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Interdisciplinary biophysical studies of membrane proteins bacteriorhodopsin and rhodopsin. Biophys Rev 2023; 15:111-125. [PMID: 36909961 PMCID: PMC9995646 DOI: 10.1007/s12551-022-01003-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/28/2022] [Indexed: 10/10/2022] Open
Abstract
The centenary of the birth of H. Gobind Khorana provides an auspicious opportunity to review the origins and evolution of parallel advances in biophysical methodology and molecular genetics technology used to study membrane proteins. Interdisciplinary work in the Khorana laboratory in the late 1970s and for the next three decades led to productive collaborations and fostered three subsequent scientific generations whose biophysical work on membrane proteins has led to detailed elucidation of the molecular mechanisms of energy transduction by the light-driven proton pump bacteriorhodopsin (bR) and signal transduction by the G protein-coupled receptor (GPCR) rhodopsin. This review will highlight the origins and advances of biophysical studies of membrane proteins made possible by the application of molecular genetics approaches to engineer site-specific alterations of membrane protein structures.
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Intramolekulare Proteindynamik untersucht mit zeitaufgelöster Fourier Transform Infrarot-Differenzspektroskopie. ACTA ACUST UNITED AC 2014. [DOI: 10.1002/bbpc.198800244] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Tavan P. Stereodynamic Coupling of Light Energy and Ion Transport in the Retinal Proteins Bacteriorhodopsin and Halorhodopsin. ACTA ACUST UNITED AC 2014. [DOI: 10.1002/bbpc.198800259] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Schulten K, Humphrey W, Logunov I, Sheves M, Xu D. Molecular Dynamics Studies of Bacteriorhodopsin's Photocycles. Isr J Chem 2013. [DOI: 10.1002/ijch.199500042] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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5
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Althaus T, Eisfeld W, Lohrmann R, Stockburger M. Application of Raman Spectroscopy to Retinal Proteins. Isr J Chem 2013. [DOI: 10.1002/ijch.199500029] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Cembran A, Bernardi F, Olivucci M, Garavelli M. The retinal chromophore/chloride ion pair: structure of the photoisomerization path and interplay of charge transfer and covalent states. Proc Natl Acad Sci U S A 2005; 102:6255-60. [PMID: 15855270 PMCID: PMC1088357 DOI: 10.1073/pnas.0408723102] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ab initio multi-reference second-order perturbation theory computations are used to explore the photochemical behavior of two ion pairs constituted by a chloride counterion interacting with either a rhodopsin or bacteriorhodopsin chromophore model (i.e., the 4-cis-gamma-methylnona-2,4,6,8-tetraeniminium and all-trans-nona-2,4,6,8-tetraeniminium cations, respectively). Significant counterion effects on the structure of the photoisomerization paths are unveiled by comparison with the paths of the same chromophores in vacuo. Indeed, we demonstrate that the counterion (i) modulates the relative stability of the S0, S1, and S2 energy surfaces leading to an S1 isomerization energy profile where the S1 and S2 states are substantially degenerate; (ii) leads to the emergence of significant S1 energy barriers along all of the isomerization paths except the one mimicking the 11-cis --> all-trans isomerization of the rhodopsin chromophore model; and (iii) changes the nature of the S1 --> S0 decay funnel that becomes a stable excited state minimum when the isomerizing double bond is located at the center of the chromophore moiety. We show that these (apparently very different) counterion effects can be rationalized on the basis of a simple qualitative electrostatic model, which also provides a crude basis for understanding the behavior of retinal protonated Schiff bases in solution.
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Affiliation(s)
- Alessandro Cembran
- Dipartimento di Chimica G. Ciamician, Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy
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Hampp N. Bacteriorhodopsin as a Photochromic Retinal Protein for Optical Memories. Chem Rev 2000; 100:1755-1776. [PMID: 11777419 DOI: 10.1021/cr980072x] [Citation(s) in RCA: 234] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Norbert Hampp
- Institute for Physical Chemistry, University of Marburg, D-35032 Marburg, Germany, and Materials Science Center, D-35032 Marburg, Germany
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Tajkhorshid E, Paizs B, Suhai S. Conformational Effects on the Proton Affinity of the Schiff Base in Bacteriorhodopsin: A Density Functional Study. J Phys Chem B 1997. [DOI: 10.1021/jp971283t] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Emadeddin Tajkhorshid
- Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, FRG
| | - Béla Paizs
- Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, FRG
| | - Sándor Suhai
- Department of Molecular Biophysics, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, FRG
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Mathies RA, Li XY. On modeling the vibrational spectra of 14-s-cis retinal conformers in bacteriorhodopsin. Biophys Chem 1995; 56:47-55. [PMID: 7662868 DOI: 10.1016/0301-4622(95)00014-o] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The vibrational properties of 13-cis, 14-s-trans and 13-cis, 14-s-cis protonated retinal Schiff base model compounds are explored with MNDO calculations. In particular, the effect of isomerization about the C14-C15 single bond on the vibrational properties of the deuterium in-plane rocking vibrations has been examined. Our MNDO calculations, using a variety of lysine models, lysine conformations and Schiff base charge environments, demonstrate that the C14-D and C15-D in-plane rocking vibrations in the 14,15-dideuterio retinal protonated Schiff base are strongly coupled in 13-cis, 14-s-cis molecules producing a splitting of ca. 80 cm-1 between the symmetric and antisymmetric rocking mode combinations but that these modes are only weakly coupled in 14-s-trans molecules. This analysis demonstrates that the 14,15-dideuterio labeling method developed earlier for determining C14-C15 conformation (S.P.A. Fodor, W. T. Pollard, R. Gebhard, E. M. M. van den Berg, J. Lugtenburg and R. A. Mathies, Proc. Natl. Acad. Sci. USA, 85, (1988) 2156-2160) is valid, and hence that the structure of the retinal chromophore in bacteriorhodopsin's L550 intermediate is 13-cis, 14-s-trans. The reasons for the misleading conclusions derived from MNDO calculations performed earlier by Schulten and Tavan are discussed.
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Affiliation(s)
- R A Mathies
- Chemistry Department, University of California, Berkeley 94720, USA
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Birge RR. Nature of the primary photochemical events in rhodopsin and bacteriorhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1016:293-327. [PMID: 2184895 DOI: 10.1016/0005-2728(90)90163-x] [Citation(s) in RCA: 302] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- R R Birge
- Department of Chemistry, Syracuse University, NY 13244
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Fahmy K, Siebert F, Großjean M, Tavan P. Photoisomerization in bacteriorhodopsin studied by FTIR, linear dichroism and photoselection experiments combined with quantum chemical theoretical analysis. J Mol Struct 1989. [DOI: 10.1016/0022-2860(89)80017-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Ottolenghi M, Sheves M. Synthetic retinals as probes for the binding site and photoreactions in rhodopsins. J Membr Biol 1989; 112:193-212. [PMID: 2693733 DOI: 10.1007/bf01870951] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- M Ottolenghi
- Department of Physical Chemistry, Hebrew University of Jerusalem, Israel
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Holzwarth AR. Applications of ultrafast laser spectroscopy for the study of biological systems. Q Rev Biophys 1989; 22:239-326. [PMID: 2695961 DOI: 10.1017/s0033583500002985] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The discovery of mode-locked laser operation now nearly two decades ago has started a development which enables researchers to probe the dynamics of ultrafast physical and chemical processes at the molecular level on shorter and shorter time scales. Naturally the first applications were in the fields of photophysics and photochemistry where it was then possible for the first time to probe electronic and vibrational relaxation processes on a sub-nanosecond timescale. The development went from lasers producing pulses of many picoseconds to the shortest pulses which are at present just a few femtoseconds long. Soon after their discovery ultrashort pulses were applied also to biological systems which has revealed a wealth of information contributing to our understanding of a broadrange of biological processes on the molecular level.It is the aim of this review to discuss the recent advances and point out some future trends in the study of ultrafast processes in biological systems using laser techniques. The emphasis will be mainly on new results obtained during the last 5 or 6 years. The term ultrafast means that I shall restrict myself to sub-nanosecond processes with a few exceptions.
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Affiliation(s)
- A R Holzwarth
- Max-Planck-Institut für Strahlenchemie, Mülheim/Ruhr, FRG
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Photochemical quantum yield of bacteriorhodopsin from resonance Raman scattering as a probe for photolysis. Chem Phys 1989. [DOI: 10.1016/0301-0104(89)87078-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abstract
Comparison of the primary structure of the chloride pump halorhodopsin with that of the proton pump bacteriorhodopsin provides insight into light-driven ion transport by retinal proteins. Several conserved amino acid residues in the membrane-spanning region of both proteins and their interaction with different isomerization states of retinal are suggested to be the key element for ion transport in both proteins.
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Light-induced polarized Fourier transform infrared spectroscopy of bacteriorhodopsin — a studyof the M412 intermediate by photoselection. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 1989. [DOI: 10.1016/s0005-2728(89)80395-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lugtenburg J, Mathies RA, Griffin RG, Herzfeld J. Structure and function of rhodopsins from solid state NMR and resonance Raman spectroscopy of isotopic retinal derivatives. Trends Biochem Sci 1988; 13:388-93. [PMID: 3072701 DOI: 10.1016/0968-0004(88)90181-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Ganter UM, Gärtner W, Siebert F. Rhodopsin-lumirhodopsin phototransition of bovine rhodopsin investigated by Fourier transform infrared difference spectroscopy. Biochemistry 1988; 27:7480-8. [PMID: 3207686 DOI: 10.1021/bi00419a046] [Citation(s) in RCA: 63] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The rhodopsin-lumirhodopsin transition has been investigated by Fourier transform infrared difference spectroscopy using isotope-labeled retinals. In the transition, two protonated carboxyl groups are involved. Another carbonyl band, located at 1725 cm-1 in rhodopsin, is shifted to 1731.5 cm-1 in lumirhodopsin. This line is tentatively assigned to a carbonyl stretching vibration of a peptide bond adjacent to the nitrogen of a proline residue. The C=N stretching vibration of rhodopsin could unequivocally be assigned to a band at 1659 cm-1. In contrast to rhodopsin and bathorhodopsin, the C=N stretching vibration of lumirhodopsin is at a low position, i.e., at 1635 cm-1, and exhibits only a downshift of 4 cm-1 upon deuteriation of the nitrogen. The C15-H rocking vibration of rhodopsin is assigned to the unusual high position of 1456 cm-1 and shifts into the normal region upon formation of lumirhodopsin. From these results, it is concluded that, whereas the environment of the Schiff base in rhodopsin, bathorhodopsin, and isorhodopsin is approximately the same, large changes occur with the formation of lumirhodopsin. From the assignment of the C10-C11 stretching vibration in bathorhodopsin and lumirhodopsin, a 10-s-cis geometry of lumirhodopsin can be excluded.
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Affiliation(s)
- U M Ganter
- Institut für Biophysik und Strahlenbiologie, Albert-Ludwig Universität Freiburg, FRG
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Grossjean MF, Tavan P. Wavelength regulation in bacteriorhodopsin and halorhodopsin: A Pariser–Parr–Pople multireference double excitation configuration interaction study of retinal dyes. J Chem Phys 1988. [DOI: 10.1063/1.454701] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Fodor SP, Pollard WT, Gebhard R, van den Berg EM, Lugtenburg J, Mathies RA. Bacteriorhodopsin's L550 intermediate contains a C14-C15 s-trans-retinal chromophore. Proc Natl Acad Sci U S A 1988; 85:2156-60. [PMID: 3353373 PMCID: PMC279948 DOI: 10.1073/pnas.85.7.2156] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Conformational changes of the retinal chromophore about the C14-C15 bond in bacteriorhodopsin (BR) have been proposed in models for the mechanism of light-driven proton transport. To determine the C14-C15 conformation in BR's L550 intermediate, we have examined the resonance Raman spectra of BR derivatives regenerated with retinal deuterated at the 14 and 15 positions. Vibrational calculations show that the C14-2H and C15-2H rocking modes form symmetric (A) and antisymmetric (B) combinations in [14,15-2H]retinal chromophores. When there is a trans conformation about the single bond between C14 and C15 (14-s-trans), a small frequency separation or splitting is observed between the A and B modes, which are found at approximately equal to 970 cm-1. In 14-s-cis molecules, the splitting is large, and the Raman-active symmetric A mode is predicted at approximately equal to 850 cm-1. In addition, the monodeuterium rock should appear at an unusually low frequency (920-930 cm-1) in the 14-2H-labeled 14-s-cis molecules. These patterns are insensitive to computational details: similar results are predicted by a modified Urey-Bradley force field and by MNDO (modified neglect of differential overlap) calculations for twisted chromophores and for highly delocalized protonated Schiff base cations. Time-resolved resonance Raman spectra were obtained of BR's L550 intermediate regenerated with [14-2H]-, [15-2H]- and [14,15-2H]retinal. The symmetric A rock in L550 is found at 968 cm-1, within 4 cm-1 of the frequencies for the monodeuterio derivatives, and no scattering is observed between 800 and 940 cm-1. The rocking frequencies of deuterated L550 are within 5 cm-1 of those observed in BR568, which contains a 14-s-trans chromophore. These results show that L550 contains a 14-s-trans chromophore and suggest that only 14-s-trans structures are involved in the proton pumping photocycle of BR.
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Affiliation(s)
- S P Fodor
- Department of Chemistry, University of California, Berkeley 94720
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Keszthelyi L. Primary charge motions and light-energy transduction in bacteriorhodopsin. Biophys Chem 1988; 29:127-36. [PMID: 17010911 DOI: 10.1016/0301-4622(88)87032-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/1987] [Indexed: 11/29/2022]
Abstract
The bacteriorhodopsin protein (bR) in the cell membrane of Halobacterium halobium is a light driven proton pump. Many details are known about its structure and the molecular mechanism of proton translocation. The events may be characterized by: (1) the changes in light absorption after photon excitation (the photocycle); (2) the charge motion cycle inside the protein: the steps taken by the proton during translocation; (3) the retinal cycle. changes in isomerization and protonation; and (4) the opsin cycle: alterations of protonation of different amino acids in the apoprotein. From a review of existing data a more or less concise picture of the parallelism of the above four cycles emerges, which may be valuable as a model for understanding other types of molecular pumps.
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Affiliation(s)
- L Keszthelyi
- Institute of Biophysics, Biological Research Center, Szeged H-6701 Hungary
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Petrich J, Breton J, Martin J, Antonetti A. Femtosecond absorption spectroscopy of light-adapted and dark-adapted bacteriorhodopsin. Chem Phys Lett 1987. [DOI: 10.1016/0009-2614(87)80902-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Femtosecond Absorption Studies of the Primary Events in Bacterial Photosynthesis and Light- and Dark-Adapted Bacteriorhodopsin. ACTA ACUST UNITED AC 1987. [DOI: 10.1007/978-3-642-72835-8_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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