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Buhrke D, Hildebrandt P. Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chem Rev 2019; 120:3577-3630. [PMID: 31814387 DOI: 10.1021/acs.chemrev.9b00429] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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Mizuno M, Nakajima A, Kandori H, Mizutani Y. Structural Evolution of a Retinal Chromophore in the Photocycle of Halorhodopsin from Natronobacterium pharaonis. J Phys Chem A 2018; 122:2411-2423. [DOI: 10.1021/acs.jpca.7b12332] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and
| | - Ayumi Nakajima
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and
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Wolter T, Elstner M, Fischer S, Smith JC, Bondar AN. Mechanism by which Untwisting of Retinal Leads to Productive Bacteriorhodopsin Photocycle States. J Phys Chem B 2014; 119:2229-40. [DOI: 10.1021/jp505818r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Tino Wolter
- Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Stefan Fischer
- IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany
| | - Jeremy C. Smith
- Center for
Molecular
Biophysics, University of Tenessee, Oak Ridge National Laboratory, PO BOX 2008 MS6164, Oak Ridge, Tennessee 37831-6164, United States
| | - Ana-Nicoleta Bondar
- Theoretical
Molecular Biophysics, Department of Physics, Freie Universitaet Berlin, Arnimallee 14, D-14195 Berlin, Germany
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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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Ujj L, Atkinson G. Picosecond Resonance Coherent Anti-Stokes Raman Spectroscopy of Light- and Dark-Adapted Bacteriorhodopsin. Isr J Chem 2013. [DOI: 10.1002/ijch.199300026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Mizuno M, Sudo Y, Homma M, Mizutani Y. Direct Observation of the Structural Change of Tyr174 in the Primary Reaction of Sensory Rhodopsin II. Biochemistry 2011; 50:3170-80. [DOI: 10.1021/bi101817y] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yuki Sudo
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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Dioumaev AK, Wang JM, Lanyi JK. Low-temperature FTIR study of multiple K intermediates in the photocycles of bacteriorhodopsin and xanthorhodopsin. J Phys Chem B 2010; 114:2920-31. [PMID: 20136108 PMCID: PMC3820168 DOI: 10.1021/jp908698f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Low-temperature FTIR spectroscopy of bacteriorhodopsin and xanthorhodopsin was used to elucidate the number of K-like bathochromic states, their sequence, and their contributions to the photoequilibrium mixtures created by illumination at 80-180 K. We conclude that in bacteriorhodopsin the photocycle includes three distinct K-like states in the sequence bR (hv)--> I* --> J --> K(0) --> K(E) --> L --> ..., and similarly in xanthorhodopsin. K(0) is the main fraction in the mixture at 77 K that is formed from J. K(0) becomes thermally unstable above approximately 50 K in both proteins. At 77 K, both J-to-K(0) and K(0)-to-K(E) transitions occur and, contrarily to long-standing belief, cryogenic trapping at 77 K does not produce a pure K state but a mixture of the two states, K(0) and K(E), with contributions from K(E) of approximately 15 and approximately 10% in the two retinal proteins, respectively. Raising the temperature leads to increasing conversion of K(0) to K(E), and the two states coexist (without contamination from non-K-like states) in the 80-140 K range in bacteriorhodopsin, and in the 80-190 K range in xanthorhodopsin. Temperature perturbation experiments in these regions of coexistence revealed that, in spite of the observation of apparently stable mixtures of K(0) and K(E), the two states are not in thermally controlled equilibrium. The K(0)-to-K(E) transition is unidirectional, and the partial transformation to K(E) is due to distributed kinetics, which governs the photocycle dynamics at temperatures below approximately 245 K (Dioumaev and Lanyi, Biochemistry 2008, 47, 11125-11133). From spectral deconvolution, we conclude that the K(E) state, which is increasingly present at higher temperatures, is the same intermediate that is detected by time-resolved FTIR prior to its decay, on a time scale of hundreds of nanoseconds at ambient temperature (Dioumaev and Braiman, J. Phys. Chem. B 1997, 101, 1655-1662), into the K(L) state. We were unable to trap the latter separately from K(E) at low temperature, due to the slow distributed kinetics and the increasingly faster overlapping formation of the L state. Formation of the two consecutive K-like states in both proteins is accompanied by distortion of two different weakly bound water molecules: one in K(0), the other in K(E). The first, well-documented in bacteriorhodopsin at 77 K where K(0) dominates, was assigned to water 401 in bacteriorhodopsin. The other water molecule, whose participation has not been described previously, is disturbed on the next step of the photocycle, in K(E), in both proteins. In bacteriorhodopsin, the most likely candidate is water 407. However, unlike bacteriorhodopsin, the crystal structure of xanthorhodopsin lacks homologous weakly bound water molecules.
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Affiliation(s)
- Andrei K. Dioumaev
- Department of Physiology & Biophysics, University of California, Irvine, CA 92697
| | - Jennifer M. Wang
- Department of Physiology & Biophysics, University of California, Irvine, CA 92697
| | - Janos K. Lanyi
- Department of Physiology & Biophysics, University of California, Irvine, CA 92697
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Mizuno M, Shibata M, Yamada J, Kandori H, Mizutani Y. Picosecond Time-Resolved Ultraviolet Resonance Raman Spectroscopy of Bacteriorhodopsin: Primary Protein Response to the Photoisomerization of Retinal. J Phys Chem B 2009; 113:12121-8. [DOI: 10.1021/jp904388w] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 454-8555, Japan
| | - Mikihiro Shibata
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 454-8555, Japan
| | - Junya Yamada
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 454-8555, Japan
| | - Hideki Kandori
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 454-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan, and Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 454-8555, Japan
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Primary events in the bacteriorhodopsin photocycle: Torsional vibrational dephasing in the first excited electronic state. Chem Phys 2005. [DOI: 10.1016/j.chemphys.2004.12.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Atkinson GH, Zhou Y, Ujj L, Aharoni A, Sheves M, Ottolenghi M. Dynamics and Retinal Structural Changes in the Photocycle of the Artificial Bacteriorhodopsin Pigment BR6.9. J Phys Chem A 2002. [DOI: 10.1021/jp011911d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- G. H. Atkinson
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, Department of Organic Chemistry, Weizmann Institute, Rehovot, Israel, Department of Physical Chemistry, Hebrew University, Jerusalem, Israel, and Department of Physics, University of West Florida, Pensacola, Florida 32503
| | - Y. Zhou
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, Department of Organic Chemistry, Weizmann Institute, Rehovot, Israel, Department of Physical Chemistry, Hebrew University, Jerusalem, Israel, and Department of Physics, University of West Florida, Pensacola, Florida 32503
| | - L. Ujj
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, Department of Organic Chemistry, Weizmann Institute, Rehovot, Israel, Department of Physical Chemistry, Hebrew University, Jerusalem, Israel, and Department of Physics, University of West Florida, Pensacola, Florida 32503
| | - A. Aharoni
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, Department of Organic Chemistry, Weizmann Institute, Rehovot, Israel, Department of Physical Chemistry, Hebrew University, Jerusalem, Israel, and Department of Physics, University of West Florida, Pensacola, Florida 32503
| | - M. Sheves
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, Department of Organic Chemistry, Weizmann Institute, Rehovot, Israel, Department of Physical Chemistry, Hebrew University, Jerusalem, Israel, and Department of Physics, University of West Florida, Pensacola, Florida 32503
| | - M. Ottolenghi
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, Department of Organic Chemistry, Weizmann Institute, Rehovot, Israel, Department of Physical Chemistry, Hebrew University, Jerusalem, Israel, and Department of Physics, University of West Florida, Pensacola, Florida 32503
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Delaney JK, Schmidt PK, Brack TL, Atkinson GH. Photochemistry of K-590 in the Room-Temperature Bacteriorhodopsin Photocycle. J Phys Chem B 2000. [DOI: 10.1021/jp000374e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. K. Delaney
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, and Department of Chemistry, Hofstra University, Hempstead, New York 11549
| | - P. K. Schmidt
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, and Department of Chemistry, Hofstra University, Hempstead, New York 11549
| | - T. L. Brack
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, and Department of Chemistry, Hofstra University, Hempstead, New York 11549
| | - G. H. Atkinson
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721, and Department of Chemistry, Hofstra University, Hempstead, New York 11549
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Atkinson GH, Ujj L, Zhou Y. Vibrational Spectrum of the J-625 Intermediate in the Room Temperature Bacteriorhodopsin Photocycle. J Phys Chem A 1999. [DOI: 10.1021/jp9918306] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- G. H. Atkinson
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721
| | - L. Ujj
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721
| | - Yidong Zhou
- Department of Chemistry and Optical Science Center, University of Arizona, Tucson, Arizona 85721
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Delaney JK, Schmidt P, Atkinson GH, Subramaniam S. Evidence for a Long-Lived 13-cis-Containing Intermediate in the Photocycle of the Leu 93 → Ala Bacteriorhodopsin Mutant. J Phys Chem B 1997. [DOI: 10.1021/jp963243f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- J. K. Delaney
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, and Department of Chemistry & Optical Science Center, University of Arizona, Tucson, Arizona 85721
| | - P. Schmidt
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, and Department of Chemistry & Optical Science Center, University of Arizona, Tucson, Arizona 85721
| | - G. H. Atkinson
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, and Department of Chemistry & Optical Science Center, University of Arizona, Tucson, Arizona 85721
| | - S. Subramaniam
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, and Department of Chemistry & Optical Science Center, University of Arizona, Tucson, Arizona 85721
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Dioumaev AK, Braiman MS. Two Bathointermediates of the Bacteriorhodopsin Photocycle, Distinguished by Nanosecond Time-Resolved FTIR Spectroscopy at Room Temperature. J Phys Chem B 1997. [DOI: 10.1021/jp961512w] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrei K. Dioumaev
- Department of Biochemistry, University of Virginia Health Sciences Center, Charlottesville, Virginia 22908
| | - Mark S. Braiman
- Department of Biochemistry, University of Virginia Health Sciences Center, Charlottesville, Virginia 22908
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Ujj L, Jäger F, Popp A, Atkinson G. Vibrational spectrum of the K-590 intermediate in the bacteriorhodopsin photocycle at room temperature: picosecond time-resolved resonance coherent anti-Raman spectroscopy. Chem Phys 1996. [DOI: 10.1016/s0301-0104(96)00201-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Jäger F, Ujj L, Atkinson GH, Sheves M, Livnah N, Ottolenghi M. Vibrational Spectrum of K-590 Containing 13C14,15 Retinal: Picosecond Time-Resolved Coherent Anti-Stokes Raman Spectroscopy of the Room Temperature Bacteriorhodopsin Photocycle. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp961131i] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | | | | | - M. Ottolenghi
- Department of Chemistry, Hebrew University, Jerusalem, Israel
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Ujj L, Popp A, Atkinson G. Picosecond resonance coherent anti-Stokes Raman spectroscopy of bacteriorhodopsin: quantitative third-order susceptibility analysis of the dark-adapted mixture. Chem Phys 1994. [DOI: 10.1016/0301-0104(94)00253-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Ujj L, Volodin B, Popp A, Delaney J, Atkinson G. Picosecond resonance coherent anti-Stokes Raman spectroscopy of bacteriorhodopsin: spectra and quantitative third-order susceptibility analysis of the light-adapted BR-570. Chem Phys 1994. [DOI: 10.1016/0301-0104(94)00005-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Picosecond-Resonance Coherent Anti-Stokes Raman Scattering in Biophysics: Power Dependence in the Bacteriorhodopsin Photocycle. ACTA ACUST UNITED AC 1994. [DOI: 10.1007/978-3-642-85060-8_37] [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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Diller R, Iannone M, Cowen BR, Maiti S, Bogomolni RA, Hochstrasser RM. Picosecond dynamics of bacteriorhodopsin, probed by time-resolved infrared spectroscopy. Biochemistry 1992; 31:5567-72. [PMID: 1610802 DOI: 10.1021/bi00139a020] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The photoinduced reaction cycle of bacteriorhodopsin (BR) has been studied by means of a recently developed picosecond infrared spectroscopic method at ambient temperature. BR - K difference spectra between 1560 and 1700 cm-1 have been recorded at delay times from 100 ps to 14 ns. The spectrum remains unchanged during this period. The negative difference OD band at 1660 cm-1 indicates the peptide backbone responds within 50 ps. A survey in the region of carboxylic side chain absorption around 1740 cm-1 reveals that perturbations of those groups, present in low-temperature FTIR spectra, are not observable within 10 ns, suggesting a slow conformational change.
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Affiliation(s)
- R Diller
- Department of Chemistry, University of Pennsylvania, Philadelphia 19104
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Blanchard D, Gilmore D, Brack T, Lemaire H, Hughes D, Atkinson G. Picosecond time-resolved absorption and fluorescence in the bacteriorhodopsin photocycle: Vibrationally-excited species. Chem Phys 1991. [DOI: 10.1016/0301-0104(91)89050-k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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