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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: 11] [Impact Index Per Article: 11.0] [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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Delage-Laurin L, Palani RS, Golota N, Mardini M, Ouyang Y, Tan KO, Swager TM, Griffin RG. Overhauser Dynamic Nuclear Polarization with Selectively Deuterated BDPA Radicals. J Am Chem Soc 2021; 143:20281-20290. [PMID: 34813311 DOI: 10.1021/jacs.1c09406] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The Overhauser effect (OE), commonly observed in NMR spectra of liquids and conducting solids, was recently discovered in insulating solids doped with the radical 1,3-bisdiphenylene-2-phenylallyl (BDPA). However, the mechanism of polarization transfer in OE-DNP in insulators is yet to be established, but hyperfine coupling of the radical to protons in BDPA has been proposed. In this paper we present a study that addresses the role of hyperfine couplings via the EPR and DNP measurements on some selectively deuterated BDPA radicals synthesized for this purpose. Newly developed synthetic routes enable selective deuteration at orthogonal positions or perdeuteration of the fluorene moieties with 2H incorporation of >93%. The fluorene moieties were subsequently used to synthesize two octadeuterated BDPA radicals, 1,3-[α,γ-d8]-BDPA and 1,3-[β,δ-d8]-BDPA, and a BDPA radical with perdeuterated fluorene moieties, 1,3-[α,β,γ,δ-d16]-BDPA. In contrast to the strong positive OE enhancement observed in degassed samples of fully protonated h21-BDPA (ε ∼ +70), perdeuteration of the fluorenes results in a negative enhancement (ε ∼ -13), while selective deuteration of α- and γ-positions (aiso ∼ 5.4 MHz) in BDPA results in a weak negative OE enhancement (ε ∼ -1). Furthermore, deuteration of β- and δ-positions (aiso ∼ 1.2 MHz) results in a positive OE enhancement (ε ∼ +36), albeit with a reduced magnitude relative to that observed in fully protonated BDPA. Our results clearly show the role of the hyperfine coupled α and γ 1H spins in the BDPA radical in determining the dominance of the zero and double-quantum cross-relaxation pathways and the polarization-transfer mechanism to the bulk matrix.
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Affiliation(s)
- Léo Delage-Laurin
- Institute for Soldier Nanotechnologies, Cambridge, Massachusetts 02139, United States
| | | | | | | | | | | | - Timothy M Swager
- Institute for Soldier Nanotechnologies, Cambridge, Massachusetts 02139, United States
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Can TV, Tan KO, Yang C, Weber RT, Griffin RG. Time domain DNP at 1.2 T. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2021; 329:107012. [PMID: 34186299 PMCID: PMC9148420 DOI: 10.1016/j.jmr.2021.107012] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 05/28/2023]
Abstract
We present the results of an experimental pulsed DNP study at 1.2 T (33.5 GHz/51 MHz electron and 1H Larmor frequencies, respectively). The results include a comparison of constant-amplitude NOVEL (CA-NOVEL), ramped-amplitude NOVEL (RA-NOVEL) and the frequency-swept integrated solid effect (FS-ISE) experiments all of which were performed at the NOVEL matching condition, ω1S=ω0I, where ω1S is the electron Rabi frequency andω0I the proton Larmor frequency. To the best of our knowledge, this is the first pulsed DNP study carried out at field higher than X-band (0.35 T) using the NOVEL condition. A combination of high microwave power (∼150 W) and a microwave cavity with a high Q (∼500) allowed us to satisfy the NOVEL matching condition. We also observed stretched solid effect (S2E) contributions in the Zeeman field profiles when chirped pulses are applied. Furthermore, the high quality factor of the cavity limits the concentration of the radical to ∼5 mM and generates a hysteresis in the FS-ISE experiments. Nevertheless, we observe very high DNP enhancements that are comparable to the results at X-band. These promising outcomes suggest the importance of further studies at even higher fields that delineate the instrumentation and methods required for time domain DNP.
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Affiliation(s)
- T V Can
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - K O Tan
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - C Yang
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - R T Weber
- Bruker BioSpin Corporation, Billerica, MA 01821, United States
| | - R G Griffin
- Francis Bitter Magnet Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, United States; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
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Abstract
The solid effect (SE) is a two spin dynamic nuclear polarization (DNP) mechanism that enhances the sensitivity in NMR experiments by irradiation of the electron-nuclear spin transitions with continuous wave (CW) microwaves at ω0S ± ω0I, where ω0S and ω0I are electron and nuclear Larmor frequencies, respectively. Using trityl (OX063), dispersed in a 60/40 glycerol/water mixture at 80 K, as a polarizing agent, we show here that application of a chirped microwave pulse, with a bandwidth comparable to the EPR line width applied at the SE matching condition, improves the enhancement by a factor of 2.4 over the CW method. Furthermore, the chirped pulse yields an enhancement that is ∼20% larger than obtained with the ramped-amplitude NOVEL (RA-NOVEL), which to date has achieved the largest enhancements in time domain DNP experiments. Numerical simulations suggest that the spins follow an adiabatic trajectory during the polarization transfer; hence, we denote this sequence as an adiabatic solid effect (ASE). We foresee that ASE will be a practical pulsed DNP experiment to be implemented at higher static magnetic fields due to the moderate power requirement. In particular, the ASE uses only 13% of the maximum microwave power required for RA-NOVEL.
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Affiliation(s)
- Kong Ooi Tan
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ralph T Weber
- Bruker BioSpin Corporation, Billerica, Massachusetts 01821, United States
| | - Thach V Can
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Robert G Griffin
- Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Stensitzki T, Yang Y, Muders V, Schlesinger R, Heberle J, Heyne K. Femtosecond infrared spectroscopy of channelrhodopsin-1 chromophore isomerization. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:043208. [PMID: 27191011 PMCID: PMC4851625 DOI: 10.1063/1.4948338] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 04/15/2016] [Indexed: 06/05/2023]
Abstract
Vibrational dynamics of the retinal all-trans to 13-cis photoisomerization in channelrhodopsin-1 from Chlamydomonas augustae (CaChR1) was investigated by femtosecond visible pump mid-IR probe spectroscopy. After photoexcitation, the transient infrared absorption of C-C stretching modes was detected. The formation of the 13-cis photoproduct marker band at 1193 cm(-1) was observed within the time resolution of 0.3 ps. We estimated the photoisomerization yield to (60 ± 6) %. We found additional time constants of (0.55 ± 0.05) ps and (6 ± 1) ps, assigned to cooling, and cooling processes with a back-reaction pathway. An additional bleaching band demonstrates the ground-state heterogeneity of retinal.
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Affiliation(s)
- T Stensitzki
- Department of Physics, Institute of Experimental Physics , Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - Y Yang
- Department of Physics, Institute of Experimental Physics , Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - V Muders
- Genetic Biophysics, Department of Physics, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - R Schlesinger
- Genetic Biophysics, Department of Physics, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - J Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
| | - K Heyne
- Department of Physics, Institute of Experimental Physics , Freie Universität Berlin , Arnimallee 14, 14195 Berlin, Germany
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Wand A, Gdor I, Zhu J, Sheves M, Ruhman S. Shedding New Light on Retinal Protein Photochemistry. Annu Rev Phys Chem 2013; 64:437-58. [DOI: 10.1146/annurev-physchem-040412-110148] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Amir Wand
- Institute of Chemistry and the Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
| | - Itay Gdor
- Institute of Chemistry and the Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
| | - Jingyi Zhu
- Institute of Chemistry and the Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
| | - Mordechai Sheves
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sanford Ruhman
- Institute of Chemistry and the Farkas Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel;
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Wand A, Rozin R, Eliash T, Jung KH, Sheves M, Ruhman S. Asymmetric Toggling of a Natural Photoswitch: Ultrafast Spectroscopy of Anabaena Sensory Rhodopsin. J Am Chem Soc 2011; 133:20922-32. [DOI: 10.1021/ja208371g] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amir Wand
- Institute of Chemistry and Farkash Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Rinat Rozin
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tamar Eliash
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Shinsu-Dong 1, Mapo-Gu, Seoul 121-742, South Korea
| | - Mordechai Sheves
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sanford Ruhman
- Institute of Chemistry and Farkash Center for Light-Induced Processes, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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9
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Gebhard R, Courtin JML, Shadid JB, van Haveren J, van Haeringen CJ, Lugtenburg J. Synthesis of retinals labelled with 13C in the cyclohexene ring. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19891080602] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Gebhard R, van der Hoef K, Lefeber AWM, Erkelens C, Lugtenburg J. Synthesis and spectroscopy of (14′-13C)- and (15′-13C)spheroidene. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19901090604] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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11
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Spijker-Assink MB, Winkel C, Baldwin GS, Lugtenburg J. 5-Demethylretinal and its 5-2H, 7-2H2 and 5,7-2H2 isotopomers. Synthesis, photochemistry and spectroscopy. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19881070304] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Goncalves JA, Ahuja S, Erfani S, Eilers M, Smith SO. Structure and function of G protein-coupled receptors using NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2010; 57:159-80. [PMID: 20633362 PMCID: PMC2907352 DOI: 10.1016/j.pnmrs.2010.04.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 04/08/2010] [Indexed: 05/15/2023]
Affiliation(s)
- Joseph A Goncalves
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
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Rajput J, Rahbek D, Andersen L, Hirshfeld A, Sheves M, Altoè P, Orlandi G, Garavelli M. Probing and Modeling the Absorption of Retinal Protein Chromophores in Vacuo. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905061] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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14
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Rajput J, Rahbek D, Andersen L, Hirshfeld A, Sheves M, Altoè P, Orlandi G, Garavelli M. Probing and Modeling the Absorption of Retinal Protein Chromophores in Vacuo. Angew Chem Int Ed Engl 2010; 49:1790-3. [DOI: 10.1002/anie.200905061] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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Ahuja S, Eilers M, Hirshfeld A, Yan ECY, Ziliox M, Sakmar TP, Sheves M, Smith SO. 6-s-cis Conformation and polar binding pocket of the retinal chromophore in the photoactivated state of rhodopsin. J Am Chem Soc 2010; 131:15160-9. [PMID: 19795853 DOI: 10.1021/ja9034768] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The visual pigment rhodopsin is unique among the G protein-coupled receptors in having an 11-cis retinal chromophore covalently bound to the protein through a protonated Schiff base linkage. The chromophore locks the visual receptor in an inactive conformation through specific steric and electrostatic interactions. This efficient inverse agonist is rapidly converted to an agonist, the unprotonated Schiff base of all-trans retinal, upon light activation. Here, we use magic angle spinning NMR spectroscopy to obtain the (13)C chemical shifts (C5-C20) of the all-trans retinylidene chromophore and the (15)N chemical shift of the Schiff base nitrogen in the active metarhodopsin II intermediate. The retinal chemical shifts are sensitive to the conformation of the chromophore and its molecular interactions within the protein-binding site. Comparison of the retinal chemical shifts in metarhodopsin II with those of retinal model compounds reveals that the Schiff base environment is polar. In particular, the (13)C15 and (15)Nepsilon chemical shifts indicate that the C horizontal lineN bond is highly polarized in a manner that would facilitate Schiff base hydrolysis. We show that a strong perturbation of the retinal (13)C12 chemical shift observed in rhodopsin is reduced in wild-type metarhodopsin II and in the E181Q mutant of rhodopsin. On the basis of the T(1) relaxation time of the retinal (13)C18 methyl group and the conjugated retinal (13)C5 and (13)C8 chemical shifts, we have determined that the conformation of the retinal C6-C7 single bond connecting the beta-ionone ring and the retinylidene chain is 6-s-cis in both the inactive and the active states of rhodopsin. These results are discussed within the general framework of ligand-activated G protein-coupled receptors.
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Affiliation(s)
- Shivani Ahuja
- Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York 11794-5215, USA
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Brown MF, Salgado GFJ, Struts AV. Retinal dynamics during light activation of rhodopsin revealed by solid-state NMR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1798:177-93. [PMID: 19716801 DOI: 10.1016/j.bbamem.2009.08.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2009] [Revised: 07/25/2009] [Accepted: 08/12/2009] [Indexed: 11/28/2022]
Abstract
Rhodopsin is a canonical member of class A of the G protein-coupled receptors (GPCRs) that are implicated in many of the drug interventions in humans and are of great pharmaceutical interest. The molecular mechanism of rhodopsin activation remains unknown as atomistic structural information for the active metarhodopsin II state is currently lacking. Solid-state (2)H NMR constitutes a powerful approach to study atomic-level dynamics of membrane proteins. In the present application, we describe how information is obtained about interactions of the retinal cofactor with rhodopsin that change with light activation of the photoreceptor. The retinal methyl groups play an important role in rhodopsin function by directing conformational changes upon transition into the active state. Site-specific (2)H labels have been introduced into the methyl groups of retinal and solid-state (2)H NMR methods applied to obtain order parameters and correlation times that quantify the mobility of the cofactor in the inactive dark state, as well as the cryotrapped metarhodopsin I and metarhodopsin II states. Analysis of the angular-dependent (2)H NMR line shapes for selectively deuterated methyl groups of rhodopsin in aligned membranes enables determination of the average ligand conformation within the binding pocket. The relaxation data suggest that the beta-ionone ring is not expelled from its hydrophobic pocket in the transition from the pre-activated metarhodopsin I to the active metarhodopsin II state. Rather, the major structural changes of the retinal cofactor occur already at the metarhodopsin I state in the activation process. The metarhodopsin I to metarhodopsin II transition involves mainly conformational changes of the protein within the membrane lipid bilayer rather than the ligand. The dynamics of the retinylidene methyl groups upon isomerization are explained by an activation mechanism involving cooperative rearrangements of extracellular loop E2 together with transmembrane helices H5 and H6. These activating movements are triggered by steric clashes of the isomerized all-trans retinal with the beta4 strand of the E2 loop and the side chains of Glu(122) and Trp(265) within the binding pocket. The solid-state (2)H NMR data are discussed with regard to the pathway of the energy flow in the receptor activation mechanism.
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Affiliation(s)
- Michael F Brown
- Department of Chemistry, University of Arizona, Tucson, AZ 85721, USA; Department of Physics, University of Arizona, Tucson, AZ 85721, USA.
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Lau PW, Grossfield A, Feller SE, Pitman MC, Brown MF. Dynamic structure of retinylidene ligand of rhodopsin probed by molecular simulations. J Mol Biol 2007; 372:906-917. [PMID: 17719606 PMCID: PMC5233727 DOI: 10.1016/j.jmb.2007.06.047] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2007] [Revised: 06/13/2007] [Accepted: 06/18/2007] [Indexed: 11/22/2022]
Abstract
Rhodopsin is currently the only available atomic-resolution template for understanding biological functions of the G protein-coupled receptor (GPCR) family. The structural basis for the phenomenal dark state stability of 11-cis-retinal bound to rhodopsin and its ultrafast photoreaction are active topics of research. In particular, the beta-ionone ring of the retinylidene inverse agonist is crucial for the activation mechanism. We analyzed a total of 23 independent, 100 ns all-atom molecular dynamics simulations of rhodopsin embedded in a lipid bilayer in the microcanonical (N,V,E) ensemble. Analysis of intramolecular fluctuations predicts hydrogen-out-of-plane (HOOP) wagging modes of retinal consistent with those found in Raman vibrational spectroscopy. We show that sampling and ergodicity of the ensemble of simulations are crucial for determining the distribution of conformers of retinal bound to rhodopsin. The polyene chain is rigidly locked into a single, twisted conformation, consistent with the function of retinal as an inverse agonist in the dark state. Most surprisingly, the beta-ionone ring is mobile within its binding pocket; interactions are non-specific and the cavity is sufficiently large to enable structural heterogeneity. We find that retinal occupies two distinct conformations in the dark state, contrary to most previous assumptions. The beta-ionone ring can rotate relative to the polyene chain, thereby populating both positively and negatively twisted 6-s-cis enantiomers. This result, while unexpected, strongly agrees with experimental solid-state (2)H NMR spectra. Correlation analysis identifies the residues most critical to controlling mobility of retinal; we find that Trp265 moves away from the ionone ring prior to any conformational transition. Our findings reinforce how molecular dynamics simulations can challenge conventional assumptions for interpreting experimental data, especially where existing models neglect conformational fluctuations.
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Affiliation(s)
- Pick-Wei Lau
- Department of Biochemistry & Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
| | - Alan Grossfield
- IBM TJ Watson Research Center, Yorktown Heights, New York 10598, USA
| | - Scott E. Feller
- Department of Chemistry, Wabash College, Crawfordsville, Indiana 47933, USA
| | - Michael C. Pitman
- IBM TJ Watson Research Center, Yorktown Heights, New York 10598, USA
| | - Michael F. Brown
- Department of Biochemistry & Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA
- Department of Physics, University of Arizona, Tucson, Arizona 85721, USA
- Corresponding author. Present address: Pick-Wei Lau, Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
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Struts AV, Salgado GFJ, Tanaka K, Krane S, Nakanishi K, Brown MF. Structural analysis and dynamics of retinal chromophore in dark and meta I states of rhodopsin from 2H NMR of aligned membranes. J Mol Biol 2007; 372:50-66. [PMID: 17640664 PMCID: PMC5233725 DOI: 10.1016/j.jmb.2007.03.046] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2006] [Revised: 03/02/2007] [Accepted: 03/19/2007] [Indexed: 11/29/2022]
Abstract
Rhodopsin is a prototype for G protein-coupled receptors (GPCRs) that are implicated in many biological responses in humans. A site-directed (2)H NMR approach was used for structural analysis of retinal within its binding cavity in the dark and pre-activated meta I states. Retinal was labeled with (2)H at the C5, C9, or C13 methyl groups by total synthesis, and was used to regenerate the opsin apoprotein. Solid-state (2)H NMR spectra were acquired for aligned membranes in the low-temperature lipid gel phase versus the tilt angle to the magnetic field. Data reduction assumed a static uniaxial distribution, and gave the retinylidene methyl bond orientations plus the alignment disorder (mosaic spread). The dark-state (2)H NMR structure of 11-cis-retinal shows torsional twisting of the polyene chain and the beta-ionone ring. The ligand undergoes restricted motion, as evinced by order parameters of approximately 0.9 for the spinning C-C(2)H(3) groups, with off-axial fluctuations of approximately 15 degrees . Retinal is accommodated within the rhodopsin binding pocket with a negative pre-twist about the C11=C12 double bond that explains its rapid photochemistry and the trajectory of 11-cis to trans isomerization. In the cryo-trapped meta I state, the (2)H NMR structure shows a reduction of the polyene strain, while torsional twisting of the beta-ionone ring is maintained. Distortion of the retinal conformation is interpreted through substituent control of receptor activation. Steric hindrance between trans retinal and Trp265 can trigger formation of the subsequent activated meta II state. Our results are pertinent to quantum and molecular mechanics simulations of ligands bound to GPCRs, and illustrate how (2)H NMR can be applied to study their biological mechanisms of action.
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Affiliation(s)
- Andrey V. Struts
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA
| | - Gilmar F. J. Salgado
- Department of Biochemistry & Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
| | - Katsunori Tanaka
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Sonja Krane
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Koji Nakanishi
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Michael F. Brown
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA
- Department of Biochemistry & Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
- Department of Physics, University of Arizona, Tucson, Arizona 85721, USA
- Corresponding author:
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Scheidt HA, Vogel A, Eckhoff A, Koenig BW, Huster D. Solid-state NMR characterization of the putative membrane anchor of TWD1 from Arabidopsis thaliana. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2006; 36:393-404. [PMID: 17033777 DOI: 10.1007/s00249-006-0094-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2006] [Revised: 08/16/2006] [Accepted: 08/25/2006] [Indexed: 10/24/2022]
Abstract
Structure and membrane interaction of a 31 amino acid residue fragment of the membrane bound FKBP-like protein twisted dwarf 1 (TWD1) from Arabidopsis thaliana was investigated by solid-state NMR spectroscopy. The studied peptide TWD1(335-365) contained the putative membrane anchor of the protein (residues 339-357) that was previously predicted by sequence hydrophobicity analysis. The TWD1 peptide was synthesized by standard solid phase peptide synthesis and contained three uniformly (13)C- and (15)N-labelled residues (Phe 340, Val 350, Ala 364). The peptide was incorporated into either multilamellar vesicles or oriented planar membranes composed of an equimolar ternary phospholipid mixture (POPC, POPE, POPG), where the POPC was sn-1 chain-deuterated. (31)P NMR spectra of the membrane in the absence and in the presence of the peptide showed axially symmetric powder patterns indicative of a lamellar bilayer phase. Further, the addition of peptide caused a decrease in the lipid hydrocarbon chain order as indicated by reduced quadrupolar splittings in the (2)H NMR spectra of the POPC in the membrane. The conformation of TWD1(335-365) was investigated by (13)C cross-polarization magic-angle spinning NMR spectroscopy. At a temperature of -30 degrees C all peptide signals were resolved and could be fully assigned in two-dimensional proton-driven (13)C spin diffusion and (13)C single quantum/double quantum correlation experiments. The isotropic chemical shift values for Phe 340 and Val 350 exhibited the signature of a regular alpha-helix. Chemical shifts typical for a random coil conformation were observed for Ala 364 located close to the C-terminus of the peptide. Static (15)N NMR spectra of TWD1(335-365) in mechanically aligned lipid bilayers demonstrated that the helical segment of TWD1(335-365) adopts an orientation perpendicular to the membrane normal. At 30 degrees C, the peptide undergoes intermediate time scale motions.
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Affiliation(s)
- Holger A Scheidt
- Junior Research Group, Structural Biology of Membrane Proteins, Institute of Biotechnology, Martin Luther University Halle-Wittenberg, Halle, Germany
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20
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Yeagle PL, Albert AD. G-protein coupled receptor structure. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2006; 1768:808-24. [PMID: 17097603 DOI: 10.1016/j.bbamem.2006.10.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Revised: 10/02/2006] [Accepted: 10/05/2006] [Indexed: 11/18/2022]
Abstract
Because of their central role in regulation of cellular function, structure/function relationships for G-protein coupled receptors (GPCR) are of vital importance, yet only recently have sufficient data been obtained to begin mapping those relationships. GPCRs regulate a wide range of cellular processes, including the senses of taste, smell, and vision, and control a myriad of intracellular signaling systems in response to external stimuli. Many diseases are linked to GPCRs. A critical need exists for structural information to inform studies on mechanism of receptor action and regulation. X-ray crystal structures of only one GPCR, in an inactive state, have been obtained to date. However considerable structural information for a variety of GPCRs has been obtained using non-crystallographic approaches. This review begins with a review of the very earliest GPCR structural information, mostly derived from rhodopsin. Because of the difficulty in crystallizing GPCRs for X-ray crystallography, the extensive published work utilizing alternative approaches to GPCR structure is reviewed, including determination of three-dimensional structure from sparse constraints. The available X-ray crystallographic analyses on bovine rhodopsin are reviewed as the only available high-resolution structures for any GPCR. Structural information available on ligand binding to several receptors is included. The limited information on excited states of receptors is also reviewed. It is concluded that while considerable basic structural information has been obtained, more data are needed to describe the molecular mechanism of activation of a GPCR.
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Affiliation(s)
- Philip L Yeagle
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
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21
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Saam J, Tajkhorshid E, Hayashi S, Schulten K. Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin. Biophys J 2002; 83:3097-112. [PMID: 12496081 PMCID: PMC1302389 DOI: 10.1016/s0006-3495(02)75314-9] [Citation(s) in RCA: 154] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Retinal cis-trans isomerization and early relaxation steps have been studied in a 10-ns molecular dynamics simulation of a fully hydrated model of membrane-embedded rhodopsin. The isomerization, induced by transiently switching the potential energy function governing the C(11)==C(12) dihedral angle of retinal, completes within 150 fs and yields a strongly distorted retinal. The most significant conformational changes in the binding pocket are straightening of retinal's polyene chain and separation of its beta-ionone ring from Trp-265. In the following 500 ps, transition of 6s-cis to 6s-trans retinal and dramatic changes in the hydrogen bonding network of the binding pocket involving the counterion for the protonated Schiff base, Glu-113, occur. Furthermore, the energy initially stored internally in the distorted retinal is transformed into nonbonding interactions of retinal with its environment. During the following 10 ns, increased mobilities of some parts of the protein, such as the kinked regions of the helices, mainly helix VI, and the intracellular loop I2, were observed, as well as transient structural changes involving the conserved salt bridge between Glu-134 and Arg-135. These features prepare the protein for major structural transformations achieved later in the photocycle. Retinal's motion, in particular, can be compared to an opening turnstile freeing the way for the proposed rotation of helix VI. This was demonstrated by a steered molecular dynamics simulation in which an applied torque enforced the rotation of helix VI.
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Affiliation(s)
- Jan Saam
- Beckman Institute, University of Illinois at Urbana-Champaign, 405 N. Mathews Avenue, Urbana, IL 61801, USA
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22
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Abstract
Bovine rhodopsin is the prototypical G protein coupled receptor (GPCR). It was the first GPCR to be obtained in quantity and studied in detail. It is also the first GPCR for which detailed three dimensional structural information has been obtained. Reviewed here are the experiments leading up to the high resolution structure determination of rhodopsin and the most recent structural information on the activation and stability of this integral membrane protein.
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Affiliation(s)
- Arlene D Albert
- Department of Molecular and Cell Biology, U-125 University of Connecticut, 75 North Eagleville Road, Storrs, CT 06269-3125, USA
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23
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Gärtner W. The Light Shall Show the Way-Or: The Conformational Changes of the Retinal Chromophore in Rhodopsin upon Light Activation. Angew Chem Int Ed Engl 2002; 40:2977-81. [PMID: 12203622 DOI: 10.1002/1521-3773(20010817)40:16<2977::aid-anie2977>3.0.co;2-e] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The visual pigment rhodopsin constitutes the interface between the physical event of light absorption and the biochemical process of visual transduction within the photoreceptor cells. The signal transduction is initiated by an 11-cis→all-trans photoisomerization of the retinal chromophore of rhodopsin which causes a series of thermally driven conformational changes of the chromophore and the protein moiety. A rhodopsin conformation is generated which allows interaction with a heterotrimeric G-protein. Two recent publications follow the chromophore motions after light absorption by cross-linking experiments and by solid-state NMR spectroscopy.
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Affiliation(s)
- W Gärtner
- Max-Planck-Institut für Strahlenchemie Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany, Fax: (+49) 208-306-3951.
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24
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Creemers AFL, Kiihne S, Bovee-Geurts PHM, DeGrip WJ, Lugtenburg J, de Groot HJM. (1)H and (13)C MAS NMR evidence for pronounced ligand-protein interactions involving the ionone ring of the retinylidene chromophore in rhodopsin. Proc Natl Acad Sci U S A 2002; 99:9101-6. [PMID: 12093898 PMCID: PMC123100 DOI: 10.1073/pnas.112677599] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2001] [Indexed: 11/18/2022] Open
Abstract
Rhodopsin is a member of the superfamily of G-protein-coupled receptors. This seven alpha-helix transmembrane protein is the visual pigment of the vertebrate rod photoreceptor cells that mediate dim light vision. In the active binding site of this protein the ligand or chromophore, 11-cis-retinal, is covalently bound via a protonated Schiff base to lysine residue 296. Here we present the complete (1)H and (13)C assignments of the 11-cis-retinylidene chromophore in its ligand-binding site determined with ultra high field magic angle spinning NMR. Native bovine opsin was regenerated with 99% enriched uniformly (13)C-labeled 11-cis-retinal. From the labeled pigment, (13)C carbon chemical shifts could be obtained by using two-dimensional radio frequency-driven dipolar recoupling in a solid-state magic angle spinning homonuclear correlation experiment. The (1)H chemical shifts were assigned by two-dimensional heteronuclear ((1)H-(13)C) dipolar correlation spectroscopy with phase-modulated Lee-Goldburg homonuclear (1)H decoupling applied during the t(1) period. The data indicate nonbonding interactions between the protons of the methyl groups of the retinylidene ionone ring and the protein. These nonbonding interactions are attributed to nearby aromatic acid residues Phe-208, Phe-212, and Trp-265 that are in close contact with, respectively, H-16/H-17 and H-18. Furthermore, binding of the chromophore involves a chiral selection of the ring conformation, resulting in equatorial and axial positions for CH(3)-16 and CH(3)-17.
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Affiliation(s)
- Alain F L Creemers
- Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
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25
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Fujimoto Y, Ishihara J, Maki S, Fujioka N, Wang T, Furuta T, Fishkin N, Borhan B, Berova N, Nakanishi K. On the bioactive conformation of the rhodopsin chromophore: absolute sense of twist around the 6-s-cis bond. Chemistry 2001; 7:4198-204. [PMID: 11686599 DOI: 10.1002/1521-3765(20011001)7:19<4198::aid-chem4198>3.0.co;2-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Incubation of opsin with synthetic 6-s-locked retinoids 2a and 2b only led to pigment formation from the alpha-locked 2a, the CD spectrum of which was similar to that of native rhodopsin (Rh). This establishes that the 6-s-bond of the chromophore in rhodopsin is cis, and that its helicity is negative. Earlier cross-linking studies showed that the 11-cis to all-trans photoisomerization occurring in the batho-Rh to lumi-Rh conversion induces a flip over of the side carrying the ring moiety. The GTP-binding assay of pigment Rh-(2a), incorporating retinal analogue 2a, has shown that its activity is 80% that of the native pigment. That is, the overall conformation around the 6-s bond is retained in the steps leading to G-protein activation.
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Affiliation(s)
- Y Fujimoto
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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26
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Gärtner W. Das Licht weise den Weg - oder: die Konformationsänderungen des Retinalchromophors im Sehpigment Rhodopsin nach Lichtanregung. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010817)113:16<3065::aid-ange3065>3.0.co;2-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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27
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Teller DC, Okada T, Behnke CA, Palczewski K, Stenkamp RE. Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of G-protein-coupled receptors (GPCRs). Biochemistry 2001; 40:7761-72. [PMID: 11425302 PMCID: PMC1698954 DOI: 10.1021/bi0155091] [Citation(s) in RCA: 513] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D C Teller
- Department of Ophthalmology, and Biological Structure and Biomolecular Structure Center, University of Washington, Seattle, Washington 98195, USA.
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28
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Sanders CR, Oxenoid K. Customizing model membranes and samples for NMR spectroscopic studies of complex membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1508:129-45. [PMID: 11090822 DOI: 10.1016/s0005-2736(00)00308-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Both solution and solid state nuclear magnetic resonance (NMR) techniques for structural determination are advancing rapidly such that it is possible to contemplate bringing these techniques to bear upon integral membrane proteins having multiple transmembrane segments. This review outlines existing and emerging options for model membrane media for use in such studies and surveys the special considerations which must be taken into account when preparing larger membrane proteins for NMR spectroscopic studies.
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Affiliation(s)
- C R Sanders
- Department of Physiology and Biophysics, Case Western Reserve University, 44106-4970, Cleveland, OH, USA.
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29
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Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M. Crystal structure of rhodopsin: A G protein-coupled receptor. Science 2000; 289:739-45. [PMID: 10926528 DOI: 10.1126/science.289.5480.739] [Citation(s) in RCA: 4169] [Impact Index Per Article: 173.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) respond to a variety of different external stimuli and activate G proteins. GPCRs share many structural features, including a bundle of seven transmembrane alpha helices connected by six loops of varying lengths. We determined the structure of rhodopsin from diffraction data extending to 2.8 angstroms resolution. The highly organized structure in the extracellular region, including a conserved disulfide bridge, forms a basis for the arrangement of the seven-helix transmembrane motif. The ground-state chromophore, 11-cis-retinal, holds the transmembrane region of the protein in the inactive conformation. Interactions of the chromophore with a cluster of key residues determine the wavelength of the maximum absorption. Changes in these interactions among rhodopsins facilitate color discrimination. Identification of a set of residues that mediate interactions between the transmembrane helices and the cytoplasmic surface, where G-protein activation occurs, also suggests a possible structural change upon photoactivation.
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Affiliation(s)
- K Palczewski
- Department of Ophthalmology, University of Washington, Seattle, WA 98195, USA.
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30
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Gröbner G, Burnett IJ, Glaubitz C, Choi G, Mason AJ, Watts A. Observations of light-induced structural changes of retinal within rhodopsin. Nature 2000; 405:810-3. [PMID: 10866205 DOI: 10.1038/35015604] [Citation(s) in RCA: 108] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Photo-isomerization of the 11-cis retinal chromophore activates the mammalian light-receptor rhodopsin, a representative member of a major superfamily of transmembrane G-protein-coupled receptor proteins (GPCRs) responsible for many cell signal communication pathways. Although low-resolution (5 A) electron microscopy studies confirm a seven transmembrane helix bundle as a principal structural component of rhodopsin, the structure of the retinal within this helical bundle is not known in detail. Such information is essential for any theoretical or functional understanding of one of the fastest occurring photoactivation processes in nature, as well as the general mechanism behind GPCR activation. Here we determine the three-dimensional structure of 11-cis retinal bound to bovine rhodopsin in the ground state at atomic level using a new high-resolution solid-state NMR method. Significant structural changes are observed in the retinal following activation by light to the photo-activated M(I) state of rhodopsin giving the all-trans isomer of the chromophore. These changes are linked directly to the activation of the receptor, providing an insight into the activation mechanism of this class of receptors at a molecular level.
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Affiliation(s)
- G Gröbner
- Department of Biochemistry, University of Oxford, UK
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31
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Ishiguro M. A Mechanism of Primary Photoactivation Reactions of Rhodopsin: Modeling of the Intermediates in the Rhodopsin Photocycle. J Am Chem Soc 2000. [DOI: 10.1021/ja9921367] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masaji Ishiguro
- Contribution from the Suntory Institute for Bioorganic Research, 1-1 Wakayamadai, Shimamoto, Osaka 618-8503, Japan
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32
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Degrip W, Rothschild K. Chapter 1 Structure and mechanism of vertebrate visual pigments. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1383-8121(00)80004-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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33
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Makino CL, Groesbeek M, Lugtenburg J, Baylor DA. Spectral tuning in salamander visual pigments studied with dihydroretinal chromophores. Biophys J 1999; 77:1024-35. [PMID: 10423447 PMCID: PMC1300393 DOI: 10.1016/s0006-3495(99)76953-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
In visual pigments, opsin proteins regulate the spectral absorption of a retinal chromophore by mechanisms that change the energy level of the excited electronic state relative to the ground state. We have studied these mechanisms by using photocurrent recording to measure the spectral sensitivities of individual red rods and red (long-wavelength-sensitive) and blue (short-wavelength-sensitive) cones of salamander before and after replacing the native 3-dehydro 11-cis retinal chromophore with retinal analogs: 11-cis retinal, 3-dehydro 9-cis retinal, 9-cis retinal, and 5,6-dihydro 9-cis retinal. The protonated Schiff's bases of analogs with unsaturated bonds in the ring had broader spectra than the same chromophores bound to opsins. Saturation of the bonds in the ring reduced the spectral bandwidths of the protonated Schiff's bases and the opsin-bound chromophores and made them similar to each other. This indicates that torsion of the ring produces spectral broadening and that torsion is limited by opsin. Saturating the 5,6 double bond in retinal reduced the perturbation of the chromophore by opsin in red and in blue cones but not in red rods. Thus an interaction between opsin and the chromophoric ring shifts the spectral maxima of the red and blue cone pigments, but not that of the red rod pigment.
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Affiliation(s)
- C L Makino
- Department of Ophthalmology, Harvard Medical School, and the Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114, USA.
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34
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Pogozheva ID, Lomize AL, Mosberg HI. The transmembrane 7-alpha-bundle of rhodopsin: distance geometry calculations with hydrogen bonding constraints. Biophys J 1997; 72:1963-85. [PMID: 9129801 PMCID: PMC1184393 DOI: 10.1016/s0006-3495(97)78842-8] [Citation(s) in RCA: 121] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A 3D model of the transmembrane 7-alpha-bundle of rhodopsin-like G-protein-coupled receptors (GPCRs) was calculated using an iterative distance geometry refinement with an evolving system of hydrogen bonds, formed by intramembrane polar side chains in various proteins of the family and collectively applied as distance constraints. The alpha-bundle structure thus obtained provides H bonding of nearly all buried polar side chains simultaneously in the 410 GPCRs considered. Forty evolutionarily conserved GPCR residues form a single continuous domain, with an aliphatic "core" surrounded by six clusters of polar and aromatic side chains. The 7-alpha-bundle of a specific GPCR can be calculated using its own set of H bonds as distance constraints and the common "average" model to restrain positions of the helices. The bovine rhodopsin model thus determined is closely packed, but has a few small polar cavities, presumably filled by water, and has a binding pocket that is complementary to 11-cis (6-s-cis, 12-s-trans, C = N anti)-retinal or to all-trans-retinal, depending on conformations of the Lys296 and Trp265 side chains. A suggested mechanism of rhodopsin photoactivation, triggered by the cis-trans isomerization of retinal, involves rotations of Glu134, Tyr223, Trp265, Lys296, and Tyr306 side chains and rearrangement of their H bonds. The model is in agreement with published electron cryomicroscopy, mutagenesis, chemical modification, cross-linking, Fourier transform infrared spectroscopy, Raman spectroscopy, electron paramagnetic resonance spectroscopy, NMR, and optical spectroscopy data. The rhodopsin model and the published structure of bacteriorhodopsin have very similar retinal-binding pockets.
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Affiliation(s)
- I D Pogozheva
- College of Pharmacy, University of Michigan, Ann Arbor 48109, USA
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35
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Abstract
For the first time the total synthesis of the peptaibol zervamicin IIB is described. Synthesis of this peptaibol was achieved by the Fmoc/tert-butyl strategy in solution using a fragment condensation approach. Three fragments of zervamicin IIB were obtained by stepwise elongation with Fmoc amino acids using BOP as a coupling reagent. For the introduction of the highly sterically hindered alpha-aminoisobutyric acid residues BOP/DMAP activation was applied. The fmoc group was removed by reaction with 0.1 M NaOH in dioxane/methanol/water (30/9/1, v/v/v). Peptide fragments were coupled by means of a new coupling reagent, CF3-PyBOP. Using the strategy developed, zervamicin IIB and two analogues specifically deuterium-labelled at different positions of the glutamine-11 residue have been synthesized in 40% overall yield based on the isotopically labelled amino acid and with 98 +/- 2% of isotope enrichment. FAB mass spectroscopy, 600 MHz 1H-NMR spectroscopy and high-performance liquid chromatography provided convincing evidence that the synthetic products, zervamicin IIB and its deuterium-labelled analogues, fully correspond to the naturally occurring zervamicin IIB.
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Affiliation(s)
- A Ogrel
- Leiden Institute of Chemistry, Leiden University, The Netherlands
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36
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Ogrel A, Bloemhoff W, Lugtenburg J, Raap J. Synthesis of the Isotopically LabelledC-Terminal Fragment of Zervamicin: An Approach to the Synthesis of Aib-Containing Peptides. ACTA ACUST UNITED AC 1997. [DOI: 10.1002/jlac.199719970109] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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37
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Abstract
The passage of molecules and information across cell membranes is mediated largely by membrane-spanning proteins acting as channels, pumps, receptors and enzymes. These proteins perform many tasks: they control electrochemical gradients across the membrane, receive signals from the environment or from other cells, convert light energy into chemical signals, transport small molecules into and out of cells, and harness proton gradients to generate the energy consumed in metabolism. Indeed, of the estimated 50000–100000 genes in the human genome, fully 20–40 % are thought to encode integral membrane proteins. If one also includes membrane-associated proteins, which are attached to the membrane surface through fatty acyl chains or electrostatic interactions, this percentage is likely to be much higher.
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Affiliation(s)
- S O Smith
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA
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38
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Maus DC, Copié V, Sun B, Griffiths JM, Griffin RG, Luo S, Schrock RR, Liu AH, Seidel SW, Davis WM, Grohmann A. A Solid-State NMR Study of Tungsten Methyl Group Dynamics in [W(η5-C5Me5)Me4][PF6]. J Am Chem Soc 1996. [DOI: 10.1021/ja960248h] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Douglas C. Maus
- Contribution from the Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Valérie Copié
- Contribution from the Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Boqin Sun
- Contribution from the Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Janet M. Griffiths
- Contribution from the Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Robert G. Griffin
- Contribution from the Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Shifang Luo
- Contribution from the Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Richard R. Schrock
- Contribution from the Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Andrew H. Liu
- Contribution from the Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Scott W. Seidel
- Contribution from the Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - William M. Davis
- Contribution from the Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Andreas Grohmann
- Contribution from the Francis Bitter Magnet Laboratory and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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39
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Houjou H, Sakurai M, Asakawa N, Inoue Y, Tamura Y. Ab InitioStudy of13C Shieldings for Linear π-Conjugated Systems. Theoretical Determination of the C12−C13 Conformation in the Chromophore of Rhodopsin. J Am Chem Soc 1996. [DOI: 10.1021/ja961023+] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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40
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Herzyk P, Hubbard RE. Automated method for modeling seven-helix transmembrane receptors from experimental data. Biophys J 1995; 69:2419-42. [PMID: 8599649 PMCID: PMC1236480 DOI: 10.1016/s0006-3495(95)80112-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A rule-based automated method is presented for modeling the structures of the seven transmembrane helices of G-protein-coupled receptors. The structures are generated by using a simulated annealing Monte Carlo procedure that positions and orients rigid helices to satisfy structural restraints. The restraints are derived from analysis of experimental information from biophysical studies on native and mutant proteins, from analysis of the sequences of related proteins, and from theoretical considerations of protein structure. Calculations are presented for two systems. The method was validated through calculations using appropriate experimental information for bacteriorhodopsin, which produced a model structure with a root mean square (rms) deviation of 1.87 A from the structure determined by electron microscopy. Calculations are also presented using experimental and theoretical information available for bovine rhodopsin to assign the helices to a projection density map and to produce a model of bovine rhodopsin that can be used as a template for modeling other G-protein-coupled receptors.
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Affiliation(s)
- P Herzyk
- Department of Chemistry, University of York, Heslington, United Kingdom.
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41
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Houjou H, Sakurai M, Asakawa N, Inoue Y, Tamura Y, Watanabe Y. Ab initioStudy of the C12-C13 Conformation of 11- cis-retinal. CHEM LETT 1995. [DOI: 10.1246/cl.1995.1039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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42
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Watts A, Ulrich AS, Middleton DA. Membrane protein structure: the contribution and potential of novel solid state NMR approaches. Mol Membr Biol 1995; 12:233-46. [PMID: 8520624 DOI: 10.3109/09687689509072423] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Alternative methods for describing molecular detail for large integral membrane proteins are required in the absence of routine crystallographic approaches. Novel solid state NMR methods, devised for the study of large molecular assemblies, are now finding applications in biological systems, including integral membrane proteins. Wild-type and genetically engineered proteins can be investigated and detailed information about side chains, prosthetic groups, ligands (e.g. drugs) and binding sites can be deduced. The molecular structure and dynamics of selected parts of the proteins are accessible by a range of different solid state NMR approaches. Inter- and intra-atomic distances can be determined rather accurately (within ångströms) and the orientation of molecular bonds (within 2 degrees) can be measured in ideal cases. Here, a brief description of the methods is given and then some specific examples described with an indication of the future potential for the approaches in studying membrane proteins. It is anticipated that this emerging NMR methodology will be more widely used in the future, not only for resolving local structure, but also for more expansive descriptions of membrane protein structure at atomic resolution.
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Affiliation(s)
- A Watts
- Department of Biochemistry, University of Oxford, UK
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43
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Fasman GD. The measurement of transmembrane helices by the deconvolution of CD spectra of membrane proteins: A review. Biopolymers 1995. [DOI: 10.1002/bip.360370505] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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44
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45
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Kinumi T, Tsujimoto K, Ohashi M, Hara R, Hara T, Ozaki K, Sakai M, Katsuta Y, Wada A, Ito M. The conformational analysis and photoisomerization of retinochrome analogs with polyenals. Photochem Photobiol 1993; 58:409-12. [PMID: 8234476 DOI: 10.1111/j.1751-1097.1993.tb09582.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
3,7-Dimethyl-2,4,6,8,10-dodecapentaenal was synthesized for reconstitution of the retinochrome analog. Its opsin shift was 1000 cm-1 smaller than that of native retinochrome, whose chromophore contains the same number of double bonds. The conformational change from 6-s-trans to 6-s-cis, as figured in a retinal molecule, plays an important role in the formation of the retinochrome analog, based on the estimation of opsin shifts for retinal analogs locked in the 6-s conformation. Thus the conformation of the 6-7 single bond in the native retinochrome was suggested to be 6-s-cis. Analysis of the circular dichroic spectra of retinochrome analogs revealed that the 6-s conformation is independent of the appearance of the beta-band. The stereoselectivity in the photoisomerization of the retinal analogs by a retinochrome template depends on the hydrophobic binding in the region of the beta-ionone ring.
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Affiliation(s)
- T Kinumi
- Department of Applied Physics and Chemistry, University of Electro-Communications, Tokyo, Japan
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46
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Park K, Perczel A, Fasman GD. Differentiation between transmembrane helices and peripheral helices by the deconvolution of circular dichroism spectra of membrane proteins. Protein Sci 1992; 1:1032-49. [PMID: 1338977 PMCID: PMC2142169 DOI: 10.1002/pro.5560010809] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The interpretation of the circular dichroism (CD) spectra of proteins to date requires additional secondary structural information of the proteins to be analyzed, such as X-ray or NMR data. Therefore, these methods are inappropriate for a CD database whose secondary structures are unknown, as in the case of the membrane proteins. The convex constraint analysis algorithm (Perczel, A., Hollósi, M., Tusnády, G., & Fasman, G. D., 1991, Protein Eng. 4, 669-679), on the other hand, operates only on a collection of spectral data to extract the common spectral components with their spectral weights. The linear combinations of these derived "pure" CD curves can reconstruct the original data set with great accuracy. For a membrane protein data set, the five-component spectra so obtained from the deconvolution consisted of two different types of alpha helices (the alpha helix in the soluble domain and the alpha T helix, for the transmembrane alpha helix), a beta-pleated sheet, a class C-like spectrum related to beta turns, and a spectrum correlated with the unordered conformation. The deconvoluted CD spectrum for the alpha T helix was characterized by a positive red-shifted band in the range 195-200 nm (+95,000 deg cm2 dmol-1), with the intensity of the negative band at 208 nm being slightly less negative than that of the 222-nm band (-50,000 and -60,000 deg cm2 dmol-1, respectively) in comparison with the regular alpha helix, with a positive band at 190 nm and two negative bands at 208 and 222 nm with magnitudes of +70,000, -30,000, and -30,000 deg cm2 dmol-1, respectively.
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Affiliation(s)
- K Park
- Graduate Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02154
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47
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Abstract
A review is given of the use of nuclear magnetic resonance (NMR) spectroscopy to study bacteriorhodopsin and bovine rhodopsin. Solution and solid-state approaches are included. The studies of the bacterial proton pump examine the chromophore, the peptide backbone, and the protein side chains. The studies of the bovine visual pigment are limited to the chromophore. Various forms of each pigment are considered. Both structural and dynamic features are addressed.
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Affiliation(s)
- L Zheng
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02254-9110
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48
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Affiliation(s)
- P F Knowles
- Department of Biochemistry and Molecular Biology, University of Leeds, U.K
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Foster KW, Saranak J, Dowben PA. Spectral sensitivity, structure and activation of eukaryotic rhodopsins: activation spectroscopy of rhodopsin analogs in Chlamydomonas. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 1991; 8:385-408. [PMID: 1828501 DOI: 10.1016/1011-1344(91)80114-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Retinal normally binds opsin forming the chromophore of the visual pigment, rhodopsin. In this investigation synthetic analogs were bound by the opsin of living cells of the alga Chlamydomonas reinhardtii; the effect was assayed by phototaxis to give an activation spectrum for each rhodopsin analog. The results show the influence of different chromophores and the protein on the absorption of light. The maxima of the phototaxis action spectra shifted systematically with the number of double bonds conjugated with the imine (C = N+H) bond of the chromophore. Chromophores lacking a beta-ionone ring, methyl groups and all C = C double bonds photoactivated the rhodopsin of Chlamydomonas with normal efficiency. On the basis of a simple model involving one-electron transitions between occupied and virtual molecular orbitals, we estimate the charge distribution along the chromophore in the binding site. With this restraint we define a unique structural model for eukaryotic rhodopsins and explain the spectral clustering of pigments, the spectral differences between red and green rhodopsins and the molecular basis of color blindness. Our results are consistent with the triggering of the activation of rhodopsin by the light-mediated change in electric dipole moment rather than the steric cis-trans isomerization of the chromophore.
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Affiliation(s)
- K W Foster
- Department of Physics, Syracuse University, NY 13244-1130
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Takahashi T, Yan B, Mazur P, Derguini F, Nakanishi K, Spudich JL. Color regulation in the archaebacterial phototaxis receptor phoborhodopsin (sensory rhodopsin II). Biochemistry 1990; 29:8467-74. [PMID: 2252905 DOI: 10.1021/bi00488a038] [Citation(s) in RCA: 98] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Phoborhodopsin, a repellent phototaxis receptor in Halobacterium halobium, exhibits vibrational fine structure, a feature that has not been identified for any other rhodopsin pigment at physiological temperatures. This conclusion follows form analysis of the absorption properties of the pigment in H. halobium membranes containing native retinal and an array of retinal analogues. The absorption spectrum of the native pigment has a maximum at 487 nm with a pronounced shoulder at 460 nm; however, the bandwidth is that expected for a single retinylidene species. Gaussian band-shape simulation with a spacing corresponding to the vibrational frequencies of polyene stretching modes reproduces the structured absorption spectra of native pigment as well as of analogue phoborhodopsin. Absorption shifts produced by a series of dihydroretinal and other retinal analogues strongly indicate that the dominant factor regulating the color of the pigment is planarization of the retinal ring with respect to the polyene chain.
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Affiliation(s)
- T Takahashi
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461
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