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Mizutani Y. Concerted Motions and Molecular Function: What Physical Chemistry We Can Learn from Light-Driven Ion-Pumping Rhodopsins. J Phys Chem B 2021; 125:11812-11819. [PMID: 34672596 DOI: 10.1021/acs.jpcb.1c06698] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transmembrane ion gradients are generated and maintained by ion-pumping proteins in cells. Light-driven ion-pumping rhodopsins are retinal-containing proteins found in archaea, bacteria, and eukarya. Photoisomerization of the retinal chromophore induces structural changes in the protein, allowing the transport of ions in a particular direction. Understanding unidirectional ion transport by ion-pumping rhodopsins is an exciting challenge for biophysical chemistry. Concerted changes in ion-binding affinities of the ion-binding sites in proteins are key to unidirectional ion transport, as is the coupling between the chromophore and the protein moiety to drive the concerted motions regulating ion-binding affinities. The commonality of ion-pumping rhodopsin protein structures and the diversity of their ion-pumping functions suggest universal principles governing ion transport, which would be widely applicable to molecular systems. In this Perspective, I review the insights obtained from previous studies on rhodopsins and discuss future perspectives.
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Affiliation(s)
- Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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Abstract
This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.
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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: 45] [Impact Index Per Article: 9.0] [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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Tahara S, Kuramochi H, Takeuchi S, Tahara T. Protein Dynamics Preceding Photoisomerization of the Retinal Chromophore in Bacteriorhodopsin Revealed by Deep-UV Femtosecond Stimulated Raman Spectroscopy. J Phys Chem Lett 2019; 10:5422-5427. [PMID: 31469573 DOI: 10.1021/acs.jpclett.9b02283] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacteriorhodopsin is a prototypical photoreceptor protein that functions as a light-driven proton pump. The retinal chromophore of bacteriorhodopsin undergoes C13═C14 trans-to-cis isomerization upon photoexcitation, and it has been believed to be the first event that triggers the cascaded structural changes in bacteriorhodopsin. We investigated the protein dynamics of bacteriorhodopsin using deep-ultraviolet resonance femtosecond stimulated Raman spectroscopy. It was found that the stimulated Raman signals of tryptophan and tyrosine residues exhibit significant changes within 0.2 ps after photoexcitation while they do not noticeably change during the isomerization process. This result implies that the protein environment changes first, and its change is small during isomerization. The obtained femtosecond stimulated Raman data indicate that ultrafast change is induced in the protein part by the sudden creation of the large dipole of the excited-state chromophore, providing an environment that realizes efficient and selective isomerization.
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Affiliation(s)
- Shinya Tahara
- Molecular Spectroscopy Laboratory , RIKEN , 2-1 Hirosawa , Wako 351-0198 , Japan
| | - Hikaru Kuramochi
- Molecular Spectroscopy Laboratory , RIKEN , 2-1 Hirosawa , Wako 351-0198 , Japan
- Ultrafast Spectroscopy Research Team , RIKEN Center for Advanced Photonics (RAP) , 2-1 Hirosawa , Wako 351-0198 , Japan
- PRESTO , Japan Science and Technology Agency , 4-1-8 Honcho , Kawaguchi 332-0012 , Japan
| | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory , RIKEN , 2-1 Hirosawa , Wako 351-0198 , Japan
- Ultrafast Spectroscopy Research Team , RIKEN Center for Advanced Photonics (RAP) , 2-1 Hirosawa , Wako 351-0198 , Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory , RIKEN , 2-1 Hirosawa , Wako 351-0198 , Japan
- Ultrafast Spectroscopy Research Team , RIKEN Center for Advanced Photonics (RAP) , 2-1 Hirosawa , Wako 351-0198 , Japan
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Mizuno M, Shimoo Y, Kandori H, Mizutani Y. Effect of a bound anion on the structure and dynamics of halorhodopsin from Natronomonas pharaonis. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:054703. [PMID: 31673569 PMCID: PMC6811361 DOI: 10.1063/1.5125621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Abstract
Active ion transport across membranes is vital to maintaining the electrochemical gradients of ions in cells and is mediated by transmembrane proteins. Halorhodopsin (HR) functions as a light-driven inward pump for chloride ions. The protein contains all-trans-retinal bound to a specific lysine residue through a protonated Schiff base. Interaction between the bound chloride ion and the protonated Schiff base is crucial for ion transport because chloride ion movement is driven by the flipping of the protonated Schiff base upon photoisomerization. However, it remains unknown how this interaction evolves in the HR photocycle. Here, we addressed the effect of the bound anion on the structure and dynamics of HR from Natronomonas pharaonis in the early stage of the photocycle. Comparison of the chloride-bound, formate-bound, and anion-depleted forms provided insights into the interaction between the bound anion and the chromophore/protein moiety. In the unphotolyzed state, the bound anion affects the π-conjugation of the polyene chain and the hydrogen bond of the protonated Schiff base of the retinal chromophore. Picosecond time scale measurements showed that the band intensities of the W16 and W18 modes of the tryptophan residues decreased instantaneously upon photoexcitation of the formate-bound form. In contrast, these intensity decreases were delayed for the chloride-bound and anion-depleted forms. These observations suggest the stronger interactions of the bound formate ion with the retinal chromophore and the chromophore pocket. On the nanosecond to microsecond timescales, we found that the interaction between the protonated Schiff base and the bound ion is broken upon formation of the K intermediate and is recovered following translocation of the bound anion toward the protonated Schiff base in the L intermediate. Our results demonstrate that the hydrogen-bonding ability of the bound anion plays an essential role in the ion transport of light-driven anion pumps.
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Affiliation(s)
- Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yumi Shimoo
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, 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
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Mizutani Y. Time-Resolved Resonance Raman Spectroscopy and Application to Studies on Ultrafast Protein Dynamics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170218] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043
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Xu W, Wu F, Zhao Y, Zhou R, Wang H, Zheng X, Ni B. Study on the noncoincidence effect phenomenon using matrix isolated Raman spectra and the proposed structural organization model of acetone in condense phase. Sci Rep 2017; 7:43835. [PMID: 28256639 PMCID: PMC5335557 DOI: 10.1038/srep43835] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 01/31/2017] [Indexed: 12/03/2022] Open
Abstract
The isotropic and anisotropic Raman spectra of acetone and deuterated acetone isolated in an argon matrix have been recorded for the understanding of noncoincidence effect (NCE) phenomenon. According to the matrix isolated Raman spectra and DFT calculations, we proposed aggregated model for the explanations of the acetone C=O vibration NCE phenomenon and its concentration effect. The experimental data were in consistence with the DFT calculations performed at the B3LYP-D3/6-311 G (d,p) levels based on the proposed model. The experimental identification of the monomer, dimer and trimer are reported here, and the dynamic of the transformation from monomer to aggregated structure can be easily controlled by tuning annealing temperature.
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Affiliation(s)
- Wenwen Xu
- Department of Chemistry and Engineering Research Center for Eco-dyeing and Finishing of Textiles, MOE, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Fengqi Wu
- Department of Chemistry and Engineering Research Center for Eco-dyeing and Finishing of Textiles, MOE, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Yanying Zhao
- Department of Chemistry and Engineering Research Center for Eco-dyeing and Finishing of Textiles, MOE, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Ran Zhou
- Department of Chemistry and Engineering Research Center for Eco-dyeing and Finishing of Textiles, MOE, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Huigang Wang
- Department of Chemistry and Engineering Research Center for Eco-dyeing and Finishing of Textiles, MOE, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xuming Zheng
- Department of Chemistry and Engineering Research Center for Eco-dyeing and Finishing of Textiles, MOE, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Bukuo Ni
- Texas A&M Univ, Dept Chem, Commerce, TX 75429, USA
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Sudo Y, Mizuno M, Wei Z, Takeuchi S, Tahara T, Mizutani Y. The Early Steps in the Photocycle of a Photosensor Protein Sensory Rhodopsin I from Salinibacter ruber. J Phys Chem B 2014; 118:1510-8. [DOI: 10.1021/jp4112662] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Yuki Sudo
- Division
of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
- Department
of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Misao Mizuno
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Zhengrong Wei
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Satoshi Takeuchi
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular
Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- RIKEN Center for Advanced Photonics (RAP), 2-1 Hirosawa, Wako 351-0198, Japan
| | - Yasuhisa Mizutani
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1
Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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Inoue K, Tsukamoto T, Sudo Y. Molecular and evolutionary aspects of microbial sensory rhodopsins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:562-77. [PMID: 23732219 DOI: 10.1016/j.bbabio.2013.05.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 05/14/2013] [Accepted: 05/16/2013] [Indexed: 02/03/2023]
Abstract
Retinal proteins (~rhodopsins) are photochemically reactive membrane-embedded proteins, with seven transmembrane α-helices which bind the chromophore retinal (vitamin A aldehyde). They are widely distributed through all three biological kingdoms, eukarya, bacteria and archaea, indicating the biological significance of the retinal proteins. Light absorption by the retinal proteins triggers a photoisomerization of the chromophore, leading to the biological function, light-energy conversion or light-signal transduction. This article reviews molecular and evolutionary aspects of the light-signal transduction by microbial sensory receptors and their related proteins. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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Affiliation(s)
- Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Takashi Tsukamoto
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan
| | - Yuki Sudo
- Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan; Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan; Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki, Japan.
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Primary structural response in tryptophan residues of Anabaena sensory rhodopsin to photochromic reactions of the retinal chromophore. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.01.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Sudo Y, Homma M. [Photosensing by membrane-embedded receptors and its application for the life scientists]. YAKUGAKU ZASSHI 2012; 132:407-16. [PMID: 22465915 DOI: 10.1248/yakushi.132.407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Light is one of the most important energy sources and signals providing critical information to biological systems. The photoreceptor rhodopsin, which possesses retinal chromophore (vitamin A aldehyde) surrounded by seven transmembrane alpha-helices, is widely dispersed in prokaryotes and in eukaryotes. Although rhodopsin molecules work as distinctly different photoreceptors, they can be divided according to their two basic functions such as light-energy conversion and light-signal transduction. Thus rhodopsin molecules have great potential for controlling cellular activity by light. Indeed, a light-energy converter channel rhodopsin is used to control neural activity. From 2001, we have been working on various microbial sensory rhodopsins functioning as light-signal converters. In this review, we will introduce rhodopsin molecules from microbes, and will describe artificial and light-dependent protein expression system in Escherichia coli using Anabeana sensory rhodopsin (ASR). The newly developed tools would be widely useful for life scientists.
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Affiliation(s)
- Yuki Sudo
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan.
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13
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Cannizzo A. Ultrafast UV spectroscopy: from a local to a global view of dynamical processes in macromolecules. Phys Chem Chem Phys 2012; 14:11205-23. [DOI: 10.1039/c2cp40567a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Fujii N, Mizuno M, Mizutani Y. Direct Observation of Vibrational Energy Flow in Cytochrome c. J Phys Chem B 2011; 115:13057-64. [DOI: 10.1021/jp207500b] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Naoki Fujii
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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