-induced difference FTIR spectroscopy of primate blue-sensitive visual pigment at 163 K. Biophys Physicobiol 2021; 18:40-49. [PMID: 33954081 PMCID: PMC8049776 DOI: 10.2142/biophysico.bppb-v18.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 02/04/2021] [Accepted: 02/10/2021] [Indexed: 12/01/2022] Open
Abstract
Structural studies of color visual pigments lag far behind those of rhodopsin for scotopic vision. Using difference FTIR spectroscopy at 77 K, we report the first structural data of three primate color visual pigments, monkey red (MR), green (MG), and blue (MB), where the batho-intermediate (Batho) exhibits photoequilibrium with the unphotolyzed state. This photochromic property is highly advantageous for limited samples since the signal-to-noise ratio is improved, but may not be applicable to late intermediates, because of large structural changes to proteins. Here we report the photochromic property of MB at 163 K, where the BL intermediate, formed by the relaxation of Batho, is in photoequilibrium with the initial MB state. A comparison of the difference FTIR spectra at 77 and 163 K provided information on what happens in the process of transition from Batho to BL in MB. The coupled C11=C12 HOOP vibration in the planer structure in MB is decoupled by distortion in Batho after retinal photoisomerization, but returns to the coupled C11=C12 HOOP vibration in the all-trans chromophore in BL. The Batho formation accompanies helical structural perturbation, which is relaxed in BL. Protein-bound water molecules that form an extended water cluster near the retinal chromophore change hydrogen bonds differently for Batho and BL, being stronger in the latter than in the initial state. In addition to structural dynamics, the present FTIR spectra show no signals of protonated carboxylic acids at 77 and 163 K, suggesting that E181 is deprotonated in MB, Batho and BL.
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Affiliation(s)
- Shunpei Hanai
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Hiroo Imai
- Primate Research Institute, Kyoto University, Inuyama, Aichi 484-8506, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
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Kvansakul M. ABA/ASB structural biology session II 2018. Biophys Rev 2019; 11:279. [PMID: 31028524 DOI: 10.1007/s12551-019-00523-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 04/15/2019] [Indexed: 10/26/2022] Open
Affiliation(s)
- Marc Kvansakul
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.
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Jardón-Valadez E, Castillo-Guajardo D, Martínez-Luis I, Gutiérrez-Sagal R, Zariñán T, Ulloa-Aguirre A. Molecular dynamics simulation of the follicle-stimulating hormone receptor. Understanding the conformational dynamics of receptor variants at positions N680 and D408 from in silico analysis. PLoS One 2018; 13:e0207526. [PMID: 30462715 PMCID: PMC6248991 DOI: 10.1371/journal.pone.0207526] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/01/2018] [Indexed: 11/18/2022] Open
Abstract
Follicle-stimulating hormone receptor (FSHR) is a G-protein coupled receptor (GPCR) and a prototype of the glycoprotein hormone receptors subfamily of GPCRs. Structural data of the FSHR ectodomain in complex with follicle-stimulating hormone suggests a "pull and lift" activation mechanism that triggers a conformational change on the seven α-helix transmembrane domain (TMD). To analyze the conformational changes of the FSHR TMD resulting from sequence variants associated with reproductive impairment in humans, we set up a computational approach combining helix modeling and molecular simulation methods to generate conformational ensembles of the receptor at room (300 K) and physiological (310 K) temperatures. We examined the receptor dynamics in an explicit membrane environment of polyunsaturated phospholipids and solvent water molecules. The analysis of the conformational dynamics of the functional (N680 and S680) and dysfunctional (mutations at D408) variants of the FSHR allowed us to validate the FSHR-TMD model. Functional variants display a concerted motion of flexible intracellular regions at TMD helices 5 and 6. Disruption of side chain interactions and conformational dynamics were detected upon mutation at D408 when replaced with alanine, arginine, or tyrosine. Dynamical network analysis confirmed that TMD helices 2 and 5 may share communication pathways in the functional FSHR variants, whereas no connectivity was detected in the dysfunctional mutants, indicating that the global dynamics of the FSHR was sensitive to mutations at amino acid residue 408, a key position apparently linked to misfolding and variable cell surface plasma membrane expression of FSHRs with distinct mutations at this position.
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Affiliation(s)
- Eduardo Jardón-Valadez
- Departamento de Recursos de la Tierra, Universidad Autónoma Metropolitana, Unidad Lerma, Estado de México, Mexico
| | - Derik Castillo-Guajardo
- Departamento de Ciencias Ambientales Universidad Autónoma Metropolitana, Unidad Lerma, Estado de México, Mexico
| | - Iván Martínez-Luis
- Red de Apoyo a la Investigación, National University of Mexico (UNAM) and Instituto Nacional de Ciencias Médicas y Nutrición SZ, Mexico City, Mexico
| | - Rubén Gutiérrez-Sagal
- Red de Apoyo a la Investigación, National University of Mexico (UNAM) and Instituto Nacional de Ciencias Médicas y Nutrición SZ, Mexico City, Mexico
| | - Teresa Zariñán
- Red de Apoyo a la Investigación, National University of Mexico (UNAM) and Instituto Nacional de Ciencias Médicas y Nutrición SZ, Mexico City, Mexico
| | - Alfredo Ulloa-Aguirre
- Red de Apoyo a la Investigación, National University of Mexico (UNAM) and Instituto Nacional de Ciencias Médicas y Nutrición SZ, Mexico City, Mexico
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Recent advances in biophysical studies of rhodopsins - Oligomerization, folding, and structure. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1512-1521. [PMID: 28844743 DOI: 10.1016/j.bbapap.2017.08.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 08/06/2017] [Accepted: 08/11/2017] [Indexed: 12/19/2022]
Abstract
Retinal-binding proteins, mainly known as rhodopsins, function as photosensors and ion transporters in a wide range of organisms. From halobacterial light-driven proton pump, bacteriorhodopsin, to bovine photoreceptor, visual rhodopsin, they have served as prototypical α-helical membrane proteins in a large number of biophysical studies and aided in the development of many cutting-edge techniques of structural biology and biospectroscopy. In the last decade, microbial and animal rhodopsin families have expanded significantly, bringing into play a number of new interesting structures and functions. In this review, we will discuss recent advances in biophysical approaches to retinal-binding proteins, primarily microbial rhodopsins, including those in optical spectroscopy, X-ray crystallography, nuclear magnetic resonance, and electron paramagnetic resonance, as applied to such fundamental biological aspects as protein oligomerization, folding, and structure.
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Melo-Nava B, Casas-González P, Pérez-Solís MA, Castillo-Badillo J, Maravillas-Montero JL, Jardón-Valadez E, Zariñán T, Aguilar-Rojas A, Gallay N, Reiter E, Ulloa-Aguirre A. Role of Cysteine Residues in the Carboxyl-Terminus of the Follicle-Stimulating Hormone Receptor in Intracellular Traffic and Postendocytic Processing. Front Cell Dev Biol 2016; 4:76. [PMID: 27489855 PMCID: PMC4951517 DOI: 10.3389/fcell.2016.00076] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 07/01/2016] [Indexed: 01/21/2023] Open
Abstract
Posttranslational modifications occurring during the biosynthesis of G protein-coupled receptors include glycosylation and palmitoylation at conserved cysteine residues located in the carboxyl-terminus of the receptor. In a number of these receptors, these modifications play an important role in receptor function and particularly, in intracellular trafficking. In the present study, the three cysteine residues present in the carboxyl-terminus of the human FSHR were replaced with glycine by site-directed mutagenesis. Wild-type and mutant (Cys627/629/655Gly) FSHRs were then transiently expressed in HEK-293 cells and analyzed for cell-surface plasma membrane expression, agonist-stimulated signaling and internalization, and postendocytic processing in the absence and presence of lysosome and/or proteasome inhibitors. Compared with the wild-type FSHR, the triple mutant FSHR exhibited ~70% reduction in plasma membrane expression as well as a profound attenuation in agonist-stimulated cAMP production and ERK1/2 phosphorylation. Incubation of HEK-293 cells expressing the wild-type FSHR with 2-bromopalmitate (palmitoylation inhibitor) for 6 h, decreased plasma membrane expression of the receptor by ~30%. The internalization kinetics and β-arrestin 1 and 2 recruitment were similar between the wild-type and triple mutant FSHR as disclosed by assays performed in non-equilibrium binding conditions and by confocal microscopy. Cells expressing the mutant FSHR recycled the internalized FSHR back to the plasma membrane less efficiently than those expressing the wild-type FSHR, an effect that was counteracted by proteasome but not by lysosome inhibition. These results indicate that replacement of the cysteine residues present in the carboxyl-terminus of the FSHR, impairs receptor trafficking from the endoplasmic reticulum/Golgi apparatus to the plasma membrane and its recycling from endosomes back to the cell surface following agonist-induced internalization. Since in the FSHR these cysteine residues are S-palmitoylated, the data presented emphasize on this posttranslational modification as an important factor for both upward and downward trafficking of this receptor.
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Affiliation(s)
- Brenda Melo-Nava
- Research Unit in Reproductive Medicine, Unidad Medica de Alta Especialidad Hospital de Ginecobstetricia "Luis Castelazo Ayala", Instituto Mexicano del Seguro Social Mexico City, Mexico
| | - Patricia Casas-González
- Research Unit in Reproductive Medicine, Unidad Medica de Alta Especialidad Hospital de Ginecobstetricia "Luis Castelazo Ayala", Instituto Mexicano del Seguro Social Mexico City, Mexico
| | - Marco A Pérez-Solís
- Research Unit in Reproductive Medicine, Unidad Medica de Alta Especialidad Hospital de Ginecobstetricia "Luis Castelazo Ayala", Instituto Mexicano del Seguro Social Mexico City, Mexico
| | - Jean Castillo-Badillo
- Research Support Network, Universidad Nacional Autónoma de México and Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán" Mexico City, Mexico
| | - José L Maravillas-Montero
- Research Support Network, Universidad Nacional Autónoma de México and Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán" Mexico City, Mexico
| | | | - Teresa Zariñán
- Research Support Network, Universidad Nacional Autónoma de México and Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán" Mexico City, Mexico
| | - Arturo Aguilar-Rojas
- Research Unit in Reproductive Medicine, Unidad Medica de Alta Especialidad Hospital de Ginecobstetricia "Luis Castelazo Ayala", Instituto Mexicano del Seguro Social Mexico City, Mexico
| | - Nathalie Gallay
- BIOS Group, UMR85, Unité Physiologie de la Reproduction et des Comportements, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, UMR7247, Université François Rabelais Tours, France
| | - Eric Reiter
- BIOS Group, UMR85, Unité Physiologie de la Reproduction et des Comportements, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, UMR7247, Université François Rabelais Tours, France
| | - Alfredo Ulloa-Aguirre
- Research Support Network, Universidad Nacional Autónoma de México and Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán" Mexico City, Mexico
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