1
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Schubert L, Chen JL, Fritz T, Marxer F, Langner P, Hoffmann K, Gamiz-Hernandez AP, Kaila VRI, Schlesinger R, Heberle J. Proton Release Reactions in the Inward H + Pump NsXeR. J Phys Chem B 2023; 127:8358-8369. [PMID: 37729557 DOI: 10.1021/acs.jpcb.3c04100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Directional ion transport across biological membranes plays a central role in many cellular processes. Elucidating the molecular determinants for vectorial ion transport is key to understanding the functional mechanism of membrane-bound ion pumps. The extensive investigation of the light-driven proton pump bacteriorhodopsin from Halobacterium salinarum(HsBR) enabled a detailed description of outward proton transport. Although the structure of inward-directed proton pumping rhodopsins is very similar to HsBR, little is known about their protonation pathway, and hence, the molecular reasons for the vectoriality of proton translocation remain unclear. Here, we employ a combined experimental and theoretical approach to tracking protonation steps in the light-driven inward proton pump xenorhodopsin from Nanosalina sp. (NsXeR). Time-resolved infrared spectroscopy reveals the transient deprotonation of D220 concomitantly with deprotonation of the retinal Schiff base. Our molecular dynamics simulations support a proton release pathway from the retinal Schiff base via a hydrogen-bonded water wire leading to D220 that could provide a putative gating point for the proton release and with allosteric interactions to the retinal Schiff base. Our findings support the key role of D220 in mediating proton release to the cytoplasmic side and provide evidence that this residue is not the primary proton acceptor of the proton transiently released by the retinal Schiff base.
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Affiliation(s)
- Luiz Schubert
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195Berlin, Germany
| | - Jheng-Liang Chen
- Genetic Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195Berlin, Germany
| | - Tobias Fritz
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Florina Marxer
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195Berlin, Germany
| | - Pit Langner
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195Berlin, Germany
| | - Kirsten Hoffmann
- Genetic Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195Berlin, Germany
| | - Ana P Gamiz-Hernandez
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ville R I Kaila
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ramona Schlesinger
- Genetic Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195Berlin, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195Berlin, Germany
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2
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Saliminasab M, Yamazaki Y, Palmateer A, Harris A, Schubert L, Langner P, Heberle J, Bondar AN, Brown LS. A Proteorhodopsin-Related Photosensor Expands the Repertoire of Structural Motifs Employed by Sensory Rhodopsins. J Phys Chem B 2023; 127:7872-7886. [PMID: 37694950 PMCID: PMC10519204 DOI: 10.1021/acs.jpcb.3c04032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/09/2023] [Indexed: 09/12/2023]
Abstract
Microbial rhodopsins are light-activated retinal-binding membrane proteins that perform a variety of ion transport and photosensory functions. They display several cases of convergent evolution where the same function is present in unrelated or very distant protein groups. Here we report another possible case of such convergent evolution, describing the biophysical properties of a new group of sensory rhodopsins. The first representative of this group was identified in 2004 but none of the members had been expressed and characterized. The well-studied haloarchaeal sensory rhodopsins interacting with methyl-accepting Htr transducers are close relatives of the halobacterial proton pump bacteriorhodopsin. In contrast, the sensory rhodopsins we describe here are relatives of proteobacterial proton pumps, proteorhodopsins, but appear to interact with Htr-like transducers likewise, even though they do not conserve the residues important for the interaction of haloarchaeal sensory rhodopsins with their transducers. The new sensory rhodopsins display many unusual amino acid residues, including those around the retinal chromophore; most strikingly, a tyrosine in place of a carboxyl counterion of the retinal Schiff base on helix C. To characterize their unique sequence motifs, we augment the spectroscopy and biochemistry data by structural modeling of the wild-type and three mutants. Taken together, the experimental data, bioinformatics sequence analyses, and structural modeling suggest that the tyrosine/aspartate complex counterion contributes to a complex water-mediated hydrogen-bonding network that couples the protonated retinal Schiff base to an extracellular carboxylic dyad.
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Affiliation(s)
- Maryam Saliminasab
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Yoichi Yamazaki
- Division
of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Alyssa Palmateer
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Andrew Harris
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Luiz Schubert
- Experimental
Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Pit Langner
- Experimental
Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Joachim Heberle
- Experimental
Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Ana-Nicoleta Bondar
- University
of Bucharest, Faculty of Physics, Atomiştilor 405, Măgurele 077125, Romania
- Forschungszentrum
Jülich, Institute for Neuroscience and Medicine and Institute
for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52428 Jülich, Germany
| | - Leonid S. Brown
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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3
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Noji T, Ishikita H. Mechanism of Absorption Wavelength Shift of Bacteriorhodopsin During Photocycle. J Phys Chem B 2022; 126:9945-9955. [PMID: 36413506 DOI: 10.1021/acs.jpcb.2c04359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Bacteriorhodopsin, a light-driven proton pump, alters the absorption wavelengths in the range of 410-617 nm during the photocycle. Here, we report the absorption wavelengths, calculated using 12 bacteriorhodopsin crystal structures (including the BR, BR13-cis, J, K0, KE, KL, L, M, N, and O state structures) and a combined quantum mechanical/molecular mechanical/polarizable continuum model (QM/MM/PCM) approach. The QM/MM/PCM calculations reproduced the experimentally measured absorption wavelengths with a standard deviation of 4 nm. The shifts in the absorption wavelengths can be explained mainly by the following four factors: (i) retinal Schiff base deformation/twist induced by the protein environment, leading to a decrease in the electrostatic interaction between the protein environment and the retinal Schiff base; (ii) changes in the protonation state of the protein environment, directly altering the electrostatic interaction between the protein environment and the retinal Schiff base; (iii) changes in the protonation state; or (iv) isomerization of the retinal Schiff base, where the absorption wavelengths of the isomers originally differ.
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Affiliation(s)
- Tomoyasu Noji
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan
| | - Hiroshi Ishikita
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo153-8904, Japan.,Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo113-8654, Japan
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4
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Kouyama T, Ihara K. Existence of two substates in the O intermediate of the bacteriorhodopsin photocycle. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183998. [PMID: 35753392 DOI: 10.1016/j.bbamem.2022.183998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 04/12/2022] [Accepted: 06/18/2022] [Indexed: 06/15/2023]
Abstract
The proton pumping cycle of bacteriorhodopsin (bR) is initiated when the retinal chromophore with the 13-trans configuration is photo-isomerized into the 13-cis configuration. To understand the recovery processes of the initial retinal configuration that occur in the late stage of the photocycle, we have performed a comprehensive analysis of absorption kinetics data collected at various pH levels and at different salt concentrations. The result of analysis revealed the following features of the late stages of the trans photocycle. i) Two substates occur in the O intermediate. ii) The visible absorption band of the first substate (O1) appears at a much shorter wavelength than that of the late substate (O2). iii) O1 is in rapid equilibrium with the preceding state (N), but O1 becomes less stable than N when an ionizable residue (X1) with a pKa value of 6.5 (in 2 M KCl) is deprotonated. iv) At a low pH and at a low salt concentration, the decay time constant of O2 is longer than those of the preceding states, but the relationship between these time constants is altered when the medium pH or the salt concentration is increased. On the basis of the present observations and previous studies on the structure of the chromophore in O, we suspect that the retinal chromophore in O1 takes on a distorted 13-cis configuration and the O1-to-O2 transition is accompanied by cis-to-trans isomerization about C13C14 bond.
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Affiliation(s)
- Tsutomu Kouyama
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
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5
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Saito K, Xu T, Ishikita H. Correlation between C═O Stretching Vibrational Frequency and p Ka Shift of Carboxylic Acids. J Phys Chem B 2022; 126:4999-5006. [PMID: 35763701 PMCID: PMC9289881 DOI: 10.1021/acs.jpcb.2c02193] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
![]()
Identifying the pKa values of aspartic
acid (Asp) and glutamic acid (Glu) in active sites is essential for
understanding enzyme reaction mechanisms. In this study, we investigated
the correlation between the C=O stretching vibrational frequency
(νC=O) of protonated carboxylic acids and
the pKa values using density functional
theory calculations. In unsaturated carboxylic acids (e.g., benzoic
acid analogues), νC=O decreases as the pKa increases (the negative correlation), whereas
in saturated carboxylic acids (e.g., acetic acid analogues, Asp, and
Glu), νC=O increases as the pKa increases (the positive correlation) as long as the
structure of the H-bond network around the acid is identical. The
negative/positive correlation between νC=O and pKa can be rationalized by the presence
or absence of the C=C double bond. The pKa shift was estimated from the νC=O shift of Asp and Glu in proteins on the basis of the negative correlation
derived from benzoic acids. The previous estimations should be revisited
by using the positive correlation derived in this study, as demonstrated
by quantum mechanical/molecular mechanical calculations of νC=O and electrostatic calculations of pKa on a key Asp85 in the proton-transfer pathway of bacteriorhodopsin.
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Affiliation(s)
- Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Tianyang Xu
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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6
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Baserga F, Vorkas A, Crea F, Schubert L, Chen JL, Redlich A, La Greca M, Storm J, Oldemeyer S, Hoffmann K, Schlesinger R, Heberle J. Membrane Protein Activity Induces Specific Molecular Changes in Nanodiscs Monitored by FTIR Difference Spectroscopy. Front Mol Biosci 2022; 9:915328. [PMID: 35769914 PMCID: PMC9234331 DOI: 10.3389/fmolb.2022.915328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/18/2022] [Indexed: 12/03/2022] Open
Abstract
It is well known that lipids neighboring integral membrane proteins directly influence their function. The opposite effect is true as well, as membrane proteins undergo structural changes after activation and thus perturb the lipidic environment. Here, we studied the interaction between these molecular machines and the lipid bilayer by observing changes in the lipid vibrational bands via FTIR spectroscopy. Membrane proteins with different functionalities have been reconstituted into lipid nanodiscs: Microbial rhodopsins that act as light-activated ion pumps (the proton pumps NsXeR and UmRh1, and the chloride pump NmHR) or as sensors (NpSRII), as well as the electron-driven cytochrome c oxidase RsCcO. The effects of the structural changes on the surrounding lipid phase are compared to mechanically induced lateral tension exerted by the light-activatable lipid analogue AzoPC. With the help of isotopologues, we show that the ν(C = O) ester band of the glycerol backbone reports on changes in the lipids’ collective state induced by mechanical changes in the transmembrane proteins. The perturbation of the nanodisc lipids seems to involve their phase and/or packing state. 13C-labeling of the scaffold protein shows that its structure also responds to the mechanical expansion of the lipid bilayer.
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Affiliation(s)
- Federico Baserga
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Antreas Vorkas
- Department of Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Fucsia Crea
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Luiz Schubert
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Jheng-Liang Chen
- Department of Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Aoife Redlich
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | | | - Julian Storm
- Department of Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Sabine Oldemeyer
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Kirsten Hoffmann
- Department of Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Ramona Schlesinger
- Department of Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
- *Correspondence: Ramona Schlesinger, ; Joachim Heberle,
| | - Joachim Heberle
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
- *Correspondence: Ramona Schlesinger, ; Joachim Heberle,
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7
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Schubert L, Langner P, Ehrenberg D, Lorenz-Fonfria VA, Heberle J. Protein conformational changes and protonation dynamics probed by a single shot using quantum-cascade-laser-based IR spectroscopy. J Chem Phys 2022; 156:204201. [PMID: 35649857 DOI: 10.1063/5.0088526] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mid-IR spectroscopy is a powerful and label-free technique to investigate protein reactions. In this study, we use quantum-cascade-laser-based dual-comb spectroscopy to probe protein conformational changes and protonation events by a single-shot experiment. By using a well-characterized membrane protein, bacteriorhodopsin, we provide a comparison between dual-comb spectroscopy and our homebuilt tunable quantum cascade laser (QCL)-based scanning spectrometer as tools to monitor irreversible reactions with high time resolution. In conclusion, QCL-based infrared spectroscopy is demonstrated to be feasible for tracing functionally relevant protein structural changes and proton translocations by single-shot experiments. Thus, we envisage a bright future for applications of this technology for monitoring the kinetics of irreversible reactions as in (bio-)chemical transformations.
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Affiliation(s)
- Luiz Schubert
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Pit Langner
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - David Ehrenberg
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Victor A Lorenz-Fonfria
- Institute of Molecular Science, Universitat de Valencia, Catedrático José Beltrán Martínez, No. 2, 46980 Paterna, Spain
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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8
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La Greca M, Chen JL, Schubert L, Kozuch J, Berneiser T, Terpitz U, Heberle J, Schlesinger R. The Photoreaction of the Proton-Pumping Rhodopsin 1 From the Maize Pathogenic Basidiomycete Ustilago maydis. Front Mol Biosci 2022; 9:826990. [PMID: 35281268 PMCID: PMC8913941 DOI: 10.3389/fmolb.2022.826990] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/25/2022] [Indexed: 01/25/2023] Open
Abstract
Microbial rhodopsins have recently been discovered in pathogenic fungi and have been postulated to be involved in signaling during the course of an infection. Here, we report on the spectroscopic characterization of a light-driven proton pump rhodopsin (UmRh1) from the smut pathogen Ustilago maydis, the causative agent of tumors in maize plants. Electrophysiology, time-resolved UV/Vis and vibrational spectroscopy indicate a pH-dependent photocycle. We also characterized the impact of the auxin hormone indole-3-acetic acid that was shown to influence the pump activity of UmRh1 on individual photocycle intermediates. A facile pumping activity test was established of UmRh1 expressed in Pichia pastoris cells, for probing proton pumping out of the living yeast cells during illumination. We show similarities and distinct differences to the well-known bacteriorhodopsin from archaea and discuss the putative role of UmRh1 in pathogenesis.
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Affiliation(s)
- Mariafrancesca La Greca
- Institute of Experimental Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Jheng-Liang Chen
- Institute of Experimental Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Luiz Schubert
- Institute of Experimental Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Jacek Kozuch
- Institute of Experimental Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Tim Berneiser
- Institute of Experimental Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Ulrich Terpitz
- Department of Biotechnology and Biophysics, Biocenter, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Joachim Heberle
- Institute of Experimental Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Ramona Schlesinger
- Institute of Experimental Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
- *Correspondence: Ramona Schlesinger,
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9
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Bozovic O, Jankovic B, Hamm P. Using azobenzene photocontrol to set proteins in motion. Nat Rev Chem 2021; 6:112-124. [PMID: 37117294 DOI: 10.1038/s41570-021-00338-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2021] [Indexed: 02/06/2023]
Abstract
Controlling the activity of proteins with azobenzene photoswitches is a potent tool for manipulating their biological function. With the help of light, it is possible to change binding affinities, control allostery or manipulate complex biological processes, for example. Additionally, owing to their intrinsically fast photoisomerization, azobenzene photoswitches can serve as triggers that initiate out-of-equilibrium processes. Such switching of the activity initiates a cascade of conformational events that can be accessed with time-resolved methods. In this Review, we show how the potency of azobenzene photoswitching can be combined with transient spectroscopic techniques to disclose the order of events and experimentally observe biomolecular interactions in real time. This strategy will further our understanding of how a protein can accommodate, adapt and readjust its structure to answer an incoming signal, revealing more of the dynamical character of proteins.
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10
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Buhrke D, Ruf J, Heckmeier P, Hamm P. A stop-flow sample delivery system for transient spectroscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2021; 92:123001. [PMID: 34972444 DOI: 10.1063/5.0068227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/06/2021] [Indexed: 06/14/2023]
Abstract
A stop-flow sample delivery system for transient spectroscopy is presented, which is, in particular, suited for laser-based instruments (quantum-cascade lasers or amplified femtosecond lasers) with excitation pulse repetition rates in the range 10-100 Hz. Two pulsing micro-valves are mounted onto a flow cuvette designed for transient IR spectroscopy, which is integrated into a flow cycle driven by a peristaltic pump. The performance of the system is demonstrated with transient IR experiments of the trans-to-cis photoisomerization of a water-soluble azobenzene derivative. The sample stands still when the micro-valves are closed and is pushed out from the probe beam focus on a 1 ms timescale when opening the micro-valves. The setup is extremely sample efficient. It needs only small sample volumes, and at the same time, it enables excitation of a large fraction of molecules in solution.
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Affiliation(s)
- David Buhrke
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Jeannette Ruf
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Philipp Heckmeier
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
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11
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Watson RA, Offenbacher AR, Barry BA. Detection of Catalytically Linked Conformational Changes in Wild-Type Class Ia Ribonucleotide Reductase Using Reaction-Induced FTIR Spectroscopy. J Phys Chem B 2021; 125:8362-8372. [PMID: 34289692 DOI: 10.1021/acs.jpcb.1c03038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzyme, ribonucleotide reductase (RNR), is essential for DNA synthesis in all cells. The class Ia Escherichia coli RNR consists of two dimeric subunits, α2 and β2, which form an active but unstable heterodimer of dimers, α2β2. The structure of the wild-type form of the enzyme has been challenging to study due to the instability of the catalytic complex. A long-range proton-coupled electron-transfer (PCET) pathway facilitates radical migration from the Y122 radical-diiron cofactor in the β subunit to an active site cysteine, C439, in the α subunit to initiate the RNR chemistry. The PCET reactions and active site chemistry are spectroscopically masked by a rate-limiting, conformational gate. Here, we present a reaction-induced Fourier transform infrared (RIFTIR) spectroscopic method to monitor the mechanism of the active, wild-type RNR α2β2 complex. This method is employed to obtain new information about conformational changes accompanying RNR catalysis, including the role of carboxylate interactions, deprotonation, and oxidation of active site cysteines, and a detailed description of reversible secondary structural changes. Labeling of tyrosine revealed a conformationally active tyrosine in the β subunit, assigned to Y356β, which is part of the intersubunit PCET pathway. New insights into the roles of the inhibitors, azidoUDP and dATP, and the sensitivity of RIFTIR spectroscopy to detect subtle conformational motions arising from protein allostery are also presented.
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Affiliation(s)
- Ryan Atlee Watson
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States
| | - Adam R Offenbacher
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States.,Department of Chemistry, East Carolina University, Greenville, North Carolina, United States
| | - Bridgette A Barry
- Department of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia, United States
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12
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Weigel A, Jacob P, Gröters D, Buberl T, Huber M, Trubetskov M, Heberle J, Pupeza I. Ultra-rapid electro-optic sampling of octave-spanning mid-infrared waveforms. OPTICS EXPRESS 2021; 29:20747-20764. [PMID: 34266157 DOI: 10.1364/oe.423818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/24/2021] [Indexed: 06/13/2023]
Abstract
We demonstrate ultra-rapid electro-optic sampling (EOS) of octave-spanning mid-infrared pulses centered at 9 μm, implemented by mechanically scanning a mirror with a sonotrode resonating at 19 kHz (forward and backward acquisition at 38 kHz). The instrument records the infrared waveform with a spectral intensity dynamic range of 1.6 × 105 for a single scan over a 1.6-ps delay range, acquired within 26 μs. The purely reflective nature of the delay scanning technique is compatible with broad optical bandwidths, short pulse durations (16 fs, centered at 1030 nm) and high average powers (Watt-level). Interferometric tracking of the sonotrode motion in combination with a predictor-corrector algorithm allows for delay-axis determination with down to single-digit attosecond precision. Ultra-rapid mid-infrared EOS will advance applications such as molecular fingerprinting of static samples as well as tracking of biological processes and chemical reactions and is likely to find new fields of application such as infrared-spectroscopic flow cytometry.
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13
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Affiliation(s)
- Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
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14
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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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15
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Ash PA, Kendall-Price SET, Vincent KA. Unifying Activity, Structure, and Spectroscopy of [NiFe] Hydrogenases: Combining Techniques To Clarify Mechanistic Understanding. Acc Chem Res 2019; 52:3120-3131. [PMID: 31675209 DOI: 10.1021/acs.accounts.9b00293] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Achieving a unified understanding of the mechanism of a multicenter redox enzyme such as [NiFe] hydrogenase is complicated by difficulties in reconciling information obtained by using different techniques and on samples in different physical forms. Measurements of the activity of the enzyme, and of factors which perturb activity, are generally carried out using biochemical assays in solution or with electrode-immobilized enzymes using protein film electrochemistry (PFE). Conversely, spectroscopy aimed at reporting on features of the metalloclusters in the enzyme, such as electron paramagnetic resonance (EPR) or X-ray absorption spectroscopy (XAS), is often conducted on frozen samples and is thus difficult to relate to catalytically relevant states as information about turnover and activity has been lost. To complicate matters further, most of our knowledge of the atomic-level structure of metalloenzymes comes from X-ray diffraction studies in the solid, crystalline state, which are again difficult to link to turnover conditions. Taking [NiFe] hydrogenases as our case study, we show here how it is possible to apply infrared (IR) spectroscopic sampling approaches to unite direct spectroscopic study with catalytic turnover. Using a method we have named protein film IR electrochemistry (PFIRE), we reveal the steady-state distribution of intermediates during catalysis and identify catalytic "bottlenecks" introduced by site-directed mutagenesis. We also show that it is possible to study dynamic transitions between active site states of enzymes in single crystals, uniting solid state and solution spectroscopic information. In all of these cases, the spectroscopic data complement and enhance interpretation of purely activity-based measurements by providing direct chemical insight that is otherwise hidden. The [NiFe] hydrogenases possess a bimetallic [NiFe] active site, coordinated by CO and CN- ligands, linked to the protein via bridging and terminal cysteine sulfur ligands, as well as an electron relay chain of iron sulfur clusters. Infrared spectroscopy is ideal for probing hydrogenases because the CO and CN- ligands are strong IR absorbers, but the suite of IR-based approaches we describe here will be equally valuable in studying substrate- or intermediate-bound states of other metalloenzymes where key mechanistic questions remain open, such as nitrogenase, formate dehydrogenase, or carbon monoxide dehydrogenase. We therefore hope that this Account will encourage future studies which unify information from different techniques across bioinorganic chemistry.
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Affiliation(s)
- Philip A. Ash
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
- School of Chemistry, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom
| | | | - Kylie A. Vincent
- Department of Chemistry, University of Oxford, Oxford OX1 3QR, United Kingdom
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16
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Ehrenberg D, Varma N, Deupi X, Koyanagi M, Terakita A, Schertler GFX, Heberle J, Lesca E. The Two-Photon Reversible Reaction of the Bistable Jumping Spider Rhodopsin-1. Biophys J 2019; 116:1248-1258. [PMID: 30902364 PMCID: PMC6451042 DOI: 10.1016/j.bpj.2019.02.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 01/16/2019] [Accepted: 02/19/2019] [Indexed: 12/22/2022] Open
Abstract
Bistable opsins are photopigments expressed in both invertebrates and vertebrates. These light-sensitive G-protein-coupled receptors undergo a reversible reaction upon illumination. A first photon initiates the cis to trans isomerization of the retinal chromophore—attached to the protein through a protonated Schiff base—and a series of transition states that eventually results in the formation of the thermally stable and active Meta state. Excitation by a second photon reverts this process to recover the original ground state. On the other hand, monostable opsins (e.g., bovine rhodopsin) lose their chromophore during the decay of the Meta II state (i.e., they bleach). Spectroscopic studies on the molecular details of the two-photon cycle in bistable opsins are limited. Here, we describe the successful expression and purification of recombinant rhodopsin-1 from the jumping spider Hasarius adansoni (JSR1). In its natural configuration, spectroscopic characterization of JSR1 is hampered by the similar absorption spectra in the visible spectrum of the inactive and active states. We solved this issue by separating their absorption spectra by replacing the endogenous 11-cis retinal chromophore with the blue-shifted 9-cis JSiR1. With this system, we used time-resolved ultraviolet-visible spectroscopy after pulsed laser excitation to obtain kinetic details of the rise and decay of the photocycle intermediates. We also used resonance Raman spectroscopy to elucidate structural changes of the retinal chromophore upon illumination. Our data clearly indicate that the protonated Schiff base is stable throughout the entire photoreaction. We additionally show that the accompanying conformational changes in the protein are different from those of monostable rhodopsin, as recorded by light-induced FTIR difference spectroscopy. Thus, we envisage JSR1 as becoming a model system for future studies on the reaction mechanisms of bistable opsins, e.g., by time-resolved x-ray crystallography.
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Affiliation(s)
- David Ehrenberg
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Niranjan Varma
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland; Department of Biology, ETH Zürich, Zürich, Switzerland
| | - Xavier Deupi
- Division of Neutrons and Muons-Laboratory for Scientific Computing and Modelling, Paul Scherrer Institute, Villigen, Switzerland
| | - Mitsumasa Koyanagi
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka, Japan
| | - Akihisa Terakita
- Department of Biology and Geosciences, Graduate School of Science, Osaka City University, Osaka, Japan
| | - Gebhard F X Schertler
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland; Department of Biology, ETH Zürich, Zürich, Switzerland.
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Berlin, Germany.
| | - Elena Lesca
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institute, Villigen, Switzerland; Department of Biology, ETH Zürich, Zürich, Switzerland.
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17
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Jawurek M, Dröden J, Peter B, Glaubitz C, Hauser K. Lipid-induced dynamics of photoreceptors monitored by time-resolved step-scan FTIR spectroscopy. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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18
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Schultz BJ, Mohrmann H, Lorenz-Fonfria VA, Heberle J. Protein dynamics observed by tunable mid-IR quantum cascade lasers across the time range from 10ns to 1s. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 188:666-674. [PMID: 28110813 DOI: 10.1016/j.saa.2017.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 12/29/2016] [Accepted: 01/04/2017] [Indexed: 06/06/2023]
Abstract
We have developed a spectrometer based on tunable quantum cascade lasers (QCLs) for recording time-resolved absorption spectra of proteins in the mid-infrared range. We illustrate its performance by recording time-resolved difference spectra of bacteriorhodopsin in the carboxylic range (1800-1700cm-1) and on the CO rebinding reaction of myoglobin (1960-1840cm-1), at a spectral resolution of 1cm-1. The spectrometric setup covers the time range from 4ns to nearly a second with a response time of 10-15ns. Absorption changes as low as 1×10-4 are detected in single-shot experiments at t>1μs, and of 5×10-6 in kinetics obtained after averaging 100 shots. While previous time-resolved IR experiments have mostly been conducted on hydrated films of proteins, we demonstrate here that the brilliance of tunable quantum cascade lasers is superior to perform ns time-resolved experiments even in aqueous solution (H2O).
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Affiliation(s)
- Bernd-Joachim Schultz
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Hendrik Mohrmann
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Victor A Lorenz-Fonfria
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany; Department of Biochemistry and Molecular Biology, Universitat de València, Dr. Moliner 50, 46100 Burjassot, Spain; Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Dr. Moliner 50, 46100 Burjassot, Spain
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
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19
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Kraack JP. Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods. Top Curr Chem (Cham) 2017; 375:86. [PMID: 29071445 DOI: 10.1007/s41061-017-0172-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 10/02/2017] [Indexed: 12/23/2022]
Abstract
Ultrafast, multi-dimensional infrared (IR) spectroscopy has been advanced in recent years to a versatile analytical tool with a broad range of applications to elucidate molecular structure on ultrafast timescales, and it can be used for samples in a many different environments. Following a short and general introduction on the benefits of 2D IR spectroscopy, the first part of this chapter contains a brief discussion on basic descriptions and conceptual considerations of 2D IR spectroscopy. Outstanding classical applications of 2D IR are used afterwards to highlight the strengths and basic applicability of the method. This includes the identification of vibrational coupling in molecules, characterization of spectral diffusion dynamics, chemical exchange of chemical bond formation and breaking, as well as dynamics of intra- and intermolecular energy transfer for molecules in bulk solution and thin films. In the second part, several important, recently developed variants and new applications of 2D IR spectroscopy are introduced. These methods focus on (i) applications to molecules under two- and three-dimensional confinement, (ii) the combination of 2D IR with electrochemistry, (iii) ultrafast 2D IR in conjunction with diffraction-limited microscopy, (iv) several variants of non-equilibrium 2D IR spectroscopy such as transient 2D IR and 3D IR, and (v) extensions of the pump and probe spectral regions for multi-dimensional vibrational spectroscopy towards mixed vibrational-electronic spectroscopies. In light of these examples, the important open scientific and conceptual questions with regard to intra- and intermolecular dynamics are highlighted. Such questions can be tackled with the existing arsenal of experimental variants of 2D IR spectroscopy to promote the understanding of fundamentally new aspects in chemistry, biology and materials science. The final part of the chapter introduces several concepts of currently performed technical developments, which aim at exploiting 2D IR spectroscopy as an analytical tool. Such developments embrace the combination of 2D IR spectroscopy and plasmonic spectroscopy for ultrasensitive analytics, merging 2D IR spectroscopy with ultra-high-resolution microscopy (nanoscopy), future variants of transient 2D IR methods, or 2D IR in conjunction with microfluidics. It is expected that these techniques will allow for groundbreaking research in many new areas of natural sciences.
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Affiliation(s)
- Jan Philip Kraack
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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20
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Abstract
The 97 amino acid bitopic membrane protein M2 of influenza A forms a tetrameric bundle in which two of the monomers are covalently linked via a cysteine bridge. In its tetrameric assembly the protein conducts protons across the viral envelope and within intracellular compartments during the infectivity cycle of the virus. A key residue in the translocation of the protons is His-37 which forms a planar tetrad in the configuration of the bundle accepting and translocating the incoming protons from the N terminal side, exterior of the virus, to the C terminal side, inside the virus. With experimentally available data from NMR spectroscopy of the transmembrane domains of the tetrameric M2 bundle classical MD simulations are conducted with the protein bundle in different protonation stages in respect to His-37. A full correlation analysis (FCA) of the data sets with the His-37 tetrad either in a fully four times unprotonated or protonated state, assumed to mimic high and low pH in vivo, respectively, in both cases reveal asymmetric backbone dynamics. His-37 side chain rotation dynamics is increased at full protonation of the tetrad compared to the dynamics in the fully unprotonated state. The data suggest that proton translocation can be achieved by decoupled side chain or backbone dynamics. Graphical abstract Visualization of the tetrameric bundle of the transmembrane domains of M2 of influenza A after 200 ns of MD simulations (upper left). The four histidine residues 37 are either not protonated as in M20 or fully protonated is in M24+. The asymmetric dynamics of the backbones are shown after a full correlation analysis (FCA) in blue (lower left). The rotational dynamics of the χ2 dihedral angles of the histidines in M20 (upper right) are less than those in M24+ (lower right).
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Affiliation(s)
- Monoj Mon Kalita
- Institute of Biophotonics and Biophotonics & Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, 155, Li-Nong St., Sec. 2, Taipei, 112, Taiwan
| | - Wolfgang B Fischer
- Institute of Biophotonics and Biophotonics & Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, 155, Li-Nong St., Sec. 2, Taipei, 112, Taiwan.
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21
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Mezzetti A, Leibl W. Time-resolved infrared spectroscopy in the study of photosynthetic systems. PHOTOSYNTHESIS RESEARCH 2017; 131:121-144. [PMID: 27678250 DOI: 10.1007/s11120-016-0305-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 09/05/2016] [Indexed: 06/06/2023]
Abstract
Time-resolved (TR) infrared (IR) spectroscopy in the nanosecond to second timescale has been extensively used, in the last 30 years, in the study of photosynthetic systems. Interesting results have also been obtained at lower time resolution (minutes or even hours). In this review, we first describe the used techniques-dispersive IR, laser diode IR, rapid-scan Fourier transform (FT)IR, step-scan FTIR-underlying the advantages and disadvantages of each of them. Then, the main TR-IR results obtained so far in the investigation of photosynthetic reactions (in reaction centers, in light-harvesting systems, but also in entire membranes or even in living organisms) are presented. Finally, after the general conclusions, the perspectives in the field of TR-IR applied to photosynthesis are described.
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Affiliation(s)
- Alberto Mezzetti
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, UMR 7197, Laboratoire de Réactivité de Surfaces, 4 Pl. Jussieu, 75005, Paris, France.
- Institut de Biologie Intégrative de la Cellule (I2BC), IBITECS, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France.
| | - Winfried Leibl
- Institut de Biologie Intégrative de la Cellule (I2BC), IBITECS, CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette, France
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22
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Kottke T, Lórenz-Fonfría VA, Heberle J. The Grateful Infrared: Sequential Protein Structural Changes Resolved by Infrared Difference Spectroscopy. J Phys Chem B 2016; 121:335-350. [PMID: 28100053 DOI: 10.1021/acs.jpcb.6b09222] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The catalytic activity of proteins is a function of structural changes. Very often these are as minute as protonation changes, hydrogen bonding changes, and amino acid side chain reorientations. To resolve these, a methodology is afforded that not only provides the molecular sensitivity but allows for tracing the sequence of these hierarchical reactions at the same time. This feature article showcases results from time-resolved IR spectroscopy on channelrhodopsin (ChR), light-oxygen-voltage (LOV) domain protein, and cryptochrome (CRY). All three proteins are activated by blue light, but their biological role is drastically different. Channelrhodopsin is a transmembrane retinylidene protein which represents the first light-activated ion channel of its kind and which is involved in primitive vision (phototaxis) of algae. LOV and CRY are flavin-binding proteins acting as photoreceptors in a variety of signal transduction mechanisms in all kingdoms of life. Beyond their biological relevance, these proteins are employed in exciting optogenetic applications. We show here how IR difference absorption resolves crucial structural changes of the protein after photonic activation of the chromophore. Time-resolved techniques are introduced that cover the time range from nanoseconds to minutes along with some technical considerations. Finally, we provide an outlook toward novel experimental approaches that are currently developed in our laboratories or are just in our minds ("Gedankenexperimente"). We believe that some of them have the potential to provide new science.
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Affiliation(s)
- Tilman Kottke
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University , Universitätsstraße 25, 33615 Bielefeld, Germany
| | | | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin , Arnimalle 14, 14195 Berlin, Germany
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23
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Süss B, Ringleb F, Heberle J. New ultrarapid-scanning interferometer for FT-IR spectroscopy with microsecond time-resolution. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:063113. [PMID: 27370432 DOI: 10.1063/1.4953658] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A novel Fourier-transform infrared (FT-IR) rapid-scan spectrometer has been developed (patent pending EP14194520.4) which yields 1000 times higher time resolution as compared to conventional rapid-scanning spectrometers. The central element to achieve faster scanning rates is based on a sonotrode whose front face represents the movable mirror of the interferometer. A prototype spectrometer with a time resolution of 13 μs was realized, capable of fully automated long-term measurements with a flow cell for liquid samples, here a photosynthetic membrane protein in solution. The performance of this novel spectrometer is demonstrated by recording the photoreaction of bacteriorhodopsin initiated by a short laser pulse that is synchronized to the data recording. The resulting data are critically compared to those obtained by step-scan spectroscopy and demonstrate the relevance of performing experiments on proteins in solution. The spectrometer allows for future investigations of fast, non-repetitive processes, whose investigation is challenging to step-scan FT-IR spectroscopy.
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Affiliation(s)
- B Süss
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - F Ringleb
- Institute for Crystal Growth, Max-Born Straße 2, 12489 Berlin, Germany
| | - J Heberle
- Department of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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24
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Mohrmann H, Kube I, Lórenz-Fonfría VA, Engelhard M, Heberle J. Transient Conformational Changes of Sensory Rhodopsin II Investigated by Vibrational Stark Effect Probes. J Phys Chem B 2016; 120:4383-7. [DOI: 10.1021/acs.jpcb.6b01900] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hendrik Mohrmann
- Department
of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Ines Kube
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Víctor A. Lórenz-Fonfría
- Department
of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Martin Engelhard
- Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227 Dortmund, Germany
| | - Joachim Heberle
- Department
of Physics, Experimental Molecular Biophysics, Freie Universität Berlin, 14195 Berlin, Germany
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25
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Temporal evolution of helix hydration in a light-gated ion channel correlates with ion conductance. Proc Natl Acad Sci U S A 2015; 112:E5796-804. [PMID: 26460012 DOI: 10.1073/pnas.1511462112] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The discovery of channelrhodopsins introduced a new class of light-gated ion channels, which when genetically encoded in host cells resulted in the development of optogenetics. Channelrhodopsin-2 from Chlamydomonas reinhardtii, CrChR2, is the most widely used optogenetic tool in neuroscience. To explore the connection between the gating mechanism and the influx and efflux of water molecules in CrChR2, we have integrated light-induced time-resolved infrared spectroscopy and electrophysiology. Cross-correlation analysis revealed that ion conductance tallies with peptide backbone amide I vibrational changes at 1,665(-) and 1,648(+) cm(-1). These two bands report on the hydration of transmembrane α-helices as concluded from vibrational coupling experiments. Lifetime distribution analysis shows that water influx proceeded in two temporally separated steps with time constants of 10 μs (30%) and 200 μs (70%), the latter phase concurrent with the start of ion conductance. Water efflux and the cessation of the ion conductance are synchronized as well, with a time constant of 10 ms. The temporal correlation between ion conductance and hydration of helices holds for fast (E123T) and slow (D156E) variants of CrChR2, strengthening its functional significance.
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Furutani Y, Shimizu H, Asai Y, Oiki S, Kandori H. Specific interactions between alkali metal cations and the KcsA channel studied using ATR-FTIR spectroscopy. Biophys Physicobiol 2015; 12:37-45. [PMID: 27493853 PMCID: PMC4736833 DOI: 10.2142/biophysico.12.0_37] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/21/2015] [Indexed: 01/20/2023] Open
Abstract
The X-ray structure of KcsA, a eubacterial potassium channel, displays a selectivity filter composed of four parallel peptide strands. The backbone carbonyl oxygen atoms of these strands solvate multiple K(+) ions. KcsA structures show different distributions of ions within the selectivity filter in solutions containing different cations. To assess the interactions of cations with the selectivity filter, we used attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy. Ion-exchange-induced ATR-FTIR difference spectra were obtained by subtracting the spectrum of KcsA soaked in K(+) solution from that obtained in Li(+), Na(+), Rb(+), and Cs(+) solutions. Large spectral changes in the amide-I and -II regions were observed upon replacing K(+) with smaller-sized cations Li(+) and Na(+) but not with larger-sized cations Rb(+) and Cs(+). These results strongly suggest that the selectivity filter carbonyls coordinating Rb(+) or Cs(+) adopt a conformation similar to those coordinating K(+) (cage configuration), but those coordinating Li(+) or Na(+) adopt a conformation (plane configuration) considerably different from those coordinating K(+). We have identified a cation-type sensitive amide-I band at 1681 cm(-1) and an insensitive amide-I band at 1659 cm(-1). The bands at 1650, 1639, and 1627 cm(-1) observed for Na(+)-coordinating carbonyls were almost identical to those observed in Li(+) solution, suggesting that KcsA forms a similar filter structure in Li(+) and Na(+) solutions. Thus, we conclude that the filter structure adopts a collapsed conformation in Li(+) solution that is similar to that in Na(+) solution but is in clear contrast to the X-ray crystal structure of KcsA with Li(+).
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Affiliation(s)
- Yuji Furutani
- Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, Okazaki, Aichi 444-8585, Japan; Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Hirofumi Shimizu
- Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Matsuoka, Fukui 910-1193, Japan
| | - Yusuke Asai
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Shigetoshi Oiki
- Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Matsuoka, Fukui 910-1193, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
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27
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FTIR spectral signature of anticancer drugs. Can drug mode of action be identified? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1864:85-101. [PMID: 26327318 DOI: 10.1016/j.bbapap.2015.08.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 08/18/2015] [Accepted: 08/25/2015] [Indexed: 12/26/2022]
Abstract
Infrared spectroscopy has brought invaluable information about proteins and about the mechanism of action of enzymes. These achievements are difficult to transpose to living organisms as all biological molecules absorb in the mid infrared, with usually a high degree of overlap. Deciphering the contribution of each enzyme is therefore almost impossible. On the other hand, small changes in the infrared spectra of cells induced by environmental conditions or drugs may provide an accurate signature of the metabolic shift experienced by the cell as a response to a change in the growth medium. The present paper aims at reviewing the contribution of infrared spectroscopy to the description of small chemical changes that occur in cells when they are exposed to a drug. In particular, this review will focus on cancer cells and anti-cancer drugs. Results accumulated so far tend to demonstrate that infrared spectroscopy could be a very accurate descriptor of the mode of action of anticancer drugs. If confirmed, such a segmentation of potential drugs according to their "mode of action" will be invaluable for the discovery of new therapeutic molecules. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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28
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Resler T, Schultz BJ, Lórenz-Fonfría VA, Schlesinger R, Heberle J. Kinetic and vibrational isotope effects of proton transfer reactions in channelrhodopsin-2. Biophys J 2015; 109:287-97. [PMID: 26200864 PMCID: PMC4621815 DOI: 10.1016/j.bpj.2015.06.023] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Revised: 05/12/2015] [Accepted: 06/10/2015] [Indexed: 12/25/2022] Open
Abstract
Channelrhodopsins (ChRs) are light-gated cation channels. After blue-light excitation, the protein undergoes a photocycle with different intermediates. Here, we have recorded transient absorbance changes of ChR2 from Chlamydomonas reinhardtii in the visible and infrared regions with nanosecond time resolution, the latter being accomplished using tunable quantum cascade lasers. Because proton transfer reactions play a key role in channel gating, we determined vibrational as well as kinetic isotope effects (VIEs and KIEs) of carboxylic groups of various key aspartic and glutamic acid residues by monitoring their C=O stretching vibrations in H2O and in D2O. D156 exhibits a substantial KIE (>2) in its deprotonation and reprotonation, which substantiates its role as the internal proton donor to the retinal Schiff base. The unusual VIE of D156, upshifted from 1736 cm(-1) to 1738 cm(-1) in D2O, was scrutinized by studying the D156E variant. The C=O stretch of E156 shifted down by 8 cm(-1) in D2O, providing evidence for the accessibility of the carboxylic group. The C=O stretching band of E90 exhibits a VIE of 9 cm(-1) and a KIE of ∼2 for the de- and the reprotonation reactions during the lifetime of the late desensitized state. The KIE of 1 determined in the time range from 20 ns to 5 ms is incompatible with early deprotonation of E90.
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Affiliation(s)
- Tom Resler
- Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany
| | | | | | - Ramona Schlesinger
- Genetic Biophysics at Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin, Berlin, Germany.
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29
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Light-Induced Infrared Difference Spectroscopy in the Investigation of Light Harvesting Complexes. Molecules 2015; 20:12229-49. [PMID: 26151118 PMCID: PMC6332223 DOI: 10.3390/molecules200712229] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 06/16/2015] [Accepted: 06/17/2015] [Indexed: 01/24/2023] Open
Abstract
Light-induced infrared difference spectroscopy (IR-DS) has been used, especially in the last decade, to investigate early photophysics, energy transfer and photoprotection mechanisms in isolated and membrane-bound light harvesting complexes (LHCs). The technique has the definite advantage to give information on how the pigments and the other constituents of the biological system (proteins, membranes, etc.) evolve during a given photoreaction. Different static and time-resolved approaches have been used. Compared to the application of IR-DS to photosynthetic Reaction Centers (RCs), however, IR-DS applied to LHCs is still in an almost pioneering age: very often sophisticated techniques (step-scan FTIR, ultrafast IR) or data analysis strategies (global analysis, target analysis, multivariate curve resolution) are needed. In addition, band assignment is usually more complicated than in RCs. The results obtained on the studied systems (chromatophores and RC-LHC supercomplexes from purple bacteria; Peridinin-Chlorophyll-a-Proteins from dinoflagellates; isolated LHCII from plants; thylakoids; Orange Carotenoid Protein from cyanobacteria) are summarized. A description of the different IR-DS techniques used is also provided, and the most stimulating perspectives are also described. Especially if used synergically with other biophysical techniques, light-induced IR-DS represents an important tool in the investigation of photophysical/photochemical reactions in LHCs and LHC-containing systems.
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Kraack JP, Lotti D, Hamm P. 2D attenuated total reflectance infrared spectroscopy reveals ultrafast vibrational dynamics of organic monolayers at metal-liquid interfaces. J Chem Phys 2015; 142:212413. [DOI: 10.1063/1.4916915] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jan Philip Kraack
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Davide Lotti
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Abstract
Absorption of infrared radiation by proteins gives important information about their structure and function. The most intense infrared bands correspond to the overlap of all the peptide bond absorption. Additionally, in many metalloproteins their prosthetic groups have intrinsic ligands or bind substrates/inhibitors that absorb intensively in the infrared. Here, we describe thoroughly several Fourier transform infrared methods for studying structure-function relationships in metalloproteins, using hydrogenases as an example.
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Inaguma A, Tsukamoto H, Kato HE, Kimura T, Ishizuka T, Oishi S, Yawo H, Nureki O, Furutani Y. Chimeras of channelrhodopsin-1 and -2 from Chlamydomonas reinhardtii exhibit distinctive light-induced structural changes from channelrhodopsin-2. J Biol Chem 2015; 290:11623-34. [PMID: 25796616 DOI: 10.1074/jbc.m115.642256] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Indexed: 01/18/2023] Open
Abstract
Channelrhodopsin-2 (ChR2) from the green alga Chlamydomonas reinhardtii functions as a light-gated cation channel that has been developed as an optogenetic tool to stimulate specific nerve cells in animals and control their behavior by illumination. The molecular mechanism of ChR2 has been extensively studied by a variety of spectroscopic methods, including light-induced difference Fourier transform infrared (FTIR) spectroscopy, which is sensitive to structural changes in the protein upon light activation. An atomic structure of channelrhodopsin was recently determined by x-ray crystallography using a chimera of channelrhodopsin-1 (ChR1) and ChR2. Electrophysiological studies have shown that ChR1/ChR2 chimeras are less desensitized upon continuous illumination than native ChR2, implying that there are some structural differences between ChR2 and chimeras. In this study, we applied light-induced difference FTIR spectroscopy to ChR2 and ChR1/ChR2 chimeras to determine the molecular basis underlying these functional differences. Upon continuous illumination, ChR1/ChR2 chimeras exhibited structural changes distinct from those in ChR2. In particular, the protonation state of a glutamate residue, Glu-129 (Glu-90 in ChR2 numbering), in the ChR chimeras is not changed as dramatically as in ChR2. Moreover, using mutants stabilizing particular photointermediates as well as time-resolved measurements, we identified some differences between the major photointermediates of ChR2 and ChR1/ChR2 chimeras. Taken together, our data indicate that the gating and desensitizing processes in ChR1/ChR2 chimeras are different from those in ChR2 and that these differences should be considered in the rational design of new optogenetic tools based on channelrhodopsins.
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Affiliation(s)
- Asumi Inaguma
- From the Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan, PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan, Department of Structural Molecular Science, Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Hisao Tsukamoto
- From the Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan, Department of Structural Molecular Science, Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Hideaki E Kato
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tetsunari Kimura
- From the Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan, Department of Structural Molecular Science, Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan
| | - Toru Ishizuka
- CREST, Japan Science and Technology Agency (JST), 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, and Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai 980-8577, Japan
| | - Satomi Oishi
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hiromu Yawo
- CREST, Japan Science and Technology Agency (JST), 5 Sanbancho, Chiyoda-ku, Tokyo 102-0075, and Department of Developmental Biology and Neuroscience, Tohoku University Graduate School of Life Sciences, Sendai 980-8577, Japan
| | - Osamu Nureki
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yuji Furutani
- From the Department of Life and Coordination-Complex Molecular Science, Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan, PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan, Department of Structural Molecular Science, Graduate University for Advanced Studies (SOKENDAI), 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585, Japan,
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Time-resolved infrared spectroscopic studies of ligand dynamics in the active site from cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1847:79-85. [PMID: 25117435 DOI: 10.1016/j.bbabio.2014.07.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 07/29/2014] [Indexed: 10/24/2022]
Abstract
The catalytic site of heme-copper oxidases encompasses two close-lying ligand binding sites: the heme, where oxygen is bound and reduced and the CuB atom, which acts as ligand entry and release port. Diatomic gaseous ligands with a dipole moment, such as the signaling molecules carbon monoxide (CO) and nitric oxide (NO), carry clear infrared spectroscopic signatures in the different states that allow characterization of the dynamics of ligand transfer within, into and out of the active site using time-resolved infrared spectroscopy. We review the nature and diversity of these processes that have in particular been characterized with CO as ligand and which take place on time scales ranging from femtoseconds to milliseconds. These studies have advanced our understanding of the functional ligand pathways and reactivity in enzymes and more globally represent intriguing model systems for mechanisms of ligand motion in a confined protein environment. This article is part of a Special Issue entitled: Vibrational spectroscopies and bioenergetic systems.
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Kraack JP, Lotti D, Hamm P. Ultrafast, Multidimensional Attenuated Total Reflectance Spectroscopy of Adsorbates at Metal Surfaces. J Phys Chem Lett 2014; 5:2325-9. [PMID: 26279554 DOI: 10.1021/jz500978z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Ultrafast dynamics of molecules at solid-liquid interfaces are of outstanding importance in chemistry and physics due to their involvement in processes of heterogeneous catalysis. We present a new spectroscopic approach to resolve coherent, time-resolved, 2D vibrational spectra as well as ultrafast vibrational relaxation dynamics of molecules adsorbed on metallic thin films in contact with liquids. The setup is based on the technique of attenuated total reflectance (ATR) spectroscopy, which is used at interfaces between materials that exhibit different refractive indices. As a sample molecule, we consider carbon monoxide adsorbed in different binding configurations on different metals and resolve its femtosecond vibrational dynamics. It is presented that mid-infrared, multidimensional ATR spectroscopy allows for obtaining a surface-sensitive characterization of adsorbates' vibrational relaxation, spectral diffusion dynamics, and sample inhomogeneity on the femtosecond time scale.
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Affiliation(s)
- Jan Philip Kraack
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Davide Lotti
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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Lórenz-Fonfría VA, Heberle J. Proton transfer and protein conformation dynamics in photosensitive proteins by time-resolved step-scan Fourier-transform infrared spectroscopy. J Vis Exp 2014:e51622. [PMID: 24998200 PMCID: PMC4208678 DOI: 10.3791/51622] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Monitoring the dynamics of protonation and protein backbone conformation changes during the function of a protein is an essential step towards understanding its mechanism. Protonation and conformational changes affect the vibration pattern of amino acid side chains and of the peptide bond, respectively, both of which can be probed by infrared (IR) difference spectroscopy. For proteins whose function can be repetitively and reproducibly triggered by light, it is possible to obtain infrared difference spectra with (sub)microsecond resolution over a broad spectral range using the step-scan Fourier transform infrared technique. With -10(2)-10(3) repetitions of the photoreaction, the minimum number to complete a scan at reasonable spectral resolution and bandwidth, the noise level in the absorption difference spectra can be as low as -10(-) (4), sufficient to follow the kinetics of protonation changes from a single amino acid. Lower noise levels can be accomplished by more data averaging and/or mathematical processing. The amount of protein required for optimal results is between 5-100 µg, depending on the sampling technique used. Regarding additional requirements, the protein needs to be first concentrated in a low ionic strength buffer and then dried to form a film. The protein film is hydrated prior to the experiment, either with little droplets of water or under controlled atmospheric humidity. The attained hydration level (g of water / g of protein) is gauged from an IR absorption spectrum. To showcase the technique, we studied the photocycle of the light-driven proton-pump bacteriorhodopsin in its native purple membrane environment, and of the light-gated ion channel channelrhodopsin-2 solubilized in detergent.
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Affiliation(s)
| | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin;
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Geibel S, Lörinczi È, Bamberg E, Friedrich T. Voltage dependence of proton pumping by bacteriorhodopsin mutants with altered lifetime of the M intermediate. PLoS One 2013; 8:e73338. [PMID: 24019918 PMCID: PMC3760879 DOI: 10.1371/journal.pone.0073338] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/29/2013] [Indexed: 11/19/2022] Open
Abstract
The light-driven proton pump bacteriorhodopsin (BR) from Halobacterium salinarum is tightly regulated by the [H(+)] gradient and transmembrane potential. BR exhibits optoelectric properties, since spectral changes during the photocycle are kinetically controlled by voltage, which predestines BR for optical storage or processing devices. BR mutants with prolonged lifetime of the blue-shifted M intermediate would be advantageous, but the optoelectric properties of such mutants are still elusive. Using expression in Xenopus oocytes and two-electrode voltage-clamping, we analyzed photocurrents of BR mutants with kinetically destabilized (F171C, F219L) or stabilized (D96N, D96G) M intermediate in response to green light (to probe H(+) pumping) and blue laser flashes (to probe accumulation/decay of M). These mutants have divergent M lifetimes. As for BR-WT, this strictly correlates with the voltage dependence of H(+) pumping. BR-F171C and BR-F219L showed photocurrents similar to BR-WT. Yet, BR-F171C showed a weaker voltage dependence of proton pumping. For both mutants, blue laser flashes applied during and after green-light illumination showed reduced M accumulation and shorter M lifetime. In contrast, BR-D96G and BR-D96N exhibited small photocurrents, with nonlinear current-voltage curves, which increased strongly in the presence of azide. Blue laser flashes showed heavy M accumulation and prolonged M lifetime, which accounts for the strongly reduced H(+) pumping rate. Hyperpolarizing potentials augmented these effects. The combination of M-stabilizing and -destabilizing mutations in BR-D96G/F171C/F219L (BR-tri) shows that disruption of the primary proton donor Asp-96 is fatal for BR as a proton pump. Mechanistically, M destabilizing mutations cannot compensate for the disruption of Asp-96. Accordingly, BR-tri and BR-D96G photocurrents were similar. However, BR-tri showed negative blue laser flash-induced currents even without actinic green light, indicating that Schiff base deprotonation in BR-tri exists in the dark, in line with previous spectroscopic investigations. Thus, M-stabilizing mutations, including the triple mutation, drastically interfere with electrochemical H(+) gradient generation.
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Affiliation(s)
- Sven Geibel
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry, Frankfurt am Main, Germany
| | - Èva Lörinczi
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry, Frankfurt am Main, Germany
| | - Ernst Bamberg
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry, Frankfurt am Main, Germany
| | - Thomas Friedrich
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry, Frankfurt am Main, Germany
- Technical University of Berlin, Institute of Chemistry, Berlin, Germany
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Kubo M, Nakashima S, Yamaguchi S, Ogura T, Mochizuki M, Kang J, Tateno M, Shinzawa-Itoh K, Kato K, Yoshikawa S. Effective pumping proton collection facilitated by a copper site (CuB) of bovine heart cytochrome c oxidase, revealed by a newly developed time-resolved infrared system. J Biol Chem 2013; 288:30259-30269. [PMID: 23996000 DOI: 10.1074/jbc.m113.473983] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
X-ray structural and mutational analyses have shown that bovine heart cytochrome c oxidase (CcO) pumps protons electrostatically through a hydrogen bond network using net positive charges created upon oxidation of a heme iron (located near the hydrogen bond network) for O2 reduction. Pumping protons are transferred by mobile water molecules from the negative side of the mitochondrial inner membrane through a water channel into the hydrogen bond network. For blockage of spontaneous proton back-leak, the water channel is closed upon O2 binding to the second heme (heme a3) after complete collection of the pumping protons in the hydrogen bond network. For elucidation of the structural bases for the mechanism of the proton collection and timely closure of the water channel, conformational dynamics after photolysis of CO (an O2 analog)-bound CcO was examined using a newly developed time-resolved infrared system feasible for accurate detection of a single C=O stretch band of α-helices of CcO in H2O medium. The present results indicate that migration of CO from heme a3 to CuB in the O2 reduction site induces an intermediate state in which a bulge conformation at Ser-382 in a transmembrane helix is eliminated to open the water channel. The structural changes suggest that, using a conformational relay system, including CuB, O2, heme a3, and two helix turns extending to Ser-382, CuB induces the conformational changes of the water channel that stimulate the proton collection, and senses complete proton loading into the hydrogen bond network to trigger the timely channel closure by O2 transfer from CuB to heme a3.
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Affiliation(s)
| | | | - Satoru Yamaguchi
- Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo 678-1297 and
| | - Takashi Ogura
- From the Picobiology Institute,; Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Kouto, Kamighori, Akoh, Hyogo 678-1297 and; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | | | | | - Masaru Tateno
- From the Picobiology Institute,; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | | | | | - Shinya Yoshikawa
- From the Picobiology Institute,; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
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Ataka K, Stripp ST, Heberle J. Surface-enhanced infrared absorption spectroscopy (SEIRAS) to probe monolayers of membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1828:2283-93. [PMID: 23816441 DOI: 10.1016/j.bbamem.2013.04.026] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Revised: 04/05/2013] [Accepted: 04/28/2013] [Indexed: 12/15/2022]
Abstract
Surface-enhanced infrared absorption spectroscopy (SEIRAS) represents a variation of conventional infrared spectroscopy and exploits the signal enhancement exerted by the plasmon resonance of nano-structured metal thin films. The surface enhancement decays in about 10nm with the distance from the surface and is, thus, perfectly suited to selectively probe monolayers of biomembranes. Peculiar to membrane proteins is their vectorial functionality, the probing of which requires proper orientation within the membrane. To this end, the metal surface used in SEIRAS is chemically modified to generate an oriented membrane protein film. Monolayers of uniformly oriented membrane proteins are formed by tethering His-tagged proteins to a nickel nitrilo-triacetic acid (Ni-NTA) modified gold surface and SEIRAS commands molecular sensitivity to probe each step of surface modification. The solid surface used as plasmonic substrate for SEIRAS, can also be employed as an electrode to investigate systems where electron transfer reactions are relevant, like e.g. cytochrome c oxidase or plant-type photosystems. Furthermore, the interaction of these membrane proteins with water-soluble proteins, like cytochrome c or hydrogenase, is studied on the molecular level by SEIRAS. The impact of the membrane potential on protein functionality is verified by monitoring light-dark difference spectra of a monolayer of sensory rhodopsin (SRII) at different applied potentials. It is demonstrated that the interpretations of all of these experiments critically depend on the orientation of the solid-supported membrane protein. Finally, future directions of SEIRAS including cellular systems are discussed. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.
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Affiliation(s)
- Kenichi Ataka
- Freie Universität Berlin, Experimental Molecular Biophysics, Arnimallee 14, 14195 Berlin, Germany
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Abbruzzetti S, Spyrakis F, Bidon-Chanal A, Luque FJ, Viappiani C. Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations. Phys Chem Chem Phys 2013; 15:10686-701. [PMID: 23733145 DOI: 10.1039/c3cp51149a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The presence of cavities and tunnels in the interior of proteins, in conjunction with the structural plasticity arising from the coupling to the thermal fluctuations of the protein scaffold, has profound consequences on the pathways followed by ligands moving through the protein matrix. In this perspective we discuss how quantitative analysis of experimental rebinding kinetics from laser flash photolysis, trapping of unstable conformational states by embedding proteins within the nanopores of silica gels, and molecular simulations can synergistically converge to gain insight into the migration mechanism of ligands. We show how the evaluation of the free energy landscape for ligand diffusion based on the outcome of computational techniques can assist the definition of sound reaction schemes, leading to a comprehensive understanding of the broad range of chemical events and time scales that encompass the transport of small ligands in hemeproteins.
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Affiliation(s)
- Stefania Abbruzzetti
- Dipartimento di Fisica e Scienze della Terra, Università degli Studi di Parma, viale delle Scienze 7A, 43124, Parma, Italy
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Marcelli A, Innocenzi P, Malfatti L, Newton MA, Rau JV, Ritter E, Schade U, Xu W. IR and X-ray time-resolved simultaneous experiments: an opportunity to investigate the dynamics of complex systems and non-equilibrium phenomena using third-generation synchrotron radiation sources. JOURNAL OF SYNCHROTRON RADIATION 2012; 19:892-904. [PMID: 23093747 DOI: 10.1107/s0909049512041106] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 09/30/2012] [Indexed: 06/01/2023]
Abstract
Third-generation storage rings are modern facilities working with high currents and designed to host powerful radiation sources, like undulators and wigglers, and to deliver high-brilliance beams to users. Many experiments at high spatial resolution, such as spectromicroscopy at the nanometre scale and with high temporal resolution to investigate kinetics down to the picosecond regime, are now possible. The next frontier is certainly the combination of different methods in a unique set-up with the ultimate available spatial and temporal resolutions. In the last decade much synchrotron-based research has exploited the advantage of complementary information provided by time-resolved X-ray techniques and optical methods in the UV/Vis and IR domains. New time-resolved and concurrent approaches are necessary to characterize complex systems where physical-chemical phenomena occur under the same experimental conditions, for example to detect kinetic intermediates via complementary but independent observations. In this contribution we present scientific cases from original works and literature reviews to support the proposed IR/X-ray simultaneous approach, with both probes exploiting synchrotron radiation sources. In addition, simple experimental layouts that may take advantage of the high brilliance and the wide spectral distribution of the synchrotron radiation emission will be given for specific researches or applications to investigate dynamic processes and non-equilibrium phenomena occurring in many condensed matter and biological systems, of great interest for both fundamental research and technological applications.
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Siderius M, Wal M, Scholten DJ, Smit MJ, Sakmar TP, Leurs R, de Graaf C. Unnatural amino acids for the study of chemokine receptor structure and dynamics. DRUG DISCOVERY TODAY. TECHNOLOGIES 2012; 9:e227-e314. [PMID: 24063744 DOI: 10.1016/j.ddtec.2012.07.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
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Xu W, Marcelli A, Hampai D, Malfatti L, Innocenzi P, Schade U, Wu Z. New opportunity to investigate physico-chemical phenomena: time-resolved X-ray and IR concurrent analysis. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2011. [DOI: 10.1007/s12210-011-0145-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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Grossman M, Sela-Passwell N, Sagi I. Achieving broad molecular insights into dynamic protein interactions by integrated structural-kinetic approaches. Curr Opin Struct Biol 2011; 21:678-85. [PMID: 21945040 DOI: 10.1016/j.sbi.2011.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 07/21/2011] [Accepted: 07/31/2011] [Indexed: 11/30/2022]
Abstract
A network of dynamic protein interactions with their protein partners, substrates, and ligands is known to be crucial for biological function. Revealing molecular and structural-based mechanisms at atomic resolution and in real-time is fundamental for achieving a basic understanding of cellular processes. These technically challenging goals may be achieved by combining time-resolved spectroscopic and structural-kinetic tools, thus providing broad insights into specific molecular events over a wide range of timescales. Here we review representative studies utilizing such an integrated real-time structural approach designed to reveal molecular mechanisms underlying protein interactions at atomic resolution.
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Affiliation(s)
- Moran Grossman
- Departments of Structural Biology and Biological Regulation, The Weizmann Institute of Science, Rehovot 76100, Israel
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Lórenz-Fonfría VA, Kandori H, Padrós E. Probing specific molecular processes and intermediates by time-resolved Fourier transform infrared spectroscopy: application to the bacteriorhodopsin photocycle. J Phys Chem B 2011; 115:7972-85. [PMID: 21615095 DOI: 10.1021/jp201739w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a general approach for probing the kinetics of specific molecular processes in proteins by time-resolved Fourier transform infrared (IR) spectroscopy. Using bacteriorhodopsin (bR) as a model we demonstrate that by appropriately monitoring some selected IR bands it is possible obtaining the kinetics of the most important events occurring in the photocycle, namely changes in the chromophore and the protein backbone conformation, and changes in the protonation state of the key residues implicated in the proton transfers. Besides confirming widely accepted views of the bR photocycle, our analysis also sheds light into some disputed issues: the degree of retinal torsion in the L intermediate to respect the ground state; the possibility of a proton transfer from Asp85 to Asp212; the relationship between the protonation/deprotonation of Asp85 and the proton release complex; and the timing of the protein backbone dynamics. By providing a direct way to estimate the kinetics of photocycle intermediates the present approach opens new prospects for a robust quantitative kinetic analysis of the bR photocycle, which could also benefit the study of other proteins involved in photosynthesis, in phototaxis, or in respiratory chains.
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Affiliation(s)
- Víctor A Lórenz-Fonfría
- Unitat de Biofísica, Departament de Bioquímica i de Biologia Molecular, and Centre d'Estudis en Biofísica, Universitat Autònoma de Barcelona, Barcelona 08193, Spain.
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Radu I, Budyak IL, Hoomann T, Kim YJ, Engelhard M, Labahn J, Büldt G, Heberle J, Schlesinger R. Signal relay from sensory rhodopsin I to the cognate transducer HtrI: Assessing the critical change in hydrogen-bonding between Tyr-210 and Asn-53. Biophys Chem 2010; 150:23-8. [DOI: 10.1016/j.bpc.2010.02.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 02/25/2010] [Accepted: 02/26/2010] [Indexed: 10/19/2022]
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Ataka K, Kottke T, Heberle J. Thinner, Smaller, Faster: IR Techniques To Probe the Functionality of Biological and Biomimetic Systems. Angew Chem Int Ed Engl 2010; 49:5416-24. [DOI: 10.1002/anie.200907114] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Ataka K, Kottke T, Heberle J. Dünner, kleiner, schneller - wie die IR-Spektroskopie zur Aufklärung des Funktionsmechanismus biologischer und biomimetischer Systeme beiträgt. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200907114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Nack M, Radu I, Gossing M, Bamann C, Bamberg E, von Mollard GF, Heberle J. The DC gate in Channelrhodopsin-2: crucial hydrogen bonding interaction between C128 and D156. Photochem Photobiol Sci 2010; 9:194-8. [PMID: 20126794 DOI: 10.1039/b9pp00157c] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The light-gated cation channel Channelrhodopsin-2 (ChR2), a retinylidene protein found in the eye-spot of Chlamydomonas reinhardtii, became an optogenetic tool to trigger neurophysiological responses by light and, thus, revolutionized spatio-temporal studies of such processes. The reaction mechanism still remains elusive but recent vibrational spectroscopic experiments started to resolve details of the associated structural changes during the photocycle. Large alterations in the polypeptide backbone were observed by FT-IR spectroscopy that precede and succeed the opening and closing of the channel, respectively. However, the molecular switch that controls gating is still unknown. Here, we present difference spectra of the D156E mutant of ChR2 and assign the observed vibrational bands to crucial hydrogen bonding changes of this residue in various intermediate states of the photoreaction. By comparison with spectra of wild-type ChR2 and the C128T mutant and correlation to electrophysiological studies, we propose the DC gate as a crucial hydrogen-bonding interaction between D156 and C128 which may represent the valve of the channel.
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Affiliation(s)
- Melanie Nack
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany
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