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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: 21] [Impact Index Per Article: 21.0] [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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Szundi I, Pitch SG, Chen E, Farrens DL, Kliger DS. Styrene-maleic acid copolymer effects on the function of the GPCR rhodopsin in lipid nanoparticles. Biophys J 2021; 120:4337-4348. [PMID: 34509506 DOI: 10.1016/j.bpj.2021.09.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/03/2021] [Accepted: 09/07/2021] [Indexed: 01/01/2023] Open
Abstract
Styrene-maleic acid (SMA) copolymers solubilize biological membranes to form lipid nanoparticles (SMALPs) that contain membrane proteins surrounded by native lipids, thus enabling the use of a variety of biophysical techniques for structural and functional studies. The question of whether SMALPs provide a truly natural environment or SMA solubilization affects the functional properties of membrane proteins, however, remains open. We address this question by comparing the photoactivation kinetics of rhodopsin, a G-protein-coupled receptor in the disk membranes of rod cells, in native membrane and SMALPs prepared at different molar ratios between SMA(3:1) and rhodopsin. Time-resolved absorption spectroscopy combined with complex kinetic analysis reveals kinetic and mechanistic differences between the native membrane and SMA-stabilized environment. The results suggest a range of molar ratios for nanoparticles suitable for kinetic studies.
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Affiliation(s)
- Istvan Szundi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Stephanie G Pitch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Eefei Chen
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - David L Farrens
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon
| | - David S Kliger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California.
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3
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Pitch SG, Yao W, Szundi I, Fay J, Chen E, Shumate A, Kliger DS, Farrens DL. Functional integrity of membrane protein rhodopsin solubilized by styrene-maleic acid copolymer. Biophys J 2021; 120:3508-3515. [PMID: 34022241 DOI: 10.1016/j.bpj.2021.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/18/2021] [Accepted: 05/13/2021] [Indexed: 11/25/2022] Open
Abstract
Membrane proteins often require solubilization to study their structure or define the mechanisms underlying their function. In this study, the functional properties of the membrane protein rhodopsin in its native lipid environment were investigated after being solubilized with styrene-maleic acid (SMA) copolymer. The static absorption spectra of rhodopsin before and after the addition of SMA were recorded at room temperature to quantify the amount of membrane protein solubilized. The samples were then photobleached to analyze the functionality of rhodopsin upon solubilization. Samples with low or high SMA/rhodopsin ratios were compared to find a threshold in which the maximal amount of active rhodopsin was solubilized from membrane suspensions. Interestingly, whereas the highest SMA/rhodopsin ratios yielded the most solubilized rhodopsin, the rhodopsin produced under these conditions could not reach the active (Meta II) state upon photoactivation. The results confirm that SMA is a useful tool for membrane protein research, but SMA added in excess can interfere with the dynamics of protein activation.
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Affiliation(s)
- Stephanie G Pitch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Weekie Yao
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon
| | - Istvan Szundi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Jonathan Fay
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon
| | - Eefei Chen
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - Anthony Shumate
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon
| | - David S Kliger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California
| | - David L Farrens
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, Oregon.
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4
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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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5
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Funatogawa C, Szundi I, Kliger DS. A Comparison between the Photoactivation Kinetics of Human and Bovine Rhodopsins. Biochemistry 2016; 55:7005-7013. [DOI: 10.1021/acs.biochem.6b00953] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chie Funatogawa
- Department of Chemistry and
Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Istvan Szundi
- 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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6
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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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Kazmin R, Rose A, Szczepek M, Elgeti M, Ritter E, Piechnick R, Hofmann KP, Scheerer P, Hildebrand PW, Bartl FJ. The Activation Pathway of Human Rhodopsin in Comparison to Bovine Rhodopsin. J Biol Chem 2015; 290:20117-27. [PMID: 26105054 DOI: 10.1074/jbc.m115.652172] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Indexed: 11/06/2022] Open
Abstract
Rhodopsin, the photoreceptor of rod cells, absorbs light to mediate the first step of vision by activating the G protein transducin (Gt). Several human diseases, such as retinitis pigmentosa or congenital night blindness, are linked to rhodopsin malfunctions. Most of the corresponding in vivo studies and structure-function analyses (e.g. based on protein x-ray crystallography or spectroscopy) have been carried out on murine or bovine rhodopsin. Because these rhodopsins differ at several amino acid positions from human rhodopsin, we conducted a comprehensive spectroscopic characterization of human rhodopsin in combination with molecular dynamics simulations. We show by FTIR and UV-visible difference spectroscopy that the light-induced transformations of the early photointermediates are very similar. Significant differences between the pigments appear with formation of the still inactive Meta I state and the transition to active Meta II. However, the conformation of Meta II and its activity toward the G protein are essentially the same, presumably reflecting the evolutionary pressure under which the active state has developed. Altogether, our results show that although the basic activation pathways of human and bovine rhodopsin are similar, structural deviations exist in the inactive conformation and during receptor activation, even between closely related rhodopsins. These differences between the well studied bovine or murine rhodopsins and human rhodopsin have to be taken into account when the influence of point mutations on the activation pathway of human rhodopsin are investigated using the bovine or murine rhodopsin template sequences.
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Affiliation(s)
- Roman Kazmin
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, 10115 Berlin, Germany, and
| | - Alexander Rose
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, AG ProteInformatics, Charitéplatz 1, 10117 Berlin, Germany
| | - Michal Szczepek
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, AG Protein X-ray Crystallography and Signal Transduction, and
| | - Matthias Elgeti
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin
| | - Eglof Ritter
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, 10115 Berlin, Germany, and
| | - Ronny Piechnick
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin
| | - Klaus Peter Hofmann
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, Zentrum für Biophysik und Bioinformatik (BPI), Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Patrick Scheerer
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, AG Protein X-ray Crystallography and Signal Transduction, and
| | - Peter W Hildebrand
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin, AG ProteInformatics, Charitéplatz 1, 10117 Berlin, Germany
| | - Franz J Bartl
- From the Institut für Medizinische Physik und Biophysik, Charité-Universitätsmedizin Berlin,
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9
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Kliger DS, Lewis JW. Spectral and Kinetic Characterization of Visual Pigment Photointermediates. Isr J Chem 2013. [DOI: 10.1002/ijch.199500032] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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10
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Chan RH, Lewis JW, Bogomolni RA. Photocycle of the LOV-STAS protein from the pathogen Listeria monocytogenes. Photochem Photobiol 2012; 89:361-9. [PMID: 23025752 DOI: 10.1111/php.12004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 09/21/2012] [Indexed: 01/06/2023]
Abstract
Listeria monocytogenes, a food-borne bacterial pathogen causing significant human mortality, propagates by expressing genes in response to environmental signals, such as temperature and pH. Listeria gene (lmo0799) encodes a protein homologous to the Bacillus subtilis YtvA, which has a flavin-light, oxygen or voltage (LOV) domain and a Sulfate Transporters Anti-Sigma factor antagonist (STAS) output domain that regulates transcription-initiation factor Sigma B in the bacterial stress response upon exposure to light. This could be significant for the pathogenesis of listeriosis because Sigma B has been linked to virulence of Listeria, and the Listeria Lmo0799 protein has recently been identified as a virulence factor activated by blue light. We have cloned, expressed heterologously in Escherichia coli and purified the full-length LM-LOV-STAS protein. Although it exhibits photochemical activity similar to that of YtvA, LM-LOV-STAS lacks an almost universally conserved arginine in the flavin-binding site, as well as another positively charged residue, a lysine in YtvA. The absence of these positive charges was found to destabilize retention of the flavin mononucleotide (FMN) chromophore in the LM-LOV-STAS protein, particularly at higher temperatures. The unusual sequence of the LM-LOV-STAS protein alters both spectral features and activation/deactivation kinetics, potentially expanding the sensory capacity of this LOV domain, e.g. to detect light plus cold.
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Affiliation(s)
- Ruby H Chan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
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11
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Elgeti M, Ritter E, Bartl FJ. New Insights into Light-Induced Deactivation of Active Rhodopsin by SVD and Global Analysis of Time-Resolved UV/Vis- and FTIR-Data. ACTA ACUST UNITED AC 2009. [DOI: 10.1524/zpch.2008.5392] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractTime-resolved Fourier transform infrared (FTIR) and UV/Vis difference spectra of light induced deactivation of the photoreceptor rhodopsin were simultaneously recorded on the same sample. The data were analyzed by a special designed combination of singular value decomposition and Global analysis to verify our recently published model of receptor deactivation. This mathematical approach enables us to obtain the pure difference spectra of the conversions between the species involved. We found two different species, which could be identified as key intermediates of the model. The new data allow deeper insights into the structural changes that come along with the formation of the deactivated state. By means of this method we can now separate and assign even strongly overlapping and highly coupled bands of the infrared difference spectra.
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12
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Epps J, Lewis JW, Szundi I, Kliger DS. Lumi I --> Lumi II: the last detergent independent process in rhodopsin photoexcitationt. Photochem Photobiol 2007; 82:1436-41. [PMID: 16553464 DOI: 10.1562/2006-02-01-ra-792] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Time-resolved absorbance difference spectra were collected at delays from 1 to 128 micros after photolysis of membrane and detergent suspensions of rhodopsin at 20 degrees C. Fitting both sets of data with two exponential decays plus a constant showed a similar fast process (lifetime 11 micros in membrane, 12 micros in 5% dodecyl maltoside) with a small but similar spectral change. This demonstrates that the Lumi I - Lumi II process, previously characterized in detergent suspensions, has similar properties in membrane without significant effect of detergent. The slower exponential process detected in the data is quite different in membrane compared to detergent solubilized samples, showing that the pronounced effect of detergent on the later rhodopsin photointermediates begins fairly abruptly near 20 micros. Besides affecting the late processes, the data collected here shows that detergent induces a small blue shift in the 1 micros difference spectrum (the Lumi I minus rhodopsin difference spectrum). The blue shift is similar to one induced by chloride ion in the E181Q rhodopsin mutant and may indicate that the ionization state of Glu181 in rhodopsin is affected by detergent.
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Affiliation(s)
- Jacqueline Epps
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, USA
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13
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Epps J, Lewis JW, Szundi I, Kliger DS. Lumi I → Lumi II: The Last Detergent Independent Process in Rhodopsin Photoexcitation. Photochem Photobiol 2006. [DOI: 10.1111/j.1751-1097.2006.tb09796.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Lüdeke S, Lórenz Fonfría VA, Siebert F, Vogel R. Time-resolved rapid-scan Fourier transform infrared difference spectroscopy on a noncyclic photosystem: rhodopsin photointermediates from Lumi to Meta II. Biopolymers 2006; 83:159-69. [PMID: 16721790 DOI: 10.1002/bip.20540] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The visual pigment rhodopsin has been extensively studied for the kinetics of its photointermediates by various spectroscopic methods. Unlike such archaeal retinal proteins as bacteriorhodopsin, visual rhodopsin does not thermally recover its dark state after photoexcitation, which precludes repeated excitation of a single sample and thereby complicates time-resolved experiments. Kinetic data on the late rhodopsin photointermediates have so far been available mainly from time-resolved ultraviolet (UV)-visible spectroscopy, but not from Fourier transform infrared (FTIR) spectroscopy. The latter has the advantage of being informative of structural changes of both chromophore and protein, but does not allow the highly reproducible, automated sample exchange procedures available to UV-visible spectroscopy. Using rapid-scan FTIR difference spectroscopy, we obtained time-resolved data sets that were analyzed by a maximum entropy inverse Laplace-transform. Covering the time range from 8 ms to 15 s at temperatures of 0 and -7 degrees C, the transitions from the Lumi to the Meta I and from the Meta I to the Meta II photoproduct states could be resolved. In the transition from Meta I to Meta II, our data reveal a partial deprotonation of the retinal Schiff base preceding the conformational change of the receptor protein to Meta II. The technique and the results are discussed in regard to its advantages as well as its limitations.
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Affiliation(s)
- Steffen Lüdeke
- Arbeitsgruppe Biophysik, Institut für Molekulare Medizin und Zellforschung, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Str. 9, D-79104 Freiburg, Germany
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Vogel R, Siebert F, Yan ECY, Sakmar TP, Hirshfeld A, Sheves M. Modulating Rhodopsin Receptor Activation by Altering the pKa of the Retinal Schiff Base. J Am Chem Soc 2006; 128:10503-12. [PMID: 16895417 DOI: 10.1021/ja0627848] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The visual pigment rhodopsin is a seven-transmembrane (7-TM) G protein-coupled receptor (GPCR). Activation of rhodopsin involves two pH-dependent steps: proton uptake at a conserved cytoplasmic motif between TM helices 3 and 6, and disruption of a salt bridge between a protonated Schiff base (PSB) and its carboxylate counterion in the transmembrane core of the receptor. Formation of an artificial pigment with a retinal chromophore fluorinated at C14 decreases the intrinsic pKa of the PSB and thereby destabilizes this salt bridge. Using Fourier transform infrared difference and UV-visible spectroscopy, we characterized the pH-dependent equilibrium between the active photoproduct Meta II and its inactive precursor, Meta I, in the 14-fluoro (14-F) analogue pigment. The 14-F chromophore decreases the enthalpy change of the Meta I-to-Meta II transition and shifts the Meta I/Meta II equilibrium toward Meta II. Combining C14 fluorination with deletion of the retinal beta-ionone ring to form a 14-F acyclic artificial pigment uncouples disruption of the Schiff base salt bridge from transition to Meta II and in particular from the cytoplasmic proton uptake reaction, as confirmed by combining the 14-F acyclic chromophore with the E134Q mutant. The 14-F acyclic analogue formed a stable Meta I state with a deprotonated Schiff base and an at least partially protonated protein counterion. The combination of retinal modification and site-directed mutagenesis reveals that disruption of the protonated Schiff base salt bridge is the most important step thermodynamically in the transition from Meta I to Meta II. This finding is particularly important since deprotonation of the retinal PSB is known to precede the transition to the active state in rhodopsin activation and is consistent with models of agonist-dependent activation of other GPCRs.
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Affiliation(s)
- Reiner Vogel
- Arbeitsgruppe Biophysik, Institut für Molekulare Medizin und Zellforschung, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 9, D-79104 Freiburg, Germany
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16
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Ruprecht JJ, Mielke T, Vogel R, Villa C, Schertler GFX. Electron crystallography reveals the structure of metarhodopsin I. EMBO J 2004; 23:3609-20. [PMID: 15329674 PMCID: PMC517614 DOI: 10.1038/sj.emboj.7600374] [Citation(s) in RCA: 231] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2004] [Accepted: 07/27/2004] [Indexed: 11/08/2022] Open
Abstract
Rhodopsin is the prototypical G protein-coupled receptor, responsible for detection of dim light in vision. Upon absorption of a photon, rhodopsin undergoes structural changes, characterised by distinct photointermediates. Currently, only the ground-state structure has been described. We have determined a density map of a photostationary state highly enriched in metarhodopsin I, to a resolution of 5.5 A in the membrane plane, by electron crystallography. The map shows density for helix 8, the cytoplasmic loops, the extracellular plug, all tryptophan residues, an ordered cholesterol molecule and the beta-ionone ring. Comparison of this map with X-ray structures of the ground state reveals that metarhodopsin I formation does not involve large rigid-body movements of helices, but there is a rearrangement close to the bend of helix 6, at the level of the retinal chromophore. There is no gradual build-up of the large conformational change known to accompany metarhodopsin II formation. The protein remains in a conformation similar to that of the ground state until late in the photobleaching process.
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Affiliation(s)
| | | | - Reiner Vogel
- Biophysics Group, Institut für Molekulare Medizin und Zellforschung, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | | | - Gebhard FX Schertler
- MRC Laboratory of Molecular Biology, Cambridge, UK
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK. Tel.: +44 1223 402328; Fax: +44 1223 213556; E-mail:
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17
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Szundi I, Swartz TE, Bogomolni RA. Multicolored protein conformation states in the photocycle of transducer-free sensory rhodopsin-I. Biophys J 2001; 80:469-79. [PMID: 11159417 PMCID: PMC1301248 DOI: 10.1016/s0006-3495(01)76029-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Sensory rhodopsin-I (SRI), a phototaxis receptor of archaebacteria, is a retinal-binding protein that exists in the cell membrane intimately associated with a signal-transducing protein (HtrI) homologous to eubacterial chemotaxis receptors. Transducer-free sensory rhodopsin-I (fSRI), from cells devoid of HtrI, undergoes a photochemical cycle kinetically different from that of native SRI. We report here on the measurement and analysis of the photochemical kinetics of fSRI reactions in the 350-750-nm spectral range and in a 10(-7) s to 1 s time window. The lack of specific intermolecular interactions between SRI and HtrI results in early return of the ground form via distinct branching reactions in fSRI, not evident in the photocycle of native SRI. The chromophore transitions are loosely coupled to protein structural transitions. The coexistence of multiple spectral forms within kinetic intermediates is interpreted within the concept of multicolored protein conformational states.
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Affiliation(s)
- I Szundi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, California 95064, USA
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18
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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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19
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Hofmann KP. Signalling states of photoactivated rhodopsin. NOVARTIS FOUNDATION SYMPOSIUM 1999; 224:158-75; discussion 175-80. [PMID: 10614051 DOI: 10.1002/9780470515693.ch10] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In microseconds after photoexcitation, rhodopsin forms the Meta I intermediate from lumirhodopsin. In this conversion, contacts between retinal and the apoprotein are formed, which result in a defined arrangement of donor and acceptor groups for proton translocations. A system of protonation-dependent coupled equilibria is now adopted, comprising Meta intermediates I, II and III, and their isospectral subforms. Some Meta states were identified as signalling states, in which the receptor interacts with transducin (Gt), rhodopsin kinase (RK) and arrestin. The binding of Gt or arrestin shifts the equilibrium to Meta II, while RK does not, indicating exposure of the RK binding site(s) before Meta II is formed. On contact with the activated receptor, each signalling protein responds with a conformational change, which transforms it into a functionally active state. The bell-shaped pH/rate profiles which are seen for the activation of both the G protein and the receptor kinase, indicate the necessary protonation and deprotonation of groups with different pKa. The right wing of the profile reflects the formation of the protonated subconformation (termed MIIb) of Meta II. For the interaction with Gt, recent work suggests a 'sequential fit' mechanism, involving the recognition of the C-terminal peptide of the Gt alpha subunit and of the farnesylated C-terminus of the gamma subunit. Isolated peptides derived from these portions of the G protein mimic the left wing of the pH/rate profile. We discuss the sequential fit as a time-ordered sequence of microscopic recognition and conformational interlocking in the interaction with the G protein.
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Affiliation(s)
- K P Hofmann
- Institut für Medizinische Physik und Biophysik, Medizinische Fakultät Charité, Humboldt-Universität zu Berlin, Germany
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Dioumaev AK. Evaluation of intrinsic chemical kinetics and transient product spectra from time-resolved spectroscopic data. Biophys Chem 1997; 67:1-25. [PMID: 17029887 DOI: 10.1016/s0301-4622(96)02268-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/1996] [Revised: 12/17/1996] [Accepted: 12/17/1996] [Indexed: 11/19/2022]
Abstract
This communication is devoted to the evaluation of true spectra and intrinsic (microscopic) rate constants from apparent kinetics measured in time-resolved spectroscopic experiments monitoring complex relaxation dynamics of multi-intermediate systems. Retinal proteins, cytochrom c oxidase, phytochrome, hemoglobin, and photoactive yellow protein are examples of natural systems in which several transient states (intermediates) overlap so strongly, both in time and spectral domains, that their isolation and full characterization by classical biochemical methods is impossible, and mathematical evaluation of their true spectra and microscopic kinetic constants is required. Most of the popular methods for analysis of kinetic data, global fitting (GF), singular value decomposition (SVD), principal component analysis (PCA) and factor analysis (FA), are applicable to two-dimensional (2D, in time and spectral domains) arrays of data. All these methods produce only a phenomenological description of data, that approximates the measured data only with apparent kinetics. A fundamental limitation, namely, insufficient information in 2D data, does not allow any of these methods to reach the final goal: to recalculate from apparent to intrinsic values in any but the most trivial cases. A strategy was proposed (J.F. Nagle, Biophys. J.. 59 (1991) 476-487) to include an additional (third) information-rich dimension, temperature, into the simultaneous computer analysis. A simultaneous direct fitting of 3D data arrays to systems of differential rate equations allows recalculation of apparent kinetics into true spectra and intrinsic rate constants. In spite of its evident theoretical advantages, this strategy has not been successful on real data. Here we describe another custom-built program, SCHEMEFIT, developed for the same purpose: to fit measured kinetics directly to the system of coupled differential rate equations describing the photochrome's relaxation dynamics. Though sharing the main strategy with the previous approach, SCHEMEFIT is based on a different set of numeric algorithms, and its application requires different tactics. Its performance is illustrated on synthetic data, and compared with GF and SVD. An example of applying SCHEMEFIT to the photocycle of halorhodopsin is also reported.
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Affiliation(s)
- A K Dioumaev
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA.
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Szundi I, Lewis JW, Kliger DS. Deriving reaction mechanisms from kinetic spectroscopy. Application to late rhodopsin intermediates. Biophys J 1997; 73:688-702. [PMID: 9251787 PMCID: PMC1180967 DOI: 10.1016/s0006-3495(97)78103-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A general algebraic approach to the kinetic analysis of time-dependent absorption data is presented that allows the calculation of possible kinetic schemes. The kinetic matrices of all possible reaction mechanisms are calculated from experimental eigenvalues and eigenvectors derived from the decay constants and amplitude spectra (b-spectra) of the global exponential fit to the time-dependence of the absorption data. The eigenvalues are directly related to the decay constants, and the eigenvectors are obtained by decomposing the b-spectra into spectral components representing the intermediates. The analysis method is applied to the late intermediates (lumi, meta I, meta I-380, and meta II) of the rhodopsin photoreaction. The b-spectra are decomposed into lumi, meta I, meta-380, and rhodopsin spectra. The meta-380 component is partitioned into isospectral meta I-380 and meta II components based on physical criteria. The calculated kinetic matrices yield a number of reaction mechanisms (linear scheme with back reactions, branched schemes with equilibrium steps, and a variety of square models) consistent with the photolysis data at 25 degrees C. The problems associated with isospectral intermediates (meta I-380 and meta II) are treated successfully with this method.
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Affiliation(s)
- I Szundi
- Department of Chemistry and Biochemistry, University of California, Santa Cruz 95064, USA
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22
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Brown MF. Chapter 8 Influence of Nonlamellar-Forming Lipids on Rhodopsin. CURRENT TOPICS IN MEMBRANES 1997. [DOI: 10.1016/s0070-2161(08)60212-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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23
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Peter Hofmann K, Heck M. Light-induced protein-protein interactions on the rod photoreceptor disc membrane. ACTA ACUST UNITED AC 1996. [DOI: 10.1016/s1874-5342(07)80006-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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Abstract
A prevalent model for the function of rhodopsin centers on the metarhodopsin I (MI) to metarhodopsin II (MII) conformational transition as the triggering event for the visual process. Flash photolysis techniques enable one to determine the [MII]/[MI] ratio for rhodopsin in various recombinant membranes, and thus investigate the roles of the phospholipid head groups and the lipid acyl chains systematically. The results obtained to date clearly show that the pK for the acid-base MI-MII equilibrium of rhodopsin is modulated by the lipid environment. In bilayers of phosphatidylcholines the MI-MII equilibrium is shifted to the left; whereas in the native rod outer segment membranes it is shifted to the right, i.e., at neutral pH near physiological temperature. The lipid mixtures sufficient to yield full photochemical function of rhodopsin include a native-like head group composition, viz, comprising phosphatidylcholine (PC), phosphatidylethanolamine (PE), and phosphatidylserine (PS), in combination with polyunsaturated docosahexaenoic acid (DHA; 22:6 omega 3) chains. Yet such a native-like lipid mixture is not necessary for the MI-MII conformational transition of rhodopsin; one can substitute other lipid compositions having similar properties. The MI-MII transition is favored by relatively small head groups which produce a condensed bilayer surface, viz, a comparatively small interfacial area as in the case of PE, together with bulky acyl chains such as DHA which prefer a relatively large cross sectional area. The resulting force imbalance across the layer gives rise to a curvature elastic stress of the lipid/water interface, such that the lipid mixtures yielding native-like behavior form reverse hexagonal (HII) phases at slightly higher temperatures. A relatively unstable membrane is needed: lipids tending to form the lamellar phase do not support full native-like photochemical function of rhodopsin. Thus chemically specific properties of the various lipids are not required, but rather average or material properties of the entire assembly, which may involve the curvature free energy of the membrane-lipid water interface. These findings reveal that the membrane lipid bilayer has a direct influence on the energetics of the conformational states of rhodopsin in visual excitation.
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Affiliation(s)
- M F Brown
- Department of Chemistry, University of Arizona, Tucson 85721
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25
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Georgiadis KE, Jhon NI, Einarsdóttir O. Time-resolved optical absorption studies of intramolecular electron transfer in cytochrome c oxidase. Biochemistry 1994; 33:9245-56. [PMID: 8049226 DOI: 10.1021/bi00197a028] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Intramolecular electron transfer and conformational changes in cytochrome c oxidase were studied at room temperature following the photodissociation of CO bound to mixed-valence enzyme (cytochrome a3(2+)-CO CuB+ cytochrome a3+ CuA2+) and fully reduced enzyme. Time-resolved optical absorption difference spectra were collected in the Soret region on time scales of nanoseconds to milliseconds using a gated optical spectrometric multichannel analyzer. A global exponential fitting procedure combined with a singular value decomposition method was used to analyze the transient difference spectra at various times following CO photolysis. The analysis shows that at least two processes, with apparent lifetimes of 1.4 microseconds and 11.1 ms, are present following the photodissociation of CO bound to the fully reduced enzyme. These are attributed to a conformational change and CO recombination at the cytochrome a3 site, respectively. Global analysis of the mixed-valence CO complex transient difference spectra showed the presence of five intermediates with apparent lifetimes of 1.0 microseconds, 5.2 microseconds, 83.7 microseconds, 10.5 ms, and 25.3 ms. The data on a microsecond time scale are consistent with a mechanism involving a conformational change at cytochrome a3, followed by electron transfer from cytochrome a3 to cytochrome a with subsequent electron transfer to CuA. One of the two processes on a millisecond time scale is attributed to CO recombination and the other to a structural rearrangement or heme-heme electron transfer. On the basis of this mechanism, the kinetics and the absorption spectra of the intermediates involved in the conformational and electron transfer dynamics of the mixed-valence enzyme were determined.
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Affiliation(s)
- K E Georgiadis
- Department of Chemistry, University of California, Santa Cruz 95064
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Straume M. Sequential versus simultaneous analysis of data: differences in reliability of derived quantitative conclusions. Methods Enzymol 1994; 240:89-121. [PMID: 7823858 DOI: 10.1016/s0076-6879(94)40045-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- M Straume
- Department of Medicine, University of Virginia, Health Sciences Center, Charlottesville 22903
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Thorgeirsson TE, Lewis JW, Wallace-Williams SE, Kliger DS. Effects of temperature on rhodopsin photointermediates from lumirhodopsin to metarhodopsin II. Biochemistry 1993; 32:13861-72. [PMID: 8268161 DOI: 10.1021/bi00213a015] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Absorbance changes following the photolysis of mildly sonicated membrane suspensions of bovine rhodopsin are monitored using multichannel detection at 15, 20, 25, 30, and 35 degrees C. Difference spectra collected with microsecond time resolution are analyzed by singular value decomposition and multiexponential fitting. Several kinetic schemes are tested using methods that compare the observed rates and associated spectral amplitudes to the eigenvalues and eigenvectors of kinetic matrices. The time evolution of the spectra is more complex than can be accounted for by the traditional lumi-->metarhodopsin I<-->metarhodopsin II scheme. Above 25 degrees C, the formation of metarhodopsin II is achieved without a large transient accumulation of metarhodopsin I. Within the framework of first-order kinetics, the observations are explained by simple kinetic schemes that lead to the formation of a deprotonated Schiff's base species temporally distinct from metarhodopsin II directly upon the decay of lumirhodopsin.
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Affiliation(s)
- T E Thorgeirsson
- Department of Chemistry and Biochemistry, University of California at Santa Cruz 95064
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Farahbakhsh ZT, Hideg K, Hubbell WL. Photoactivated conformational changes in rhodopsin: a time-resolved spin label study. Science 1993; 262:1416-9. [PMID: 8248781 DOI: 10.1126/science.8248781] [Citation(s) in RCA: 112] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Rhodopsin has been selectively spin-labeled near the cytoplasmic termini of helices C and G. Photoactivation with a light flash induces an electron paramagnetic resonance spectral change in the millisecond time domain, coincident with the appearance of the active metarhodopsin II intermediate. The spectral change is consistent with a small movement near the cytoplasmic termination of the C helix and reverses upon formation of the MIII state. These results provide an important link between the optical changes associated with the retinal chromophore and protein conformational states.
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Arnis S, Hofmann KP. Two different forms of metarhodopsin II: Schiff base deprotonation precedes proton uptake and signaling state. Proc Natl Acad Sci U S A 1993; 90:7849-53. [PMID: 8356093 PMCID: PMC47240 DOI: 10.1073/pnas.90.16.7849] [Citation(s) in RCA: 139] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Rhodopsin is a retinal protein and a G-protein-coupled receptor; it shares with both of these families the seven helix structure. To generate the G-interacting helix-loop conformation, generally identified with the 380-nm absorbing metarhodopsin II (MII) photoproduct, the retinal Schiff base bond to the apoprotein must be deprotonated. This occurs as a key event also in the related retinal proteins, sensory rhodopsins, and the proton pump bacteriorhodopsin. In MII, proton uptake from the aqueous phase must be involved as well, since its formation increases the pH of the aqueous medium and is accelerated under acidic conditions. In the native membrane, the pH effect matches MII formation kinetically, suggesting that intramolecular and aqueous protonation changes contribute in concert to the protein transformation. We show here, however, that proton uptake, as indicated by bromocresol purple, and Schiff base deprotonation (380-nm absorption change) show different kinetics when the protein is solubilized in suitable detergents. Our data are consistent with a two-step reaction:
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Affiliation(s)
- S Arnis
- Institut für Biophysik und Strahlenbiologie, Albert-Ludwigs-Universität, Freiburg, Germany
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