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Hunt NT. Biomolecular infrared spectroscopy: making time for dynamics. Chem Sci 2024; 15:414-430. [PMID: 38179520 PMCID: PMC10763549 DOI: 10.1039/d3sc05223k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/24/2023] [Indexed: 01/06/2024] Open
Abstract
Time resolved infrared spectroscopy of biological molecules has provided a wealth of information relating to structural dynamics, conformational changes, solvation and intermolecular interactions. Challenges still exist however arising from the wide range of timescales over which biological processes occur, stretching from picoseconds to minutes or hours. Experimental methods are often limited by vibrational lifetimes of probe groups, which are typically on the order of picoseconds, while measuring an evolving system continuously over some 18 orders of magnitude in time presents a raft of technological hurdles. In this Perspective, a series of recent advances which allow biological molecules and processes to be studied over an increasing range of timescales, while maintaining ultrafast time resolution, will be reviewed, showing that the potential for real-time observation of biomolecular function draws ever closer, while offering a new set of challenges to be overcome.
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Affiliation(s)
- Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York Heslington York YO10 5DD UK
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2
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Bühl E, Resler T, Lam R, Asido M, Bamberg E, Schlesinger R, Bamann C, Heberle J, Wachtveitl J. Assessing the Role of R120 in the Gating of CrChR2 by Time-Resolved Spectroscopy from Femtoseconds to Seconds. J Am Chem Soc 2023; 145:21832-21840. [PMID: 37773976 DOI: 10.1021/jacs.3c05399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
The light-gated ion channel channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2) is the most frequently used optogenetic tool in neurosciences. However, the precise molecular mechanism of the channel opening and the correlation among retinal isomerization, the photocycle, and the channel activity of the protein are missing. Here, we present electrophysiological and spectroscopic investigations on the R120H variant of CrChR2. R120 is a key residue in an extended network linking the retinal chromophore to several gates of the ion channel. We show that despite the deficient channel activity, the photocycle of the variant is intact. In a comparative study for R120H and the wild type, we resolve the vibrational changes in the spectral range of the retinal and amide I bands across the time range from femtoseconds to seconds. Analysis of the amide I mode reveals a significant impairment of the ultrafast protein response after retinal excitation. We conclude that channel opening in CrChR2 is prepared immediately after retinal excitation. Additionally, chromophore isomerization is essential for both photocycle and channel activities, although both processes can occur independently.
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Affiliation(s)
- Elena Bühl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Strasse 7, 60438 Frankfurt, Germany
| | - Tom Resler
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Rebecca Lam
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany
| | - Marvin Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Strasse 7, 60438 Frankfurt, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany
| | - Ramona Schlesinger
- Department of Physics, Genetic Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Christian Bamann
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt am Main, Germany
| | - Joachim Heberle
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Strasse 7, 60438 Frankfurt, Germany
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3
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Shibata K, Oda K, Nishizawa T, Hazama Y, Ono R, Takaramoto S, Bagherzadeh R, Yawo H, Nureki O, Inoue K, Akiyama H. Twisting and Protonation of Retinal Chromophore Regulate Channel Gating of Channelrhodopsin C1C2. J Am Chem Soc 2023; 145:10779-10789. [PMID: 37129501 DOI: 10.1021/jacs.3c01879] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Channelrhodopsins (ChRs) are light-gated ion channels and central optogenetic tools that can control neuronal activity with high temporal resolution at the single-cell level. Although their application in optogenetics has rapidly progressed, it is unsolved how their channels open and close. ChRs transport ions through a series of interlocking elementary processes that occur over a broad time scale of subpicoseconds to seconds. During these processes, the retinal chromophore functions as a channel regulatory domain and transfers the optical input as local structural changes to the channel operating domain, the helices, leading to channel gating. Thus, the core question on channel gating dynamics is how the retinal chromophore structure changes throughout the photocycle and what rate-limits the kinetics. Here, we investigated the structural changes in the retinal chromophore of canonical ChR, C1C2, in all photointermediates using time-resolved resonance Raman spectroscopy. Moreover, to reveal the rate-limiting factors of the photocycle and channel gating, we measured the kinetic isotope effect of all photoreaction processes using laser flash photolysis and laser patch clamp, respectively. Spectroscopic and electrophysiological results provided the following understanding of the channel gating: the retinal chromophore highly twists upon the retinal Schiff base (RSB) deprotonation, causing the surrounding helices to move and open the channel. The ion-conducting pathway includes the RSB, where inflowing water mediates the proton to the deprotonated RSB. The twisting of the retinal chromophore relaxes upon the RSB reprotonation, which closes the channel. The RSB reprotonation rate-limits the channel closing.
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Affiliation(s)
- Keisei Shibata
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Kazumasa Oda
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo 113-0034, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo 113-0034, Japan
| | - Yuji Hazama
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Ryohei Ono
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
| | - Shunki Takaramoto
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Reza Bagherzadeh
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Hiromu Yawo
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Osamu Nureki
- Department of Biological Sciences Graduate School of Science, The University of Tokyo, Tokyo 113-0034, Japan
| | - Keiichi Inoue
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Hidefumi Akiyama
- Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
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4
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Abstract
Microbial rhodopsins represent the most abundant phototrophic systems known today. A similar molecular architecture with seven transmembrane helices and a retinal cofactor linked to a lysine in helix 7 enables a wide range of functions including ion pumping, light-controlled ion channel gating, or sensing. Deciphering their molecular mechanisms therefore requires a combined consideration of structural, functional, and spectroscopic data in order to identify key factors determining their function. Important insight can be gained by solid-state NMR spectroscopy by which the large homo-oligomeric rhodopsin complexes can be studied directly within lipid bilayers. This chapter describes the methodological background and the necessary sample preparation requirements for the study of photointermediates, for the analysis of protonation states, H-bonding and chromophore conformations, for 3D structure determination, and for probing oligomer interfaces of microbial rhodopsins. The use of data extracted from these NMR experiments is discussed in the context of complementary biophysical methods.
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Affiliation(s)
- Clara Nassrin Kriebel
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johanna Becker-Baldus
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Clemens Glaubitz
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
- Centre for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Frankfurt am Main, Germany.
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5
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Ultrafast proton release reaction and primary photochemistry of phycocyanobilin in solution observed with fs-time-resolved mid-IR and UV/Vis spectroscopy. Photochem Photobiol Sci 2021; 20:715-732. [PMID: 34002345 DOI: 10.1007/s43630-021-00045-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022]
Abstract
Deactivation processes of photoexcited (λex = 580 nm) phycocyanobilin (PCB) in methanol were investigated by means of UV/Vis and mid-IR femtosecond (fs) transient absorption (TA) as well as static fluorescence spectroscopy, supported by density-functional-theory calculations of three relevant ground state conformers, PCBA, PCBB and PCBC, their relative electronic state energies and normal mode vibrational analysis. UV/Vis fs-TA reveals time constants of 2.0, 18 and 67 ps, describing decay of PCBB*, of PCBA* and thermal re-equilibration of PCBA, PCBB and PCBC, respectively, in line with the model by Dietzek et al. (Chem Phys Lett 515:163, 2011) and predecessors. Significant substantiation and extension of this model is achieved first via mid-IR fs-TA, i.e. identification of molecular structures and their dynamics, with time constants of 2.6, 21 and 40 ps, respectively. Second, transient IR continuum absorption (CA) is observed in the region above 1755 cm-1 (CA1) and between 1550 and 1450 cm-1 (CA2), indicative for the IR absorption of highly polarizable protons in hydrogen bonding networks (X-H…Y). This allows to characterize chromophore protonation/deprotonation processes, associated with the electronic and structural dynamics, on a molecular level. The PCB photocycle is suggested to be closed via a long living (> 1 ns), PCBC-like (i.e. deprotonated), fluorescent species.
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6
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Oda K, Nomura T, Nakane T, Yamashita K, Inoue K, Ito S, Vierock J, Hirata K, Maturana AD, Katayama K, Ikuta T, Ishigami I, Izume T, Umeda R, Eguma R, Oishi S, Kasuya G, Kato T, Kusakizako T, Shihoya W, Shimada H, Takatsuji T, Takemoto M, Taniguchi R, Tomita A, Nakamura R, Fukuda M, Miyauchi H, Lee Y, Nango E, Tanaka R, Tanaka T, Sugahara M, Kimura T, Shimamura T, Fujiwara T, Yamanaka Y, Owada S, Joti Y, Tono K, Ishitani R, Hayashi S, Kandori H, Hegemann P, Iwata S, Kubo M, Nishizawa T, Nureki O. Time-resolved serial femtosecond crystallography reveals early structural changes in channelrhodopsin. eLife 2021; 10:62389. [PMID: 33752801 PMCID: PMC7987342 DOI: 10.7554/elife.62389] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 02/15/2021] [Indexed: 01/17/2023] Open
Abstract
Channelrhodopsins (ChRs) are microbial light-gated ion channels utilized in optogenetics to control neural activity with light . Light absorption causes retinal chromophore isomerization and subsequent protein conformational changes visualized as optically distinguished intermediates, coupled with channel opening and closing. However, the detailed molecular events underlying channel gating remain unknown. We performed time-resolved serial femtosecond crystallographic analyses of ChR by using an X-ray free electron laser, which revealed conformational changes following photoactivation. The isomerized retinal adopts a twisted conformation and shifts toward the putative internal proton donor residues, consequently inducing an outward shift of TM3, as well as a local deformation in TM7. These early conformational changes in the pore-forming helices should be the triggers that lead to opening of the ion conducting pore.
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Affiliation(s)
- Kazumasa Oda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takashi Nomura
- Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Takanori Nakane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Keitaro Yamashita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Keiichi Inoue
- Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
| | - Shota Ito
- Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
| | - Johannes Vierock
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Kunio Hirata
- RIKEN SPring-8 Center, Hyogo, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Japan
| | - Andrés D Maturana
- Department of Bioengineering Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Kota Katayama
- Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
| | - Tatsuya Ikuta
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Itsuki Ishigami
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tamaki Izume
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Rie Umeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ryuun Eguma
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Satomi Oishi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Go Kasuya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Takafumi Kato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroto Shimada
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Tomoyuki Takatsuji
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Mizuki Takemoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Reiya Taniguchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Atsuhiro Tomita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Ryoki Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Masahiro Fukuda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hirotake Miyauchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yongchan Lee
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, Hyogo, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Rie Tanaka
- RIKEN SPring-8 Center, Hyogo, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tomoyuki Tanaka
- RIKEN SPring-8 Center, Hyogo, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | | | - Tetsunari Kimura
- Department of Chemistry, Graduate School of Science, Kobe University, Kobe, Japan
| | - Tatsuro Shimamura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takaaki Fujiwara
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasuaki Yamanaka
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shigeki Owada
- RIKEN SPring-8 Center, Hyogo, Japan.,Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Yasumasa Joti
- RIKEN SPring-8 Center, Hyogo, Japan.,Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Kensuke Tono
- RIKEN SPring-8 Center, Hyogo, Japan.,Japan Synchrotron Radiation Research Institute, Hyogo, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Hideki Kandori
- Graduate School of Engineering, Nagoya Institute of Technology, Nagoya, Japan
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Berlin, Germany
| | - So Iwata
- RIKEN SPring-8 Center, Hyogo, Japan.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Minoru Kubo
- Graduate School of Life Science, University of Hyogo, Hyogo, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Kawaguchi, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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7
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Kaufmann JCD, Krause BS, Adam S, Ritter E, Schapiro I, Hegemann P, Bartl FJ. Modulation of Light Energy Transfer from Chromophore to Protein in the Channelrhodopsin ReaChR. Biophys J 2020; 119:705-716. [PMID: 32697975 DOI: 10.1016/j.bpj.2020.06.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/10/2020] [Accepted: 06/26/2020] [Indexed: 10/23/2022] Open
Abstract
The function of photoreceptors relies on efficient transfer of absorbed light energy from the chromophore to the protein to drive conformational changes that ultimately generate an output signal. In retinal-binding proteins, mainly two mechanisms exist to store the photon energy after photoisomerization: 1) conformational distortion of the prosthetic group retinal, and 2) charge separation between the protonated retinal Schiff base (RSBH+) and its counterion complex. Accordingly, energy transfer to the protein is achieved by chromophore relaxation and/or reduction of the charge separation in the RSBH+-counterion complex. Combining FTIR and UV-Vis spectroscopy along with molecular dynamics simulations, we show here for the widely used, red-activatable Volvox carteri channelrhodopsin-1 derivate ReaChR that energy storage and transfer into the protein depends on the protonation state of glutamic acid E163 (Ci1), one of the counterions of the RSBH+. Ci1 retains a pKa of 7.6 so that both its protonated and deprotonated forms equilibrate at physiological conditions. Protonation of Ci1 leads to a rigid hydrogen-bonding network in the active-site region. This stabilizes the distorted conformation of the retinal after photoactivation and decelerates energy transfer into the protein by impairing the release of the strain energy. In contrast, with deprotonated Ci1 or removal of the Ci1 glutamate side chain, the hydrogen-bonded system is less rigid, and energy transfer by chromophore relaxation is accelerated. Based on the hydrogen out-of-plane (HOOP) band decay kinetics, we determined the activation energy for these processes in dependence of the Ci1 protonation state.
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Affiliation(s)
- Joel C D Kaufmann
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Berlin, Germany; Institut für Medizinische Physik und Biophysik, Charité Berlin, Berlin, Germany
| | - Benjamin S Krause
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Suliman Adam
- Fritz Haber Center for Molecular Dynamics Research at the Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eglof Ritter
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Berlin, Germany; Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research at the Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Peter Hegemann
- Institut für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Franz J Bartl
- Institut für Biologie, Biophysikalische Chemie, Humboldt-Universität zu Berlin, Berlin, Germany.
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8
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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Ultrafast Backbone Protonation in Channelrhodopsin-1 Captured by Polarization Resolved Fs Vis-pump-IR-Probe Spectroscopy and Computational Methods. Molecules 2020; 25:molecules25040848. [PMID: 32075128 PMCID: PMC7070883 DOI: 10.3390/molecules25040848] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/03/2020] [Accepted: 02/12/2020] [Indexed: 12/19/2022] Open
Abstract
Channelrhodopsins (ChR) are light-gated ion-channels heavily used in optogenetics. Upon light excitation an ultrafast all-trans to 13-cis isomerization of the retinal chromophore takes place. It is still uncertain by what means this reaction leads to further protein changes and channel conductivity. Channelrhodopsin-1 in Chlamydomonas augustae exhibits a 100 fs photoisomerization and a protonated counterion complex. By polarization resolved ultrafast spectroscopy in the mid-IR we show that the initial reaction of the retinal is accompanied by changes in the protein backbone and ultrafast protonation changes at the counterion complex comprising Asp299 and Glu169. In combination with homology modelling and quantum mechanics/molecular mechanics (QM/MM) geometry optimization we assign the protonation dynamics to ultrafast deprotonation of Glu169, and transient protonation of the Glu169 backbone, followed by a proton transfer from the backbone to the carboxylate group of Asp299 on a timescale of tens of picoseconds. The second proton transfer is not related to retinal dynamics and reflects pure protein changes in the first photoproduct. We assume these protein dynamics to be the first steps in a cascade of protein-wide changes resulting in channel conductivity.
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10
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Vieira Pinto SM, Tasinato N, Barone V, Amadei A, Zanetti-Polzi L, Daidone I. Modeling amino-acid side chain infrared spectra: the case of carboxylic residues. Phys Chem Chem Phys 2020; 22:3008-3016. [DOI: 10.1039/c9cp04774c] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Infrared (IR) spectroscopy is commonly utilized for the investigation of protein structures and protein-mediated processes.
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Affiliation(s)
- Sandra Mónica Vieira Pinto
- Scuola Normale Superiore
- I-56126 Pisa
- Italy
- Department of Physical and Chemical Sciences
- University of L'Aquila
| | | | | | - Andrea Amadei
- Department of Chemical and Technological Sciences
- University of Rome “Tor Vergata
- I-00185 Rome
- Italy
| | - Laura Zanetti-Polzi
- Department of Physical and Chemical Sciences
- University of L'Aquila
- I-67010 L'Aquila
- Italy
- CNR Institute of Nanoscience
| | - Isabella Daidone
- Department of Physical and Chemical Sciences
- University of L'Aquila
- I-67010 L'Aquila
- Italy
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11
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Chakraborty S, Nandi S, Bhattacharyya K, Mukherjee S. Time Evolution of Local pH Around a Photo-Acid in Water and a Polymer Hydrogel: Time Resolved Fluorescence Spectroscopy of Pyranine. Chemphyschem 2019; 20:3221-3227. [PMID: 31596029 DOI: 10.1002/cphc.201900845] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 09/19/2019] [Indexed: 12/31/2022]
Abstract
In this work, we propose a new analysis of the time resolved emission spectra of a photo-acid, HA, pyranine (8-hydroxypyrene-1,3,6-trisulphonic acid, HPTS) based on time resolved area normalized emission spectra (TRANES). Presence of an isoemissive point in TRANES confirms the presence of two emissive species (HA and A- ) inside the system in bulk water and inside a co-polymer hydrogel [F127, (PEO)100 -(PPO)70 -(PEO)100 ]. We show that following electronic excitation, the local pH around HPTS, is much lower than the bulk pH presumably because of ejection of proton from the photo-acid in the excited state. With increase in time, the local pH increases and reaches the bulk value. We further, demonstrate that the excited state pKa of HPTS may be estimated from the emission intensities of HA and A- at long time. The time constant for time evolution of pH is ∼630 ps in water, ∼1300 ps in F127 gel and ∼4700 ps in CTAB micelle. The location and local viscosity sensed by the probe is ascertained using fluorescence correlation spectroscopy (FCS) and fluorescence anisotropy decay. The different values of the local viscosity reported by these two methods are reconciled.
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Affiliation(s)
- Subhajit Chakraborty
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal, 462 066, Madhya Pradesh, India
| | - Somen Nandi
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal, 462 066, Madhya Pradesh, India
| | - Kankan Bhattacharyya
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal, 462 066, Madhya Pradesh, India
| | - Saptarshi Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal, 462 066, Madhya Pradesh, India
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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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