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Interdisciplinary biophysical studies of membrane proteins bacteriorhodopsin and rhodopsin. Biophys Rev 2023; 15:111-125. [PMID: 36909961 PMCID: PMC9995646 DOI: 10.1007/s12551-022-01003-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/28/2022] [Indexed: 10/10/2022] Open
Abstract
The centenary of the birth of H. Gobind Khorana provides an auspicious opportunity to review the origins and evolution of parallel advances in biophysical methodology and molecular genetics technology used to study membrane proteins. Interdisciplinary work in the Khorana laboratory in the late 1970s and for the next three decades led to productive collaborations and fostered three subsequent scientific generations whose biophysical work on membrane proteins has led to detailed elucidation of the molecular mechanisms of energy transduction by the light-driven proton pump bacteriorhodopsin (bR) and signal transduction by the G protein-coupled receptor (GPCR) rhodopsin. This review will highlight the origins and advances of biophysical studies of membrane proteins made possible by the application of molecular genetics approaches to engineer site-specific alterations of membrane protein structures.
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2
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Colozo AT, Vasudevan S, Park PSH. Retinal degeneration in mice expressing the constitutively active G90D rhodopsin mutant. Hum Mol Genet 2021; 29:881-891. [PMID: 31960909 DOI: 10.1093/hmg/ddaa008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/11/2019] [Accepted: 01/15/2020] [Indexed: 11/13/2022] Open
Abstract
Rhodopsin is the G protein-coupled receptor in rod photoreceptor cells that initiates vision upon photon capture. The light receptor is normally locked in an inactive state in the dark by the covalently bound inverse agonist 11-cis retinal. Mutations can render the receptor active even in the absence of light. This constitutive activity can desensitize rod photoreceptor cells and lead to night blindness. A G90D mutation in rhodopsin causes the receptor to be constitutively active and leads to congenital stationary night blindness, which is generally thought to be devoid of retinal degeneration. The constitutively active species responsible for the night blindness phenotype is unclear. Moreover, the classification as a stationary disease devoid of retinal degeneration is also misleading. A transgenic mouse model for congenital stationary night blindness that expresses the G90D rhodopsin mutant was examined to better understand the origin of constitutive activity and the potential for retinal degeneration. Heterozygous mice for the G90D mutation did not exhibit retinal degeneration whereas homozygous mice exhibited progressive retinal degeneration. Only a modest reversal of retinal degeneration was observed when transducin signaling was eliminated genetically, indicating that some of the retinal degeneration occurred in a transducin-independent manner. Biochemical studies on purified rhodopsin from mice indicated that multiple species can potentially contribute to the constitutive activity causing night blindness.
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Affiliation(s)
- Alejandro T Colozo
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sreelakshmi Vasudevan
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Paul S-H Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
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El Hage K, Brickel S, Hermelin S, Gaulier G, Schmidt C, Bonacina L, van Keulen SC, Bhattacharyya S, Chergui M, Hamm P, Rothlisberger U, Wolf JP, Meuwly M. Implications of short time scale dynamics on long time processes. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2017; 4:061507. [PMID: 29308419 PMCID: PMC5741438 DOI: 10.1063/1.4996448] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/15/2017] [Indexed: 05/02/2023]
Abstract
This review provides a comprehensive overview of the structural dynamics in topical gas- and condensed-phase systems on multiple length and time scales. Starting from vibrationally induced dissociation of small molecules in the gas phase, the question of vibrational and internal energy redistribution through conformational dynamics is further developed by considering coupled electron/proton transfer in a model peptide over many orders of magnitude. The influence of the surrounding solvent is probed for electron transfer to the solvent in hydrated I-. Next, the dynamics of a modified PDZ domain over many time scales is analyzed following activation of a photoswitch. The hydration dynamics around halogenated amino acid side chains and their structural dynamics in proteins are relevant for iodinated TyrB26 insulin. Binding of nitric oxide to myoglobin is a process for which experimental and computational analyses have converged to a common view which connects rebinding time scales and the underlying dynamics. Finally, rhodopsin is a paradigmatic system for multiple length- and time-scale processes for which experimental and computational methods provide valuable insights into the functional dynamics. The systems discussed here highlight that for a comprehensive understanding of how structure, flexibility, energetics, and dynamics contribute to functional dynamics, experimental studies in multiple wavelength regions and computational studies including quantum, classical, and more coarse grained levels are required.
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Affiliation(s)
- Krystel El Hage
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Sebastian Brickel
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
| | - Sylvain Hermelin
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Geoffrey Gaulier
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Cédric Schmidt
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Luigi Bonacina
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Siri C van Keulen
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, Switzerland
| | | | - Majed Chergui
- Institute of Chemical Sciences and Engineering, EPFL, Lausanne, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | | | - Jean-Pierre Wolf
- Department of Applied Physics (GAP), University of Geneva, 22 Ch. de Pinchat, 1211 Geneva 4, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
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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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Park PSH. Constitutively active rhodopsin and retinal disease. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2014; 70:1-36. [PMID: 24931191 DOI: 10.1016/b978-0-12-417197-8.00001-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Rhodopsin is the light receptor in rod photoreceptor cells of the retina that initiates scotopic vision. In the dark, rhodopsin is bound to the chromophore 11-cis retinal, which locks the receptor in an inactive state. The maintenance of an inactive rhodopsin in the dark is critical for rod photoreceptor cells to remain highly sensitive. Perturbations by mutation or the absence of 11-cis retinal can cause rhodopsin to become constitutively active, which leads to the desensitization of photoreceptor cells and, in some instances, retinal degeneration. Constitutive activity can arise in rhodopsin by various mechanisms and can cause a variety of inherited retinal diseases including Leber congenital amaurosis, congenital night blindness, and retinitis pigmentosa. In this review, the molecular and structural properties of different constitutively active forms of rhodopsin are overviewed, and the possibility that constitutive activity can arise from different active-state conformations is discussed.
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Affiliation(s)
- Paul Shin-Hyun Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, Ohio, USA.
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Gensch T, Strassburger JM, Gärtner W, Braslavsky SE. Volume and Enthalpy Changes upon Photoexcitation of Bovine Rhodopsin Derived from Optoacoustic Studies by Using an Equilibrium between Bathorhodopsin and Blue-Shifted Intermediate. Isr J Chem 2013. [DOI: 10.1002/ijch.199800025] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Kawamura S, Colozo AT, Ge L, Müller DJ, Park PSH. Structural, energetic, and mechanical perturbations in rhodopsin mutant that causes congenital stationary night blindness. J Biol Chem 2012; 287:21826-35. [PMID: 22549882 DOI: 10.1074/jbc.m112.340182] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Several point mutations in rhodopsin cause retinal diseases including congenital stationary night blindness and retinitis pigmentosa. The mechanism by which a single amino acid residue substitution leads to dysfunction is poorly understood at the molecular level. A G90D point mutation in rhodopsin causes constitutive activity and leads to congenital stationary night blindness. It is unclear which perturbations the mutation introduces and how they can cause the receptor to be constitutively active. To reveal insight into these mechanisms, we characterized the perturbations introduced into dark state G90D rhodopsin from a transgenic mouse model expressing exclusively the mutant rhodopsin in rod photoreceptor cells. UV-visible absorbance spectroscopy revealed hydroxylamine accessibility to the chromophore-binding pocket of dark state G90D rhodopsin, which is not detected in dark state wild-type rhodopsin but is detected in light-activated wild-type rhodopsin. Single-molecule force spectroscopy suggested that the structural changes introduced by the mutation are small. Dynamic single-molecule force spectroscopy revealed that, compared with dark state wild-type rhodopsin, the G90D mutation decreased energetic stability and increased mechanical rigidity of most structural regions in the dark state mutant receptor. The observed structural, energetic, and mechanical changes in dark state G90D rhodopsin provide insights into the nature of perturbations caused by a pathological point mutation. Moreover, these changed properties observed for dark state G90D rhodopsin are consistent with properties expected for an active state.
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Affiliation(s)
- Shiho Kawamura
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
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Crozier PS, Stevens MJ, Woolf TB. How a small change in retinal leads to G-protein activation: initial events suggested by molecular dynamics calculations. Proteins 2007; 66:559-74. [PMID: 17109408 PMCID: PMC2848121 DOI: 10.1002/prot.21175] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Rhodopsin is the prototypical G-protein coupled receptor, coupling light activation with high efficiency to signaling molecules. The dark-state X-ray structures of the protein provide a starting point for consideration of the relaxation from initial light activation to conformational changes that may lead to signaling. In this study we create an energetically unstable retinal in the light activated state and then use molecular dynamics simulations to examine the types of compensation, relaxation, and conformational changes that occur following the cis-trans light activation. The results suggest that changes occur throughout the protein, with changes in the orientation of Helices 5 and 6, a closer interaction between Ala 169 on Helix 4 and retinal, and a shift in the Schiff base counterion that also reflects changes in sidechain interactions with the retinal. Taken together, the simulation is suggestive of the types of changes that lead from local conformational change to light-activated signaling in this prototypical system.
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Affiliation(s)
- Paul S Crozier
- Sandia National Laboratories, MS 1322, Albuquerque, New Mexico 87185-1322, USA.
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Abstract
Invertebrates are sensitive to a broad spectrum of light that ranges from UV to red. Color sensitivity in the UV plays an important role in foraging, navigation, and mate selection in both flying and terrestrial invertebrate animals. Here, we show that a single amino acid polymorphism is responsible for invertebrate UV vision. This residue (UV: lysine vs blue:asparagine or glutamate) corresponds to amino acid position glycine 90 (G90) in bovine rhodopsin, a site affected in autosomal dominant human congenital night blindness. Introduction of the positively charged lysine in invertebrates is likely to deprotonate the Schiff base chromophore and produce an UV visual pigment. This same position is responsible for regulating UV versus blue sensitivity in several bird species, suggesting that UV vision has arisen independently in invertebrate and vertebrate lineages by a similar molecular mechanism.
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10
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Abstract
The crystal structure of rod cell visual pigment rhodopsin was recently solved at 2.8-A resolution. A critical evaluation of a decade of structure-function studies is now possible. It is also possible to begin to explain the structural basis for several unique physiological properties of the vertebrate visual system, including extremely low dark noise levels as well as high gain and color detection. The ligand-binding pocket of rhodopsin is remarkably compact, and several apparent chromophore-protein interactions were not predicted from extensive mutagenesis or spectroscopic studies. The transmembrane helices are interrupted or kinked at multiple sites. An extensive network of interhelical interactions stabilizes the ground state of the receptor. The helix movement model of receptor activation, which might apply to all G protein-coupled receptors (GPCRs) of the rhodopsin family, is supported by several structural elements that suggest how light-induced conformational changes in the ligand-binding pocket are transmitted to the cytoplasmic surface. The cytoplasmic domain of the receptor is remarkable for a carboxy-terminal helical domain extending from the seventh transmembrane segment parallel to the bilayer surface. Thus the cytoplasmic surface appears to be approximately the right size to bind to the transducin heterotrimer in a one-to-one complex. Future high-resolution structural studies of rhodopsin and other GPCRs will form a basis to elucidate the detailed molecular mechanism of GPCR-mediated signal transduction.
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Affiliation(s)
- S T Menon
- Howard Hughes Medical Institute, Laboratory of Molecular Biology and Biochemistry, The Rockefeller University, New York, New York 10021, USA
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Lewis JW, Kliger DS. Absorption spectroscopy in studies of visual pigments: spectral and kinetic characterization of intermediates. Methods Enzymol 2000; 315:164-78. [PMID: 10736701 DOI: 10.1016/s0076-6879(00)15842-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- J W Lewis
- Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA
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Chapter 3 Late photoproducts and signaling states of bovine rhodopsin. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1383-8121(00)80006-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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13
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Konno T. Conformational diversity of acid-denatured cytochrome c studied by a matrix analysis of far-UV CD spectra. Protein Sci 1998; 7:975-82. [PMID: 9568904 PMCID: PMC2143977 DOI: 10.1002/pro.5560070415] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The singular value decomposition (SVD) analysis was applied to a large set of far-ultraviolet circular dichroism (far-UV CD) spectra (100-400 spectra) of horse heart cytochrome c (cyt c). The spectra were collected at pH 1.7-5.0 in (NH4)2SO4, sorbitol and 2,2,2-trifluoroethanol (TFE) solutions. The present purpose is to develop a rigorous matrix method applied to far-UV CD spectra to resolve in details conformational properties of proteins in the non-native (or denatured) regions. The analysis established that three basis spectral components are contained in a data set of difference spectra (referred to the spectrum of the native state) used here. By a further matrix transformation, any observed spectrum could be decomposed into fractions of the native (N), the molten-globule (MG), the highly denatured (D), and the alcohol-induced helical (H) spectral forms. This method could determine fractional transition curves of each conformer as a function of solution conditions, which gave the results consistent with denaturation curves of cyt c monitored by other spectroscopic methods. The results in sorbitol solutions, for example, suggested that the preferential hydration effect of the co-solvent stabilizes the MG conformer of cyt c. This report has found that the systematic SVD analysis of the far-UV CD spectra is a powerful tool for the conformational analysis of the non-native species of a protein when it is suitably supplemented with other experimental methods.
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Affiliation(s)
- T Konno
- National Institute for Physiological Science, Myodaiji, Okazaki, Japan.
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Lewis JW, Jäger S, Kliger DS. Absorbance changes by aromatic amino acid side chains in early rhodopsin photointermediates. Photochem Photobiol 1997; 66:741-6. [PMID: 9421960 DOI: 10.1111/j.1751-1097.1997.tb03218.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Absorbance changes were monitored from 250 to 650 nm during the first microsecond after photolysis of detergent suspensions of bovine rhodopsin at 20 degrees C. Global analysis of the resulting data produced difference spectra for bathorhodopsin, BSI and lumirhodopsin which give the change in absorbance of the aromatic amino acid side chains in these photointermediates relative to rhodopsin. These spectra show that the significant bleaching of absorbance near 280 nm, which has been seen previously for the lumirhodopsin, metarhodopsin I and metarhodopsin II intermediates, extends to times as early as bathorhodopsin. Because no corresponding absorbance increase is observed in the 250-275 nm region, the earliest bleaching of the 280 nm absorbance in rhodopsin is attributed to disruption of a hyperchromic interaction affecting Trp265. Partial decay of this 280 nm bleaching as bathorhodopsin converts to BSI takes place maximally near 290 nm, where Trp265 has been shown to absorb, and could be due to the ring of the retinylidene chromophore resuming a position at the BSI stage that reestablishes the hyperchromic interaction with Trp265. A subsequent change in the 250-300 nm region, which has no counterpart in the visible chromophore bands, indicates the possible presence of a protein-localized process as lumirhodopsin is formed.
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Affiliation(s)
- J W Lewis
- Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA
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Jäger S, Lewis JW, Zvyaga TA, Szundi I, Sakmar TP, Kliger DS. Chromophore structural changes in rhodopsin from nanoseconds to microseconds following pigment photolysis. Proc Natl Acad Sci U S A 1997; 94:8557-62. [PMID: 9238015 PMCID: PMC23009 DOI: 10.1073/pnas.94.16.8557] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Rhodopsin is a prototypical G protein-coupled receptor that is activated by photoisomerization of its 11-cis-retinal chromophore. Mutant forms of rhodopsin were prepared in which the carboxylic acid counterion was moved relative to the positively charged chromophore Schiff base. Nanosecond time-resolved laser photolysis measurements of wild-type recombinant rhodopsin and two mutant pigments then were used to determine reaction schemes and spectra of their early photolysis intermediates. These results, together with linear dichroism data, yielded detailed structural information concerning chromophore movements during the first microsecond after photolysis. These chromophore structural changes provide a basis for understanding the relative movement of rhodopsin's transmembrane helices 3 and 6 required for activation of rhodopsin. Thus, early structural changes following isomerization of retinal are linked to the activation of this G protein-coupled receptor. Such rapid structural changes lie at the heart of the pharmacologically important signal transduction mechanisms in a large variety of receptors, which use extrinsic activators, but are impossible to study in receptors using diffusible agonist ligands.
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Affiliation(s)
- S Jäger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
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