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Inukai S, Katayama K, Koyanagi M, Terakita A, Kandori H. Counterion at an atypical position: Investigating the mechanism of photoisomerization in jellyfish rhodopsin. J Biol Chem 2023; 299:104726. [PMID: 37094700 DOI: 10.1016/j.jbc.2023.104726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/11/2023] [Accepted: 04/15/2023] [Indexed: 04/26/2023] Open
Abstract
The position of the counterion in animal rhodopsins plays a crucial role in maintaining visible light sensitivity and facilitating the photoisomerization of their retinal chromophore. The counterion displacement is thought to be closely related to the evolution of rhodopsins, with different positions found in invertebrates and vertebrates. Interestingly, box jellyfish rhodopsin (JelRh) acquired the counterion in transmembrane 2 (TM2) independently. This is a unique feature, as in most animal rhodopsins, the counterion is found in a different location. In this study, we used Fourier Transform Infrared spectroscopy to examine the structural changes that occur in the early photointermediate state of JelRh. We aimed to determine whether the photochemistry of JelRh is similar to that of other animal rhodopsins by comparing its spectra to those of vertebrate bovine rhodopsin (BovRh) and invertebrate squid rhodopsin (SquRh). We observed that the N-D stretching band of the retinal Schiff base was similar to that of BovRh, indicating the interaction between the Schiff base and the counterion is similar in both rhodopsins, despite their different counterion positions. Furthermore, we found that the chemical structure of the retinal in JelRh is similar to that in BovRh, including the changes in the hydrogen-out-of-plane band that indicates a retinal distortion. Overall, the protein conformational changes induced by the photoisomerization of JelRh yielded spectra that resemble an intermediate between BovRh and SquRh, suggesting a unique spectral property of JelRh, and making it the only animal rhodopsin with a counterion in TM2 and an ability to activate Gs protein.
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Affiliation(s)
- Shino Inukai
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Kota Katayama
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
| | - Mitsumasa Koyanagi
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, 3-3-138, Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Akihisa Terakita
- Department of Biology, Graduate School of Science, Osaka Metropolitan University, 3-3-138, Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
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Shigaev AS, Feldman TB, Nadtochenko VA, Ostrovsky MA, Lakhno VD. Quantum-classical model of the rhodopsin retinal chromophore cis–trans photoisomerization with modified inter-subsystem coupling. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Brunk E, Rothlisberger U. Mixed Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations of Biological Systems in Ground and Electronically Excited States. Chem Rev 2015; 115:6217-63. [PMID: 25880693 DOI: 10.1021/cr500628b] [Citation(s) in RCA: 296] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Elizabeth Brunk
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,‡Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, California 94618, United States
| | - Ursula Rothlisberger
- †Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,§National Competence Center of Research (NCCR) MARVEL-Materials' Revolution: Computational Design and Discovery of Novel Materials, 1015 Lausanne, Switzerland
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Campomanes P, Neri M, Horta BAC, Röhrig UF, Vanni S, Tavernelli I, Rothlisberger U. Origin of the Spectral Shifts among the Early Intermediates of the Rhodopsin Photocycle. J Am Chem Soc 2014; 136:3842-51. [DOI: 10.1021/ja411303v] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Pablo Campomanes
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Marilisa Neri
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Bruno A. C. Horta
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Ute F. Röhrig
- Molecular Modeling
Group, Swiss Institute of
Bioinformatics, CH-1015 Lausanne, Switzerland
| | - Stefano Vanni
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Ivano Tavernelli
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale Lausanne, CH-1015 Lausanne, Switzerland
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G-protein-coupled receptor structure, ligand binding and activation as studied by solid-state NMR spectroscopy. Biochem J 2013; 450:443-57. [DOI: 10.1042/bj20121644] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
GPCRs (G-protein-coupled receptors) are versatile signalling molecules at the cell surface and make up the largest and most diverse family of membrane receptors in the human genome. They convert a large variety of extracellular stimuli into intracellular responses through the activation of heterotrimeric G-proteins, which make them key regulatory elements in a broad range of normal and pathological processes, and are therefore one of the most important targets for pharmaceutical drug discovery. Knowledge of a GPCR structure enables us to gain a mechanistic insight into its function and dynamics, and further aid rational drug design. Despite intensive research carried out over the last three decades, resolving the structural basis of GPCR function is still a major activity. The crystal structures obtained in the last 5 years provide the first opportunity to understand how protein structure dictates the unique functional properties of these complex signalling molecules. However, owing to the intrinsic hydrophobicity, flexibility and instability of membrane proteins, it is still a challenge to crystallize GPCRs, and, when this is possible, it is no longer in its native membrane environment and no longer without modification. Furthermore, the conformational change of the transmembrane α-helices associated with the structure activation increases the difficulty of capturing the activation state of a GPCR to a higher resolution by X-ray crystallography. On the other hand, solid-state NMR may offer a unique opportunity to study membrane protein structure, ligand binding and activation at atomic resolution in the native membrane environment, as well as described functionally significant dynamics. In the present review, we discuss some recent achievements of solid-state NMR for understanding GPCRs, the largest mammalian proteome at ~1% of the total expressed proteins. Structural information, details of determination, details of ligand conformations and the consequences of ligand binding to initiate activation can all be explored with solid-state NMR.
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Kim JE, McCamant DW, Zhu L, Mathies RA. Resonance Raman Structural Evidence that the Cis-to-Trans Isomerization in Rhodopsin Occurs in Femtoseconds. J Phys Chem B 2012; 105:1240-9. [PMID: 16755302 PMCID: PMC1473983 DOI: 10.1021/jp001236s] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Picosecond time-resolved resonance Raman spectroscopy is used to probe the structural changes of rhodopsin's retinal chromophore as the cis-to-trans isomerization reaction occurs that initiates vision. Room-temperature resonance Raman spectra of rhodopsin's photoproduct with time delays from -0.7 to 20.8 ps are measured using 2.2 ps, 480 nm pump and 1.5 ps, 600 nm probe pulses. Hydrogen-out-of-plane (HOOP) modes at 852, 871, and 919 cm(-1), fingerprint peaks at 1272, 1236, 1211, and 1166 cm(-1), and a broad red-shifted ethylenic band at 1530 cm(-1) are present at the earliest positive pump-probe time delay of 0.8 ps, indicating that the chromophore is already in a strained, all-trans configuration. Kinetic analyses of both the HOOP and ethylenic regions of the photoproduct spectra reveal that these features grow in with fast ( approximately 200 fs) and slow ( approximately 2-3 ps) components. These data provide the first structural evidence that photorhodopsin has a thermally unrelaxed, torsionally strained all-trans chromophore within approximately 1 ps, and possibly within 200 fs, of photon absorption. Following this ultrafast product formation, the all-trans chromophore cools and conformationally relaxes within a few picoseconds to form bathorhodopsin. This cooling process is revealed as an ethylenic frequency blue-shift of 6 cm(-1) (tau approximately 3.5 ps) as well as an ethylenic width narrowing (tau approximately 2 ps). The ultrafast production of photorhodopsin is likely accompanied by an impulsively driven, localized protein response. More delocalized protein modes are unable to relax on this ultrafast time scale enabling the chromophore-protein complex to store the large amounts of photon energy (30-35 kcal/mol) that are subsequently used to drive activating protein conformational changes.
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Affiliation(s)
- J E Kim
- Department of Chemistry, University of California, Berkeley, California 94720
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Murakami M, Kouyama T. Crystallographic Analysis of the Primary Photochemical Reaction of Squid Rhodopsin. J Mol Biol 2011; 413:615-27. [DOI: 10.1016/j.jmb.2011.08.044] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Revised: 08/19/2011] [Accepted: 08/23/2011] [Indexed: 10/17/2022]
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Sekharan S, Morokuma K. QM/MM study of the structure, energy storage, and origin of the bathochromic shift in vertebrate and invertebrate bathorhodopsins. J Am Chem Soc 2011; 133:4734-7. [PMID: 21391708 PMCID: PMC3075117 DOI: 10.1021/ja200322w] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
By comparing the results from a hybrid quantum mechanics/molecular mechanics method (SORCI+Q//B3LYP/6-31G*:Amber) between vertebrate (bovine) and invertebrate (squid) visual pigments, the mechanism of molecular rearrangements, energy storage, and origin of the bathochromic shift accompanying the transformation of rhodopsin to bathorhodopsin have been evaluated. The analysis reveals that, in the presence of an unrelaxed binding site, bathorhodopsin was found to carry almost 27 kcal/mol energy in both visual pigments and absorb (λ(max)) at 528 nm in bovine and 554 nm in squid. However, when the residues within 4.0 Å radius of the retinal are relaxed during the isomerization event, almost ∼16 kcal/mol energy is lost in squid compared to only ∼8 kcal/mol in bovine. Loss of a larger amount of energy in squid is attributed to the presence of a flexible binding site compared to a rigid binding site in bovine. Structure of the squid bathorhodopsin is characterized by formation of a direct H-bond between the Schiff base and Asn87.
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Schapiro I, Ryazantsev MN, Frutos LM, Ferré N, Lindh R, Olivucci M. The Ultrafast Photoisomerizations of Rhodopsin and Bathorhodopsin Are Modulated by Bond Length Alternation and HOOP Driven Electronic Effects. J Am Chem Soc 2011; 133:3354-64. [DOI: 10.1021/ja1056196] [Citation(s) in RCA: 143] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Igor Schapiro
- Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403, United States
| | | | - Luis Manuel Frutos
- Departamento de Química Física, Universidad de Alcalá, 28871 Alcalá de Henares, Madrid, Spain
| | - Nicolas Ferré
- Laboratoire Chimie Provence UMR 6264, Université de Provence, Campus Saint Jérôme Case 521, 13397 Marseille Cedex 20, France
| | - Roland Lindh
- Department of Quantum Chemistry, Ångströmlab, Lägerhyddsv. 1, Box 518, 751 20 Uppsala University, Sweden
| | - Massimo Olivucci
- Chemistry Department, Bowling Green State University, Bowling Green, Ohio 43403, United States
- Dipartimento di Chimica, Università degli Studi di Siena, via Aldo Moro 2, I-53100 Siena, Italy
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Frähmcke JS, Wanko M, Phatak P, Mroginski MA, Elstner M. The protonation state of Glu181 in rhodopsin revisited: interpretation of experimental data on the basis of QM/MM calculations. J Phys Chem B 2010; 114:11338-52. [PMID: 20698519 DOI: 10.1021/jp104537w] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The structure and spectroscopy of rhodopsin have been intensely studied in the past decade both experimentally and theoretically; however, important issues still remain unresolved. Of central interest is the protonation state of Glu181, where controversial and contradictory experimental evidence has appeared. While FTIR measurements indicate this residue to be unprotonated, preresonance Raman and UV-vis spectra have been interpreted in favor of a protonated Glu181. Previous computational approaches were not able to resolve this issue, providing contradicting data as well. Here, we perform hybrid QM/MM calculations using DFT methods for the electronic ground state, MRCI methods for the electronically excited states, and a polarization model for the MM part in order to investigate this issue systematically. We constructed various active-site models for protonated as well as unprotonated Glu181, which were evaluated by computing NMR, IR, Raman, and UV-vis spectroscopic data. The resulting differences in the UV-vis and Raman spectra between protonated and unprotonated models are very subtle, which has two major consequences. First, the common interpretation of prior Raman and UV-vis experiments in favor of a neutral Glu181 appears questionable, as it is based on the assumption that a charge at the Glu181 location would have a sizable impact. Second, also theoretical results should be interpreted with care. Spectroscopic differences between the structural models must be related to modeling uncertainties and intrinsic methodological errors. Despite a detailed comparison of various rhodopsins and mutants and consistently favorite results with charged Glu181 models, we find merely weak evidence from UV-vis and Raman calculations. On the contrary, difference FTIR and NMR chemical shift measurements on Rh mutants are indicative of the protonation state of Glu181. Supported by our results, they provide strong and independent evidence for a charged Glu181.
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Affiliation(s)
- Jan S Frähmcke
- Institute for Physical and Theoretical Chemistry, TU Braunschweig, Hans-Sommer-Str. 10, D-38106 Braunschweig, Germany
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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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Schmidt HLF, Shah GJ, Sperling LJ, Rienstra CM. NMR Determination of Protein pK(a) Values in the Solid State. J Phys Chem Lett 2010; 1:1623-1628. [PMID: 20563223 PMCID: PMC2885713 DOI: 10.1021/jz1004413] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Charged residues play an important role in defining key mechanistic features in many biomolecules. Determining the pK(a) values of large, membrane or fibrillar proteins can be challenging with traditional methods. In this study we show how solid-state NMR is used to monitor chemical shift changes during a pH titration for the small soluble β1 immunoglobulin binding domain of protein G. The chemical shifts of all the amino acids with charged side-chains throughout the uniformly-(13)C,(15)N-labeled protein were monitored over several samples varying in pH; pK(a) values were determined from these shifts for E27, D36, and E42, and the bounds for the pK(a) of other acidic side-chain resonances were determined. Additionally, this study shows how the calculated pK(a) values give insights into the crystal packing of the protein.
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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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Is the lifetime of light-stimulated cGMP phosphodiesterase regulated by recoverin through its regulation of rhodopsin phosphorylation? Behav Brain Sci 2010. [DOI: 10.1017/s0140525x00039522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Das S, Varghese S, Kumar NSS. Butadiene-based photoresponsive soft materials. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:1598-1609. [PMID: 19627077 DOI: 10.1021/la901962k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The creation of stimuli-responsive materials offers considerable challenges in the area of material science. The use of light as an external stimulus has particular advantages because it can bring about rapid transformations in remote regions in a very precise manner. Naturally occurring photoresponsive systems provide the motivation for developing corresponding artificial systems using molecular self-assembly to address issues such as quantum efficiency, selectivity, and amplification. A practical strategy for developing photoresponsive materials is to utilize molecules that can undergo considerable change in shape on photoisomerization. Although the photoisomerization of polyenes between their linear all-trans isomer and bent cis isomers has been extensively investigated in solution and in organized media because of its relevance to naturally occurring photoresponsive systems, its use in developing artificial photoresponsive systems has not been well explored. This feature article provides an overview of photoresponsive soft materials such as liquid crystals and gels with special emphasis on our recent studies related to the use of the butadiene chromophore for the design of such materials. The role of molecular self-assembly in controlling the photochemical and photophysical properties of these molecules is also discussed.
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Affiliation(s)
- Suresh Das
- Photosciences and Photonics Section, Chemical Sciences and Technology Division, National Institute for Interdisciplinary Science and Technology, Trivandrum-695 019, Kerala, India
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Concistrè M, Gansmüller A, McLean N, Johannessen OG, Marín Montesinos I, Bovee-Geurts PHM, Brown RCD, DeGrip WJ, Levitt MH. Light penetration and photoisomerization in rhodopsin studied by numerical simulations and double-quantum solid-state NMR spectroscopy. J Am Chem Soc 2009; 131:6133-40. [PMID: 19354207 DOI: 10.1021/ja809878c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The penetration of light into optically thick samples containing the G-protein-coupled receptor rhodopsin is studied by numerical finite-element simulations and double-quantum solid-state NMR experiments. Illumination with white light leads to the generation of the active bathorhodopsin photostate in the outer layer of the sample but generates a large amount of the side product, isorhodopsin, in the sample interior. The overall yield of bathorhodopsin is improved by using monochromatic 420 nm illumination and by mixing the sample with transparent glass beads. The implications of these findings on the interpretation of previously published rhodopsin NMR data are discussed.
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Gansmüller A, Concistrè M, McLean N, Johannessen OG, Marín-Montesinos I, Bovee-Geurts PHM, Verdegem P, Lugtenburg J, Brown RCD, Degrip WJ, Levitt MH. Towards an interpretation of 13C chemical shifts in bathorhodopsin, a functional intermediate of a G-protein coupled receptor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:1350-7. [PMID: 19265671 DOI: 10.1016/j.bbamem.2009.02.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 02/13/2009] [Accepted: 02/18/2009] [Indexed: 10/21/2022]
Abstract
Photoisomerization of the membrane-bound light receptor protein rhodopsin leads to an energy-rich photostate called bathorhodopsin, which may be trapped at temperatures of 120 K or lower. We recently studied bathorhodopsin by low-temperature solid-state NMR, using in situ illumination of the sample in a purpose-built NMR probe. In this way we acquired (13)C chemical shifts along the retinylidene chain of the chromophore. Here we compare these results with the chemical shifts of the dark state chromophore in rhodopsin, as well as with the chemical shifts of retinylidene model compounds in solution. An earlier solid-state NMR study of bathorhodopsin found only small changes in the (13)C chemical shifts upon isomerization, suggesting only minor perturbations of the electronic structure in the isomerized retinylidene chain. This is at variance with our recent measurements which show much larger perturbations of the (13)C chemical shifts. Here we present a tentative interpretation of our NMR results involving an increased charge delocalization inside the polyene chain of the bathorhodopsin chromophore. Our results suggest that the bathochromic shift of bathorhodopsin is due to modified electrostatic interactions between the chromophore and the binding pocket, whereas both electrostatic interactions and torsional strain are involved in the energy storage mechanism of bathorhodopsin.
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Affiliation(s)
- Axel Gansmüller
- School of Chemistry, University of Southampton, SO17 1BJ Southampton, England, UK
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Concistrè M, Gansmüller A, McLean N, Johannessen OG, Marín Montesinos I, Bovee-Geurts PHM, Verdegem P, Lugtenburg J, Brown RCD, DeGrip WJ, Levitt MH. Double-Quantum 13C Nuclear Magnetic Resonance of Bathorhodopsin, the First Photointermediate in Mammalian Vision. J Am Chem Soc 2008; 130:10490-1. [DOI: 10.1021/ja803801u] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maria Concistrè
- School of Chemistry, University of Southampton, SO17 1BJ Southampton, U.K., Leiden Institute of Chemistry, Gorlaeus Laboratories, NL-2300 RA Leiden, The Netherlands, and Nijmegen Centre for Molecular Life Sciences, Radboud University, NL-6500 HB Nijmegen, The Netherlands
| | - Axel Gansmüller
- School of Chemistry, University of Southampton, SO17 1BJ Southampton, U.K., Leiden Institute of Chemistry, Gorlaeus Laboratories, NL-2300 RA Leiden, The Netherlands, and Nijmegen Centre for Molecular Life Sciences, Radboud University, NL-6500 HB Nijmegen, The Netherlands
| | - Neville McLean
- School of Chemistry, University of Southampton, SO17 1BJ Southampton, U.K., Leiden Institute of Chemistry, Gorlaeus Laboratories, NL-2300 RA Leiden, The Netherlands, and Nijmegen Centre for Molecular Life Sciences, Radboud University, NL-6500 HB Nijmegen, The Netherlands
| | - Ole G. Johannessen
- School of Chemistry, University of Southampton, SO17 1BJ Southampton, U.K., Leiden Institute of Chemistry, Gorlaeus Laboratories, NL-2300 RA Leiden, The Netherlands, and Nijmegen Centre for Molecular Life Sciences, Radboud University, NL-6500 HB Nijmegen, The Netherlands
| | - Ildefonso Marín Montesinos
- School of Chemistry, University of Southampton, SO17 1BJ Southampton, U.K., Leiden Institute of Chemistry, Gorlaeus Laboratories, NL-2300 RA Leiden, The Netherlands, and Nijmegen Centre for Molecular Life Sciences, Radboud University, NL-6500 HB Nijmegen, The Netherlands
| | - Petra H. M. Bovee-Geurts
- School of Chemistry, University of Southampton, SO17 1BJ Southampton, U.K., Leiden Institute of Chemistry, Gorlaeus Laboratories, NL-2300 RA Leiden, The Netherlands, and Nijmegen Centre for Molecular Life Sciences, Radboud University, NL-6500 HB Nijmegen, The Netherlands
| | - Peter Verdegem
- School of Chemistry, University of Southampton, SO17 1BJ Southampton, U.K., Leiden Institute of Chemistry, Gorlaeus Laboratories, NL-2300 RA Leiden, The Netherlands, and Nijmegen Centre for Molecular Life Sciences, Radboud University, NL-6500 HB Nijmegen, The Netherlands
| | - Johan Lugtenburg
- School of Chemistry, University of Southampton, SO17 1BJ Southampton, U.K., Leiden Institute of Chemistry, Gorlaeus Laboratories, NL-2300 RA Leiden, The Netherlands, and Nijmegen Centre for Molecular Life Sciences, Radboud University, NL-6500 HB Nijmegen, The Netherlands
| | - Richard C. D. Brown
- School of Chemistry, University of Southampton, SO17 1BJ Southampton, U.K., Leiden Institute of Chemistry, Gorlaeus Laboratories, NL-2300 RA Leiden, The Netherlands, and Nijmegen Centre for Molecular Life Sciences, Radboud University, NL-6500 HB Nijmegen, The Netherlands
| | - Willem J. DeGrip
- School of Chemistry, University of Southampton, SO17 1BJ Southampton, U.K., Leiden Institute of Chemistry, Gorlaeus Laboratories, NL-2300 RA Leiden, The Netherlands, and Nijmegen Centre for Molecular Life Sciences, Radboud University, NL-6500 HB Nijmegen, The Netherlands
| | - Malcolm H. Levitt
- School of Chemistry, University of Southampton, SO17 1BJ Southampton, U.K., Leiden Institute of Chemistry, Gorlaeus Laboratories, NL-2300 RA Leiden, The Netherlands, and Nijmegen Centre for Molecular Life Sciences, Radboud University, NL-6500 HB Nijmegen, The Netherlands
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27
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Altun A, Yokoyama S, Morokuma K. Spectral tuning in visual pigments: an ONIOM(QM:MM) study on bovine rhodopsin and its mutants. J Phys Chem B 2008; 112:6814-27. [PMID: 18473437 DOI: 10.1021/jp709730b] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have investigated geometries and excitation energies of bovine rhodopsin and some of its mutants by hybrid quantum mechanical/molecular mechanical (QM/MM) calculations in ONIOM scheme, employing B3LYP and BLYP density functionals as well as DFTB method for the QM part and AMBER force field for the MM part. QM/MM geometries of the protonated Schiff-base 11- cis-retinal with B3LYP and DFTB are very similar to each other. TD-B3LYP/MM excitation energy calculations reproduce the experimental absorption maximum of 500 nm in the presence of native rhodopsin environment and predict spectral shifts due to mutations within 10 nm, whereas TD-BLYP/MM excitation energies have red-shift error of at least 50 nm. In the wild-type rhodopsin, Glu113 shifts the first excitation energy to blue and accounts for most of the shift found. Other amino acids individually contribute to the first excitation energy but their net effect is small. The electronic polarization effect is essential for reproducing experimental bond length alternation along the polyene chain in protonated Schiff-base retinal, which correlates with the computed first excitation energy. It also corrects the excitation energies and spectral shifts in mutants, more effectively for deprotonated Schiff-base retinal than for the protonated form. The protonation state and conformation of mutated residues affect electronic spectrum significantly. The present QM/MM calculations estimate not only the experimental excitation energies but also the source of spectral shifts in mutants.
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Affiliation(s)
- Ahmet Altun
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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28
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Altun A, Yokoyama S, Morokuma K. Quantum mechanical/molecular mechanical studies on spectral tuning mechanisms of visual pigments and other photoactive proteins. Photochem Photobiol 2008; 84:845-54. [PMID: 18331400 DOI: 10.1111/j.1751-1097.2008.00308.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The protein environments surrounding the retinal tune electronic absorption maximum from 350 to 630 nm. Hybrid quantum mechanical/molecular mechanical (QM/MM) methods can be used in calculating excitation energies of retinal in its native protein environments and in studying the molecular basis of spectral tuning. We hereby review recent QM/MM results on the phototransduction of bovine rhodopsin, bacteriorhodopsin, sensory rhodopsin II, nonretinal photoactive yellow protein and their mutants.
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Affiliation(s)
- Ahmet Altun
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, GA, USA
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29
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Nakane N, Nicolaides A, Tomioka H, Asato AE, Liu RSH. Hula-twist photoisomerization of a styrene derivative examined by argon-matrix-infrared-spectroscopic method. Mol Phys 2007. [DOI: 10.1080/00268970500417747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Norio Nakane
- a Faculty of Engineering, Chemistry Department for Materials , Mie University , Tsu, Mie, 514-8507, Japan
| | | | - Hideo Tomioka
- a Faculty of Engineering, Chemistry Department for Materials , Mie University , Tsu, Mie, 514-8507, Japan
| | - Alfred E. Asato
- c Department of Chemistry , University of Hawaii , 2545 The Mall, Honolulu, HI 96822, USA
| | - Robert S. H. Liu
- c Department of Chemistry , University of Hawaii , 2545 The Mall, Honolulu, HI 96822, USA
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30
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Affiliation(s)
- Hitoshi Nakamichi
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-41-6 Aomi, Koto-ku, Tokyo 135-0064, Japan
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31
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Nakamichi H, Okada T. Crystallographic Analysis of Primary Visual Photochemistry. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600595] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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32
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Yan ECY, Ganim Z, Kazmi MA, Chang BSW, Sakmar TP, Mathies RA. Resonance Raman analysis of the mechanism of energy storage and chromophore distortion in the primary visual photoproduct. Biochemistry 2004; 43:10867-76. [PMID: 15323547 PMCID: PMC1428786 DOI: 10.1021/bi0400148] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The vibrational structure of the chromophore in the primary photoproduct of vision, bathorhodopsin, is examined to determine the cause of the anomalously decoupled and intense C(11)=C(12) hydrogen-out-of-plane (HOOP) wagging modes and their relation to energy storage in the primary photoproduct. Low-temperature (77 K) resonance Raman spectra of Glu181 and Ser186 mutants of bovine rhodopsin reveal only mild mutagenic perturbations of the photoproduct spectrum suggesting that dipolar, electrostatic, or steric interactions with these residues do not cause the HOOP mode frequencies and intensities. Density functional theory calculations are performed to investigate the effect of geometric distortion on the HOOP coupling. The decoupled HOOP modes can be simulated by imposing approximately 40 degrees twists in the same direction about the C(11)=C(12) and C(12)-C(13) bonds. Sequence comparison and examination of the binding site suggests that these distortions are caused by three constraints consisting of an electrostatic anchor between the protonated Schiff base and the Glu113 counterion, as well as steric interactions of the 9- and 13-methyl groups with surrounding residues. This distortion stores light energy that is used to drive the subsequent protein conformational changes that activate rhodopsin.
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Affiliation(s)
- Elsa C Y Yan
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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33
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Liu RSH, Colmenares LU. The molecular basis for the high photosensitivity of rhodopsin. Proc Natl Acad Sci U S A 2003; 100:14639-44. [PMID: 14657350 PMCID: PMC299751 DOI: 10.1073/pnas.2536769100] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2003] [Indexed: 11/18/2022] Open
Abstract
Based on structural information derived from the F NMR data of labeled rhodopsins, rhodopsin crystal structure, and excited-state properties of model polyenes, we propose a molecular mechanism that accounts specifically for the causes of the well-known enhanced photoreactivity of rhodopsin (increased rates and quantum yield of isomerization). It involves the key features of close proximity of C-187 to H-12 and chromophore bond lengthening upon light absorption. The resultant "sudden punch" to H-12 triggers dual processes of decay of the Franck-Condon-excited rhodopsin, a productive directed photoisomerization and a nonproductive decay returning to the ground state as two separate molecular pathways [based on real-time fluorescence results of Chosrowjan, H., Mataga, N., Shibata, Y., Tachibanaki, S., Kandori, H., Shichida, Y., Okada, T. & Kouyama, T. (1998) J. Am. Chem. Soc. 120, 9706-9707]. The two processes are controlled by the local protein structure: an empty space provided by the intradiscal loop connecting transmembrane helices 4 and 5 and a protein wall composed of amino acid units in transmembrane 3. Suggestions, involving retinal analogs and rhodopsin mutants, to improve the unusually high photosensitivity of rhodopsin are proposed.
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Affiliation(s)
- Robert S H Liu
- Department of Chemistry, University of Hawaii, Honolulu, HI 96822, USA.
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34
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Schobert B, Cupp-Vickery J, Hornak V, Smith S, Lanyi J. Crystallographic structure of the K intermediate of bacteriorhodopsin: conservation of free energy after photoisomerization of the retinal. J Mol Biol 2002; 321:715-26. [PMID: 12206785 DOI: 10.1016/s0022-2836(02)00681-2] [Citation(s) in RCA: 181] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The K state, an early intermediate of the bacteriorhodopsin photocycle, contains the excess free energy used for light-driven proton transport. The energy gain must reside in or near the photoisomerized retinal, but in what form has long been an open question. We produced the K intermediate in bacteriorhodopsin crystals in a photostationary state at 100K, with 40% yield, and determined its X-ray diffraction structure to 1.43 A resolution. In independent refinements of data from four crystals, the changes are confined mainly to the photoisomerized retinal. The retinal is 13-cis,15-anti, as known from vibrational spectroscopy. The C13=C14 bond is rotated nearly fully to cis from the initial trans configuration, but the C14-C15 and C15=NZ bonds are partially counter-rotated. This strained geometry keeps the direction of the Schiff base N-H bond vector roughly in the extracellular direction, but the angle of its hydrogen bond with water 402, that connects it to the anionic Asp85 and Asp212, is not optimal. Weakening of this hydrogen bond may account for many of the reported features of the infrared spectrum of K, and for its photoelectric signal, as well as the deprotonation of the Schiff base later in the cycle. Importantly, although 13-cis, the retinal does not assume the expected bent shape of this configuration. Comparison of the calculated energy of the increased angle of C12-C13=C14, that allows this distortion, with the earlier reported calorimetric measurement of the enthalpy gain of the K state indicates that a significant part of the excess energy is conserved in the bond strain at C13.
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Affiliation(s)
- Brigitte Schobert
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
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35
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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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36
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Pan D, Ganim Z, Kim JE, Verhoeven MA, Lugtenburg J, Mathies RA. Time-resolved resonance Raman analysis of chromophore structural changes in the formation and decay of rhodopsin's BSI intermediate. J Am Chem Soc 2002; 124:4857-64. [PMID: 11971736 PMCID: PMC1440918 DOI: 10.1021/ja012666e] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Time-resolved resonance Raman microchip flow experiments are performed to obtain the vibrational spectrum of the chromophore in rhodopsin's BSI intermediate and to probe structural changes in the bathorhodopsin-to-BSI and BSI-to-lumirhodopsin transitions. Kinetic Raman spectra from 250 ns to 3 micros identify the key vibrational features of BSI. BSI exhibits relatively intense HOOP modes at 886 and 945 cm(-1) that are assigned to C(14)H and C(11)H=C(12)H A(u) wags, respectively. This result suggests that in the bathorhodopsin-to-BSI transition the highly strained all-trans chromophore has relaxed in the C(10)-C(11)=C(12)-C(13) region, but is still distorted near C(14). The low frequency of the 11,12 A(u) HOOP mode in BSI compared with that of lumirhodopsin and metarhodopsin I indicates weaker coupling between the 11H and 12H wags due to residual distortion of the BSI chromophore near C(11)=C(12). The C=NH(+) stretching mode in BSI at 1653 cm(-1) exhibits a normal deuteriation induced downshift of 23 cm(-1), implying that there is no significant structural rearrangement of the Schiff base counterion region in the transition of bathorhodopsin to BSI. However, a dramatic Schiff base environment change occurs in the BSI-to-lumirhodopsin transition, because the 1638 cm(-1) C=NH(+) stretching mode in lumirhodopsin is unusually low and shifts only 7 cm(-1) in D(2)O, suggesting that it has essentially no H-bonding acceptor. With these data we can for the first time compare and discuss the room temperature resonance Raman vibrational structure of all the key intermediates in visual excitation.
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Affiliation(s)
- Duohai Pan
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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37
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Eilers M, Ying W, Reeves PJ, Khorana HG, Smith SO. Magic angle spinning nuclear magnetic resonance of isotopically labeled rhodopsin. Methods Enzymol 2002; 343:212-22. [PMID: 11675791 DOI: 10.1016/s0076-6879(02)43137-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Markus Eilers
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, New York 11794, USA
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38
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Abstract
CASSCF and GAUSSIAN CIS calculations were performed on ground and excited states of different conformations of 11-cis-retinal protonated Schiff bases, the chromophore of rhodopsin, in order to study their chiroptical properties and attempt a correlation between absolute conformation and CD-spectral data. Geometries were taken from molecular models, from published rhodopsin models, and from retinal conformations obtained from molecular dynamics with geometry restraints. In all the cases studied we find that a positive sense of twist about the C12-C13 bond correlates with a calculated positive CD of the long wavelength absorption band; the twist of the C6-C7 bond modulates this primary contribution of the C12-C13 bond. The correlation of the beta-band with structural features is not straightforward. Calculations on bathorhodopsin lend support to the idea that this intermediate is a highly twisted all-trans-conformation.
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Affiliation(s)
- V Buss
- Institut für Physikalische und Theoretische Chemie der Gerhard-Mercator-Universität, D47048 Duisburg, Germany.
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39
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Abstract
One major remaining problem in structural biology is to elucidate the structure and mechanism of function of membrane proteins. On the basis of preliminary information from genome projects, it is now estimated that up to 50,000 different membrane proteins may exist in the human being and that virtually every life process proceeds, sooner or later, through a membrane protein. Solid-state NMR spectroscopy in high magnetic field is rapidly developing into a widely applicable tool to describe the structure and help understand the mechanism of function of a membrane protein. Recent work in applied solid-state NMR spectroscopy crosses the boundary between the biological and the physical sciences, and aims at increasing the predictive range of this biophysical method.
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Affiliation(s)
- H J de Groot
- Leiden Institute of Chemistry, Gorlaeus Laboratories, POB 9502, 2300 RA, Leiden, Netherlands.
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40
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Abstract
Movement of the ligand/receptor complex in rhodopsin (Rh) has been traced. Bleaching of diazoketo rhodopsin (DK-Rh) containing 11-cis-3-diazo-4-oxo-retinal yields batho-, lumi-, meta-I-, and meta-II-Rh intermediates corresponding to those of native Rh but at lower temperatures. Photoaffinity labeling of DK-Rh and these bleaching intermediates shows that the ionone ring cross-links to tryptophan-265 on helix F in DK-Rh and batho-Rh, and to alanine-169 on helix D in lumi-, meta-I-, and meta-II-Rh intermediates. It is likely that these movements involving a flip-over of the chromophoric ring trigger changes in cytoplasmic membrane loops resulting in heterotrimeric guanine nucleotide-binding protein (G protein) activation.
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Affiliation(s)
- B Borhan
- Department of Chemistry, Columbia University, New York, NY 10027, USA
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41
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Birge RR, Vought BW. Energetics of rhodopsin photobleaching: photocalorimetric studies of energy storage in early and later intermediates. Methods Enzymol 2000; 315:143-63. [PMID: 10736700 DOI: 10.1016/s0076-6879(00)15841-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Affiliation(s)
- R R Birge
- Department of Chemistry, Syracuse University, New York 13244-4100, USA
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42
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Mathies R, Lugtenburg J. Chapter 2 The primary photoreaction of rhodopsin. HANDBOOK OF BIOLOGICAL PHYSICS 2000. [DOI: 10.1016/s1383-8121(00)80005-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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43
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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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44
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Verdegem PJ, Bovee-Geurts PH, de Grip WJ, Lugtenburg J, de Groot HJ. Retinylidene ligand structure in bovine rhodopsin, metarhodopsin-I, and 10-methylrhodopsin from internuclear distance measurements using 13C-labeling and 1-D rotational resonance MAS NMR. Biochemistry 1999; 38:11316-24. [PMID: 10471281 DOI: 10.1021/bi983014e] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rhodopsin is the G-protein coupled photoreceptor that initiates the rod phototransduction cascade in the vertebrate retina. Using specific isotope enrichment and magic angle spinning (MAS) NMR, we examine the spatial structure of the C10-C11=C12-C13-C20 motif in the native retinylidene chromophore, its 10-methyl analogue, and the predischarge photoproduct metarhodopsin-I. For the rhodopsin study 11-Z-[10,20-(13)C(2)]- and 11-Z-[11,20-(13)C(2)]-retinal were synthesized and incorporated into bovine opsin while maintaining a natural lipid environment. The ligand is covalently bound to Lys(296) in the photoreceptor. The C10-C20 and C11-C20 distances were measured using a novel 1-D CP/MAS NMR rotational resonance experimental procedure that was specifically developed for the purpose of these measurements [Verdegem, P. J. E., Helmle, M., Lugtenburg, J., and de Groot, H. J. M. (1997) J. Am. Chem. Soc. 119, 169]. We obtain r(10,20) = 0.304 +/- 0.015 nm and r(11,20) = 0.293 +/- 0.015 nm, which confirms that the retinylidene is 11-Z and shows that the C10-C13 unit is conformationally twisted. The corresponding torsional angle is about 44 degrees as indicated by Car-Parrinello modeling studies. To increase the nonplanarity in the chromophore, 11-Z-[10,20-(13)C(2)]-10-methylretinal and 11-Z-[(10-CH(3)), 13-(13)C(2)]-10-methylretinal were prepared and incorporated in opsin. For the resulting analogue pigment r(10,20) = 0.347 +/- 0.015 nm and r((10)(-)(CH)()3())(,)(13) = 0.314 +/- 0.015 nm were obtained, consistent with a more distorted chromophore. The analogue data are in agreement with the induced fit principle for the interaction of opsin with modified retinal chromophores. Finally, we determined the intraligand distances r(10,20) and r(11,20) also for the photoproduct metarhodopsin-I, which has a relaxed all-E structure. The results (r(10,20) >/= 0.435 nm and r(11,20) = 0.283 +/- 0.015 nm) fully agree with such a relaxed all-E structure, which further validates the 1-D rotational resonance technique for measuring intraligand distances and probing ligand structure. As far as we are aware, these results represent the first highly precise distance determinations in a ligand at the active site of a membrane protein. Overall, the MAS NMR data indicate a tight binding pocket, well defined to bind specifically only one enantiomer out of four possibilities and providing a steric complement to the chromophore in an ultrafast ( approximately 200 fs) isomerization process.
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Affiliation(s)
- P J Verdegem
- Leiden Institute of Chemistry, Gorlaeus Laboratories, The Netherlands
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45
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La Penna G, Buda F, Bifone A, de Groot HJ. The transition state in the isomerization of rhodopsin. Chem Phys Lett 1998. [DOI: 10.1016/s0009-2614(98)00870-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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46
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Jäger S, Lewis JW, Zvyaga TA, Szundi I, Sakmar TP, Kliger DS. Chromophore structural changes in rhodopsin from nanoseconds to microseconds following pigment photolysis. Proc Natl Acad Sci U S A 1997; 94:8557-62. [PMID: 9238015 PMCID: PMC23009 DOI: 10.1073/pnas.94.16.8557] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Rhodopsin is a prototypical G protein-coupled receptor that is activated by photoisomerization of its 11-cis-retinal chromophore. Mutant forms of rhodopsin were prepared in which the carboxylic acid counterion was moved relative to the positively charged chromophore Schiff base. Nanosecond time-resolved laser photolysis measurements of wild-type recombinant rhodopsin and two mutant pigments then were used to determine reaction schemes and spectra of their early photolysis intermediates. These results, together with linear dichroism data, yielded detailed structural information concerning chromophore movements during the first microsecond after photolysis. These chromophore structural changes provide a basis for understanding the relative movement of rhodopsin's transmembrane helices 3 and 6 required for activation of rhodopsin. Thus, early structural changes following isomerization of retinal are linked to the activation of this G protein-coupled receptor. Such rapid structural changes lie at the heart of the pharmacologically important signal transduction mechanisms in a large variety of receptors, which use extrinsic activators, but are impossible to study in receptors using diffusible agonist ligands.
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Affiliation(s)
- S Jäger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064, USA
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47
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Abstract
Rhodopsin is the seven transmembrane helix receptor responsible for dim light vision in vertebrate rod cells. The protein has structural homology with the other G protein-coupled receptors, which suggests that the tertiary structures and activation mechanisms are likely to be similar. However, rhodopsin is unique in several respects. The most striking is the fact that the receptor "ligand", 11-cis retinal, is covalently bound to the protein and is converted from an "antagonist" to an "agonist" upon absorption of light. NMR studies of rhodopsin and its primary photoproduct, bathorhodopsin, have generated structural constraints that enabled docking of the 11-cis and all-trans retinal chromophores into a low-resolution model of the protein proposed by Baldwin. These studies also suggest a mechanism for how retinal isomerization leads to rhodopsin activation. More recently, mutagenesis studies have extended these results by showing how the selectivity of the retinal-binding site can be modified to favor the all-trans over the 11-cis isomer. The structural constraints produced from these studies, when placed in the context of a high-resolution model of the protein, provide a coherent picture of the activation mechanism, which we show involves a direct steric interaction between the retinal chromophore and transmembrane helix 3 in the region of Gly121.
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Affiliation(s)
- T Shieh
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA
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48
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Bifone A, de Groot HJM, Buda F. Energy Storage in the Primary Photoproduct of Vision. J Phys Chem B 1997. [DOI: 10.1021/jp9623397] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Angelo Bifone
- Leiden Institute of Chemistry, Gorlaeus Laboratoria, University of Leiden, 2300 RA Leiden, The Netherlands, and Istituto Nazionale per la Fisica della Materia, Laboratorio Forum, Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Huub J. M. de Groot
- Leiden Institute of Chemistry, Gorlaeus Laboratoria, University of Leiden, 2300 RA Leiden, The Netherlands, and Istituto Nazionale per la Fisica della Materia, Laboratorio Forum, Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Francesco Buda
- Leiden Institute of Chemistry, Gorlaeus Laboratoria, University of Leiden, 2300 RA Leiden, The Netherlands, and Istituto Nazionale per la Fisica della Materia, Laboratorio Forum, Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
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49
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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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50
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Popp A, Ujj L, Atkinson GH. Bathorhodopsin structure in the room-temperature rhodopsin photosequence: picosecond time-resolved coherent anti-Stokes Raman scattering. Proc Natl Acad Sci U S A 1996; 93:372-6. [PMID: 8552641 PMCID: PMC40240 DOI: 10.1073/pnas.93.1.372] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Structural changes in the retinal chromophore during the formation of the bathorhodopsin intermediate (bathoRT) in the room-temperature rhodopsin (RhRT) photosequence (i.e., vision) are examined using picosecond time-resolved coherent anti-Stokes Raman scattering. Specifically, the retinal structure assignable to bathoRT following 8-ps excitation of RhRT is measured via vibrational Raman spectroscopy at a 200-ps time delay where the only intermediate present is bathoRT. Significant differences are observed between the C=C stretching frequencies of the retinal chromophore at low temperature where bathorhodopsin is stabilized and at room temperature where bathorhodopsin is a transient species in the RhRT photosequence. These vibrational data are discussed in terms of the formation of bathoRT, an important step in the energy storage/transduction mechanism of RhRT.
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Affiliation(s)
- A Popp
- Department of Chemistry, University of Arizona, Tucson 85721, USA
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