1
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Kaziannis S, Broser M, van Stokkum IHM, Dostal J, Busse W, Munhoven A, Bernardo C, Kloz M, Hegemann P, Kennis JTM. Multiple retinal isomerizations during the early phase of the bestrhodopsin photoreaction. Proc Natl Acad Sci U S A 2024; 121:e2318996121. [PMID: 38478688 PMCID: PMC10962995 DOI: 10.1073/pnas.2318996121] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/13/2024] [Indexed: 03/27/2024] Open
Abstract
Bestrhodopsins constitute a class of light-regulated pentameric ion channels that consist of one or two rhodopsins in tandem fused with bestrophin ion channel domains. Here, we report on the isomerization dynamics in the rhodopsin tandem domains of Phaeocystis antarctica bestrhodopsin, which binds all-trans retinal Schiff-base (RSB) absorbing at 661 nm and, upon illumination, converts to the meta-stable P540 state with an unusual 11-cis RSB. The primary photoproduct P682 corresponds to a mixture of highly distorted 11-cis and 13-cis RSB directly formed from the excited state in 1.4 ps. P673 evolves from P682 in 500 ps and contains highly distorted 13-cis RSB, indicating that the 11-cis fraction in P682 converts to 13-cis. Next, P673 establishes an equilibrium with P595 in 1.2 µs, during which RSB converts to 11-cis and then further proceeds to P560 in 48 µs and P540 in 1.0 ms while remaining 11-cis. Hence, extensive isomeric switching occurs on the early ground state potential energy surface (PES) on the hundreds of ps to µs timescale before finally settling on a metastable 11-cis photoproduct. We propose that P682 and P673 are trapped high up on the ground-state PES after passing through either of two closely located conical intersections that result in 11-cis and 13-cis RSB. Co-rotation of C11=C12 and C13=C14 bonds results in a constricted conformational landscape that allows thermal switching between 11-cis and 13-cis species of highly strained RSB chromophores. Protein relaxation may release RSB strain, allowing it to evolve to a stable 11-cis isomeric configuration in microseconds.
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Affiliation(s)
- Spyridon Kaziannis
- The Extreme Light Infrastructure ERIC, Dolní Břežany252 41, Czech Republic
- Department of Physics, University of Ioannina, IoanninaGr-45110, Greece
| | - Matthias Broser
- Faculty of Life Sciences, Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, BerlinD-10115, Germany
| | - Ivo H. M. van Stokkum
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
| | - Jakub Dostal
- The Extreme Light Infrastructure ERIC, Dolní Břežany252 41, Czech Republic
| | - Wayne Busse
- Faculty of Life Sciences, Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, BerlinD-10115, Germany
| | - Arno Munhoven
- Faculty of Life Sciences, Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, BerlinD-10115, Germany
| | - Cesar Bernardo
- The Extreme Light Infrastructure ERIC, Dolní Břežany252 41, Czech Republic
| | - Miroslav Kloz
- The Extreme Light Infrastructure ERIC, Dolní Břežany252 41, Czech Republic
| | - Peter Hegemann
- Faculty of Life Sciences, Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, BerlinD-10115, Germany
| | - John T. M. Kennis
- Department of Physics and Astronomy, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam1081 HV, The Netherlands
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2
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Leonarski F, Nan J, Matej Z, Bertrand Q, Furrer A, Gorgisyan I, Bjelčić M, Kepa M, Glover H, Hinger V, Eriksson T, Cehovin A, Eguiraun M, Gasparotto P, Mozzanica A, Weinert T, Gonzalez A, Standfuss J, Wang M, Ursby T, Dworkowski F. Kilohertz serial crystallography with the JUNGFRAU detector at a fourth-generation synchrotron source. IUCRJ 2023; 10:729-737. [PMID: 37830774 PMCID: PMC10619449 DOI: 10.1107/s2052252523008618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
Serial and time-resolved macromolecular crystallography are on the rise. However, beam time at X-ray free-electron lasers is limited and most third-generation synchrotron-based macromolecular crystallography beamlines do not offer the necessary infrastructure yet. Here, a new setup is demonstrated, based on the JUNGFRAU detector and Jungfraujoch data-acquisition system, that enables collection of kilohertz serial crystallography data at fourth-generation synchrotrons. More importantly, it is shown that this setup is capable of collecting multiple-time-point time-resolved protein dynamics at kilohertz rates, allowing the probing of microsecond to second dynamics at synchrotrons in a fraction of the time needed previously. A high-quality complete X-ray dataset was obtained within 1 min from lysozyme microcrystals, and the dynamics of the light-driven sodium-pump membrane protein KR2 with a time resolution of 1 ms could be demonstrated. To make the setup more accessible for researchers, downstream data handling and analysis will be automated to allow on-the-fly spot finding and indexing, as well as data processing.
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Affiliation(s)
- Filip Leonarski
- Photon Science Division, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Jie Nan
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Zdenek Matej
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Quentin Bertrand
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Antonia Furrer
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | | | - Monika Bjelčić
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Michal Kepa
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Hannah Glover
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Viktoria Hinger
- Photon Science Division, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Thomas Eriksson
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | | | - Mikel Eguiraun
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Piero Gasparotto
- Scientific Computing, Theory and Data, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Aldo Mozzanica
- Photon Science Division, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Ana Gonzalez
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Jörg Standfuss
- Division of Biology and Chemistry, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Meitian Wang
- Photon Science Division, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
| | - Thomas Ursby
- MAX IV Laboratory, Lund University, POB. 118, SE-22100 Lund, Sweden
| | - Florian Dworkowski
- Photon Science Division, Paul Scherrer Institut, CH-5303 Villigen PSI, Switzerland
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3
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Yang Q, Chen D. Na + Binding and Transport: Insights from Light-Driven Na +-Pumping Rhodopsin. Molecules 2023; 28:7135. [PMID: 37894614 PMCID: PMC10608830 DOI: 10.3390/molecules28207135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/07/2023] [Accepted: 10/16/2023] [Indexed: 10/29/2023] Open
Abstract
Na+ plays a vital role in numerous physiological processes across humans and animals, necessitating a comprehensive understanding of Na+ transmembrane transport. Among the various Na+ pumps and channels, light-driven Na+-pumping rhodopsin (NaR) has emerged as a noteworthy model in this field. This review offers a concise overview of the structural and functional studies conducted on NaR, encompassing ground/intermediate-state structures and photocycle kinetics. The primary focus lies in addressing key inquiries: (1) unraveling the translocation pathway of Na+; (2) examining the role of structural changes within the photocycle, particularly in the O state, in facilitating Na+ transport; and (3) investigating the timing of Na+ uptake/release. By delving into these unresolved issues and existing debates, this review aims to shed light on the future direction of Na+ pump research.
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Affiliation(s)
- Qifan Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Deliang Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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4
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Xu J, Yang Q, Ma B, Li L, Kong F, Xiao L, Chen D. K +-Dependent Photocycle and Photocurrent Reveal the Uptake of K + in Light-Driven Sodium Pump. Int J Mol Sci 2023; 24:14414. [PMID: 37833864 PMCID: PMC10572131 DOI: 10.3390/ijms241914414] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 10/15/2023] Open
Abstract
Engineering light-controlled K+ pumps from Na+-pumping rhodopsins (NaR) greatly expands the scope of optogenetic applications. However, the limited knowledge regarding the kinetic and selective mechanism of K+ uptake has significantly impeded the modification and design of light-controlled K+ pumps, as well as their practical applications in various fields, including neuroscience. In this study, we presented K+-dependent photocycle kinetics and photocurrent of a light-driven Na+ pump called Nonlabens dokdonensis rhodopsin 2 (NdR2). As the concentration of K+ increased, we observed the accelerated decay of M intermediate in the wild type (WT) through flash photolysis. In 100 mM KCl, the lifetime of the M decay was approximately 1.0 s, which shortened to around 0.6 s in 1 M KCl. Additionally, the K+-dependent M decay kinetics were also observed in the G263W/N61P mutant, which transports K+. In 100 mM KCl, the lifetime of the M decay was approximately 2.5 s, which shortened to around 0.2 s in 1 M KCl. According to the competitive model, in high KCl, K+ may be taken up from the cytoplasmic surface, competing with Na+ or H+ during M decay. This was further confirmed by the K+-dependent photocurrent of WT liposome. As the concentration of K+ increased to 500 mM, the amplitude of peak current significantly dropped to approximately ~60%. Titration experiments revealed that the ratio of the rate constant of H+ uptake (kH) to that of K+ uptake (kK) is >108. Compared to the WT, the G263W/N61P mutant exhibited a decrease of approximately 40-fold in kH/kK. Previous studies focused on transforming NaR into K+ pumps have primarily targeted the intracellular ion uptake region of Krokinobacter eikastus rhodopsin 2 (KR2) to enhance K+ uptake. However, our results demonstrate that the naturally occurring WT NdR2 is capable of intracellular K+ uptake without requiring structural modifications on the intracellular region. This discovery provides diverse options for future K+ pump designs. Furthermore, we propose a novel photocurrent-based approach to evaluate K+ uptake, which can serve as a reference for similar studies on other ion pumps. In conclusion, our research not only provides new insights into the mechanism of K+ uptake but also offers a valuable point of reference for the development of optogenetic tools and other applications in this field.
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Affiliation(s)
- Jikang Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Qifan Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Baofu Ma
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Longjie Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Fei Kong
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Lan Xiao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
| | - Deliang Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China (B.M.)
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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5
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Kriebel CN, Asido M, Kaur J, Orth J, Braun P, Becker-Baldus J, Wachtveitl J, Glaubitz C. Structural and functional consequences of the H180A mutation of the light-driven sodium pump KR2. Biophys J 2023; 122:1003-1017. [PMID: 36528791 PMCID: PMC10111219 DOI: 10.1016/j.bpj.2022.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 12/04/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Krokinobacter eikastus rhodopsin 2 (KR2) is a light-driven pentameric sodium pump. Its ability to translocate cations other than protons and to create an electrochemical potential makes it an attractive optogenetic tool. Tailoring its ion-pumping characteristics by mutations is therefore of great interest. In addition, understanding the functional and structural consequences of certain mutations helps to derive a functional mechanism of ion selectivity and transfer of KR2. Based on solid-state NMR spectroscopy, we report an extensive chemical shift resonance assignment of KR2 within lipid bilayers. This data set was then used to probe site-resolved allosteric effects of sodium binding, which revealed multiple responsive sites including the Schiff base nitrogen and the NDQ motif. Based on this data set, the consequences of the H180A mutation are probed. The mutant is silenced in the presence of sodium while in its absence proton pumping is observed. Our data reveal specific long-range effects along the sodium transfer pathway. These experiments are complemented by time-resolved optical spectroscopy. Our data suggest a model in which sodium uptake by the mutant can still take place, while sodium release and backflow control are disturbed.
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Affiliation(s)
- Clara Nassrin Kriebel
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marvin Asido
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jagdeep Kaur
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jennifer Orth
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Philipp Braun
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johanna Becker-Baldus
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany.
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6
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Asido M, Wachtveitl J. Photochemistry of the Light-Driven Sodium Pump Krokinobacter eikastus Rhodopsin 2 and Its Implications on Microbial Rhodopsin Research: Retrospective and Perspective. J Phys Chem B 2023; 127:3766-3773. [PMID: 36919947 DOI: 10.1021/acs.jpcb.2c08933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
The discovery of the light-driven sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) in 2013 has changed the paradigm that cation transport in microbial rhodopsins is restricted to the translocation of protons. Even though this finding is already remarkable by itself, it also reignited more general discussions about the functional mechanism of ion transport. The unique composition of the retinal binding pocket in KR2 with a tight interaction between the retinal Schiff base and its respective counterion D116 also has interesting implications on the photochemical pathway of the chromophore. Here, we discuss the most recent advances in our understanding of the KR2 functionality from the primary event of photon absorption by all-trans retinal up to the actual protein response in the later phases of the photocycle, mainly from the point of view of optical spectroscopy. In this context, we furthermore highlight some of the ongoing debates on the photochemistry of microbial rhodopsins and give some perspectives for promising future directions in this field of research.
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Affiliation(s)
- Marvin Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
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7
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van Stokkum IH, Hontani Y, Vierock J, Krause BS, Hegemann P, Kennis JT. Reaction Dynamics in the Chrimson Channelrhodopsin: Observation of Product-State Evolution and Slow Diffusive Protein Motions. J Phys Chem Lett 2023; 14:1485-1493. [PMID: 36745035 PMCID: PMC9940203 DOI: 10.1021/acs.jpclett.2c03110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Chrimson is a red-light absorbing channelrhodopsin useful for deep-tissue optogenetics applications. Here, we present the Chrimson reaction dynamics from femtoseconds to seconds, analyzed with target analysis methods to disentangle spectrally and temporally overlapping excited- and product-state dynamics. We found multiple phases ranging from ≈100 fs to ≈20 ps in the excited-state decay, where spectral features overlapping with stimulated emission components were assigned to early dynamics of K-like species on a 10 ps time scale. Selective excitation at the maximum or the blue edge of the absorption spectrum resulted in spectrally distinct but kinetically similar excited-state and product-state species, which gradually became indistinguishable on the μs to 100 μs time scales. Hence, by removing specific protein conformations within an inhomogeneously broadened ensemble, we resolved slow protein backbone and amino acid side-chain motions in the dark that underlie inhomogeneous broadening, demonstrating that the latter represents a dynamic interconversion between protein substates.
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Affiliation(s)
- Ivo H.M. van Stokkum
- Department
of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HVAmsterdam, The Netherlands
| | - Yusaku Hontani
- Department
of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HVAmsterdam, The Netherlands
| | - Johannes Vierock
- Institut
für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115Berlin, Germany
| | - Benjamin S. Krause
- Institut
für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115Berlin, Germany
| | - Peter Hegemann
- Institut
für Biologie, Experimentelle Biophysik, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115Berlin, Germany
| | - John T.M. Kennis
- Department
of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HVAmsterdam, The Netherlands
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8
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Hontani Y, Mehlhorn J, Domratcheva T, Beck S, Kloz M, Hegemann P, Mathes T, Kennis JTM. Spectroscopic and Computational Observation of Glutamine Tautomerization in the Blue Light Sensing Using Flavin Domain Photoreaction. J Am Chem Soc 2023; 145:1040-1052. [PMID: 36607126 PMCID: PMC9853863 DOI: 10.1021/jacs.2c10621] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Blue light sensing using flavin (BLUF) domains constitute a family of flavin-binding photoreceptors of bacteria and eukaryotic algae. BLUF photoactivation proceeds via a light-driven hydrogen-bond switch among flavin adenine dinucleotide (FAD) and glutamine and tyrosine side chains, whereby FAD undergoes electron and proton transfer with tyrosine and is subsequently re-oxidized by a hydrogen back-shuttle in picoseconds, constituting an important model system to understand proton-coupled electron transfer in biology. The specific structure of the hydrogen-bond patterns and the prevalence of glutamine tautomeric states in dark-adapted (DA) and light-activated (LA) states have remained controversial. Here, we present a combined femtosecond stimulated Raman spectroscopy (FSRS), computational chemistry, and site-selective isotope labeling Fourier-transform infrared spectroscopy (FTIR) study of the Slr1694 BLUF domain. FSRS showed distinct vibrational bands from the FADS1 singlet excited state. We observed small but significant shifts in the excited-state vibrational frequency patterns of the DA and LA states, indicating that these frequencies constitute a sensitive probe for the hydrogen-bond arrangement around FAD. Excited-state model calculations utilizing four different realizations of hydrogen bond patterns and glutamine tautomeric states were consistent with a BLUF reaction model that involved glutamine tautomerization to imidic acid, accompanied by a rotation of its side chain. A combined FTIR and double-isotope labeling study, with 13C labeling of FAD and 15N labeling of glutamine, identified the glutamine imidic acid C═N stretch vibration in the LA state and the Gln C═O in the DA state. Hence, our study provides support for glutamine tautomerization and side-chain rotation in the BLUF photoreaction.
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Affiliation(s)
- Yusaku Hontani
- Department
of Physics and Astronomy, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, De Boelelaan, The Netherlands
| | - Jennifer Mehlhorn
- Institut
für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Tatiana Domratcheva
- Department
of Biomolecular Mechanisms, Max Planck Institute
for Medical Research, 69120 Heidelberg, Germany,Department
of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Sebastian Beck
- Department
of Chemistry, Humboldt-Universität
zu Berlin, Brook-Taylor-Str.
2, 12489 Berlin, Germany
| | - Miroslav Kloz
- Department
of Physics and Astronomy, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, De Boelelaan, The Netherlands,Institute
of Physics, ELI-Beamlines, Na Slovance 2, 182
21 Praha 8, Czech Republic
| | - Peter Hegemann
- Institut
für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Tilo Mathes
- Department
of Physics and Astronomy, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, De Boelelaan, The Netherlands,Institut
für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - John T. M. Kennis
- Department
of Physics and Astronomy, Vrije Universiteit
Amsterdam, 1081 HV Amsterdam, De Boelelaan, The Netherlands,
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9
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Urui T, Das I, Mizuno M, Sheves M, Mizutani Y. Origin of a Double-Band Feature in the Ethylenic C═C Stretching Modes of the Retinal Chromophore in Heliorhodopsins. J Phys Chem B 2022; 126:8680-8688. [PMID: 36281583 DOI: 10.1021/acs.jpcb.2c04883] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Photoreceptor proteins play a critical role in light utilization for energy conversion and environmental sensing. Rhodopsin is a prototypical photoreceptor protein containing a retinal group that functions as a light-receptive site. It is essential to characterize the structure of the retinal chromophore because the chromophore structure, along with retinal-protein interactions, regulates which wavelengths of light are absorbed. Resonance Raman spectroscopy is a powerful tool to characterize chromophore structures in proteins. The resonance Raman spectra of heliorhodopsins, a recently discovered rhodopsin family, were previously reported to exhibit two intense ethylenic C═C stretching bands never observed for type-1 rhodopsins. Here, we show that the double-band feature in the ethylenic C═C stretching modes is not due to structural inhomogeneity but rather to the retinal polyene chain's linear structure. It contrasts with bent all-trans chromophore in type-1 rhodopsins. The linear structure of the chromophore results from weak atomic contacts between the 13-methyl group and a nearby Trp side chain, which can slow thermal reisomerization in the photocycle. It is possible that the deceleration of reisomerization increases the lifetime of the signaling intermediate for photosensory function.
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Affiliation(s)
- Taito Urui
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
| | - Ishita Das
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76305, Israel
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
| | - Mordechai Sheves
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 76305, Israel
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, Osaka, Japan
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10
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van Stokkum IHM, Kloz M, Polli D, Viola D, Weißenborn J, Peerbooms E, Cerullo G, Kennis JTM. Vibronic dynamics resolved by global and target analysis of ultrafast transient absorption spectra. J Chem Phys 2021; 155:114113. [PMID: 34551543 DOI: 10.1063/5.0060672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a methodology that provides a complete parametric description of the time evolution of the electronically and vibrationally excited states as detected by ultrafast transient absorption (TA). Differently from previous approaches, which started fitting the data after ≈100 fs, no data are left out in our methodology, and the "coherent artifact" and the instrument response function are fully taken into account. In case studies, the method is applied to solvents, the dye Nile blue, and all-trans β-carotene in cyclohexane solution. The estimated Damped Oscillation Associated Spectra (DOAS) and phases express the most important vibrational frequencies present in the molecular system. By global fit alone of the experimental data, it is difficult to interpret in detail the underlying dynamics. Since it is unfeasible to directly fit the data by a theoretical simulation, our enhanced DOAS methodology thus provides a useful "middle ground" where the theoretical description and the fit of the experimental data can meet. β-carotene in cyclohexane was complementarily studied with femtosecond stimulated Raman spectroscopy (FSRS). The fs-ps dynamics of β-carotene in cyclohexane in TA and FSRS experiments can be described by a sequential scheme S2 → hot S1 → S1' → S1 → S0 with lifetimes of 167 fs (fixed), 0.35, 1.1, and 9.6 ps. The correspondence of DOAS decaying concomitantly with hot S1 and the Species Associated Difference Spectra of hot S1 in TA and FSRS suggest that we observe here features of the vibrational relaxation and nuclear reorganization responsible for the hot S1 to S1 transition.
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Affiliation(s)
- Ivo H M van Stokkum
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Miroslav Kloz
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, CZ-18221 Prague, Czech Republic
| | - Dario Polli
- IFN-CNR, Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Daniele Viola
- IFN-CNR, Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Jörn Weißenborn
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Ebo Peerbooms
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Giulio Cerullo
- IFN-CNR, Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - John T M Kennis
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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11
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Kusochek PA, Scherbinin AV, Bochenkova AV. Insights into the Early-Time Excited-State Dynamics of Structurally Inhomogeneous Rhodopsin KR2. J Phys Chem Lett 2021; 12:8664-8671. [PMID: 34472871 DOI: 10.1021/acs.jpclett.1c02312] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The light-driven sodium-pump rhodopsin KR2 exhibits ultrafast photoisomerization dynamics of its all-trans protonated Schiff-base retinal (PSBR). However, the excited-state decay of KR2 also shows slow picosecond time constants, which are attributed to nonreactive states. The mechanism that produces long-lived states is unclear. Here, by using molecular dynamics simulations and large-scale XMCQDPT2-based QM/MM modeling, we explore the origin of reactive and nonreactive states in KR2. By calculating the S0-S1 vibronic band shapes, we gain insight into the early-time excited-state dynamics of PSBR and show that the protein environment can significantly alter vibrational modes that are active upon photoexcitation, thus facilitating photoisomerization from all-trans to 13-cis PSBR. Importantly, we reveal structural heterogeneity of the retinal-binding pocket of KR2, characterized by three distinct conformations, and conclude that the formation of a strong hydrogen bond between the retinal Schiff base and its counterion is essential for the ultrafast reaction dynamics.
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Affiliation(s)
- Pavel A Kusochek
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Andrei V Scherbinin
- Department of Chemistry, Lomonosov Moscow State University, 119991 Moscow, Russia
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12
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Asido M, Kar RK, Kriebel CN, Braun M, Glaubitz C, Schapiro I, Wachtveitl J. Transient Near-UV Absorption of the Light-Driven Sodium Pump Krokinobacter eikastus Rhodopsin 2: A Spectroscopic Marker for Retinal Configuration. J Phys Chem Lett 2021; 12:6284-6291. [PMID: 34213348 DOI: 10.1021/acs.jpclett.1c01436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report a transient signature in the near-UV absorption of Krokinobacter eikastus rhodopsin 2 (KR2), which spans from the femtosecond up to the millisecond time scale. The signature rises with the all-trans to 13-cis isomerization of retinal and decays with the reisomerization to all-trans in the late photocycle, making it a promising marker band for retinal configuration. Hybrid quantum mechanics/molecular mechanics simulations show that the near-UV absorption signal corresponds to an S0 → S3 and/or an S0 → S5 transition, which is present in all photointermediates. These transitions exhibit a negligible spectral shift by the altering protein environment, in contrast to the main absorption band. This is rationalized by the extension of the transition densities that omits the Schiff base nitrogen. Further characterization and first steps into possible optogenetic applications were performed with near-UV quenching experiments of an induced photostationary state, yielding an ultrafast regeneration of the parent state of KR2.
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Affiliation(s)
- Marvin Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
| | - Rajiv K Kar
- Fritz Haber Center for Molecular Dynamics Research at the Institute of Chemistry, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Clara Nassrin Kriebel
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Markus Braun
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt am Main, Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research at the Institute of Chemistry, The Hebrew University of Jerusalem, 9190401 Jerusalem, Israel
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany
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13
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Kato T, Tsukamoto T, Demura M, Kikukawa T. Real-time identification of two substrate-binding intermediates for the light-driven sodium pump rhodopsin. J Biol Chem 2021; 296:100792. [PMID: 34019877 PMCID: PMC8219890 DOI: 10.1016/j.jbc.2021.100792] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 11/29/2022] Open
Abstract
Membrane transport proteins undergo critical conformational changes during substrate uptake and release, as the substrate-binding site is believed to switch its accessibility from one side of the membrane to the other. Thus, at least two substrate-binding intermediates should appear during the process, that is, after uptake and before the release of the substrate. However, this view has not been verified for most transporters because of the difficulty in detecting short-lived intermediates. Here, we report real-time identification of these intermediates for the light-driven outward current-generating Na+-pump rhodopsin. We triggered the transport cycle of Na+-pump rhodopsin using a short laser pulse, and subsequent formation and decay of various intermediates was detected by time-resolved measurements of absorption changes. We used this method to analyze transport reactions and elucidated the sequential formation of the Na+-binding intermediates O1 and O2. Both intermediates exhibited red-shifted absorption spectra and generated transient equilibria with short-wavelength intermediates. The equilibria commonly shifted toward O1 and O2 with increasing Na+ concentration, indicating that Na+ is bound to these intermediates. However, these equilibria were formed independently; O1 reached equilibrium with preceding intermediates, indicating Na+ uptake on the cytoplasmic side. In contrast, O2 reached equilibrium with subsequent intermediates, indicating Na+ release on the extracellular side. Thus, there is an irreversible switch in “accessibility” during the O1 to O2 transition, which could represent one of the key processes governing unidirectional Na+ transport.
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Affiliation(s)
- Tomoya Kato
- Graduate School of Life Science, Hokkaido University, Sapporo, Japan
| | - Takashi Tsukamoto
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan; Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.
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14
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Nakamizo Y, Fujisawa T, Kikukawa T, Okamura A, Baba H, Unno M. Low-temperature Raman spectroscopy of sodium-pump rhodopsin from Indibacter alkaliphilus: insight of Na + binding for active Na + transport. Phys Chem Chem Phys 2021; 23:2072-2079. [PMID: 33433533 DOI: 10.1039/d0cp05652a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We carried out the low-temperature Raman measurement of a sodium pump rhodopsin from Indibacter alkaliphilus (IaNaR) and examined the primary structural change for the light-driven Na+ pump. We observed that photoexcitation of IaNaR produced the distorted 13-cis retinal chromophore in the presence of Na+, while the structural distortion was significantly relaxed in the absence of Na+. This structural difference of the chromophore with/without Na+ was attributed to the Na+ binding to the protein, which alters the active site. Using the spectral sensitivity to the ion binding, we found that IaNaR had a second Na+ binding site in addition to the one already specified on the extracellular surface. To date, the Na+ binding has not been considered as a prerequisite for Na+ transport. However, this study provides insight that the protein structural change induced by the ion binding involved the formation of an R108-D250 salt bridge, which has critical importance in the active transport of Na+.
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Affiliation(s)
- Yushi Nakamizo
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan.
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15
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Jakdetchai O, Eberhardt P, Asido M, Kaur J, Kriebel CN, Mao J, Leeder AJ, Brown LJ, Brown RCD, Becker-Baldus J, Bamann C, Wachtveitl J, Glaubitz C. Probing the photointermediates of light-driven sodium ion pump KR2 by DNP-enhanced solid-state NMR. SCIENCE ADVANCES 2021; 7:7/11/eabf4213. [PMID: 33712469 PMCID: PMC7954446 DOI: 10.1126/sciadv.abf4213] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/29/2021] [Indexed: 06/10/2023]
Abstract
The functional mechanism of the light-driven sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) raises fundamental questions since the transfer of cations must differ from the better-known principles of rhodopsin-based proton pumps. Addressing these questions must involve a better understanding of its photointermediates. Here, dynamic nuclear polarization-enhanced solid-state nuclear magnetic resonance spectroscopy on cryo-trapped photointermediates shows that the K-state with 13-cis retinal directly interconverts into the subsequent L-state with distinct retinal carbon chemical shift differences and an increased out-of-plane twist around the C14-C15 bond. The retinal converts back into an all-trans conformation in the O-intermediate, which is the key state for sodium transport. However, retinal carbon and Schiff base nitrogen chemical shifts differ from those observed in the KR2 dark state all-trans conformation, indicating a perturbation through the nearby bound sodium ion. Our findings are supplemented by optical and infrared spectroscopy and are discussed in the context of known three-dimensional structures.
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Affiliation(s)
- Orawan Jakdetchai
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Peter Eberhardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max von Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Marvin Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max von Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Jagdeep Kaur
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Clara Nassrin Kriebel
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Jiafei Mao
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Alexander J Leeder
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, Great Britain
| | - Lynda J Brown
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, Great Britain
| | - Richard C D Brown
- Department of Chemistry, University of Southampton, Southampton SO17 1BJ, Great Britain
| | - Johanna Becker-Baldus
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Christian Bamann
- Max Planck Institute of Biophysics, Max von Laue Strasse 3, 60438 Frankfurt am Main, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max von Laue Strasse 7, 60438 Frankfurt am Main, Germany.
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Max von Laue Strasse 9, 60438 Frankfurt am Main, Germany.
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16
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Hontani Y, Baloban M, Escobar FV, Jansen SA, Shcherbakova DM, Weißenborn J, Kloz M, Mroginski MA, Verkhusha VV, Kennis JTM. Real-time observation of tetrapyrrole binding to an engineered bacterial phytochrome. Commun Chem 2021; 4:3. [PMID: 34746444 PMCID: PMC8570541 DOI: 10.1038/s42004-020-00437-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/09/2020] [Indexed: 01/27/2023] Open
Abstract
Near-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes are widely used for structural and functional deep-tissue imaging in vivo. To fluoresce, NIR FPs covalently bind a chromophore, such as biliverdin IXa tetrapyrrole. The efficiency of biliverdin binding directly affects the fluorescence properties, rendering understanding of its molecular mechanism of major importance. miRFP proteins constitute a family of bright monomeric NIR FPs that comprise a Per-ARNT-Sim (PAS) and cGMP-specific phosphodiesterases - Adenylyl cyclases - FhlA (GAF) domain. Here, we structurally analyze biliverdin binding to miRFPs in real time using time-resolved stimulated Raman spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations. Biliverdin undergoes isomerization, localization to its binding pocket, and pyrrolenine nitrogen protonation in <1 min, followed by hydrogen bond rearrangement in ~2 min. The covalent attachment to a cysteine in the GAF domain was detected in 4.3 min and 19 min in miRFP670 and its C20A mutant, respectively. In miRFP670, a second C-S covalent bond formation to a cysteine in the PAS domain occurred in 14 min, providing a rigid tetrapyrrole structure with high brightness. Our findings provide insights for the rational design of NIR FPs and a novel method to assess cofactor binding to light-sensitive proteins.
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Affiliation(s)
- Yusaku Hontani
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV The Netherlands
- Present Address: School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853 USA
| | - Mikhail Baloban
- Departments of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Francisco Velazquez Escobar
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Straße des 17. Juni 135, Berlin, D-10623 Germany
| | - Swetta A. Jansen
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV The Netherlands
| | - Daria M. Shcherbakova
- Departments of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Jörn Weißenborn
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV The Netherlands
| | - Miroslav Kloz
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV The Netherlands
- ELI-Beamlines, Institute of Physics, Na Slovance 2, 182 21 Praha 8, Czech Republic
| | - Maria Andrea Mroginski
- Institut für Chemie, Technische Universität Berlin, Sekr. PC 14, Straße des 17. Juni 135, Berlin, D-10623 Germany
| | - Vladislav V. Verkhusha
- Departments of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461 USA
- Medicum, Faculty of Medicine, University of Helsinki, Helsinki, 00290 Finland
| | - John T. M. Kennis
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, 1081 HV The Netherlands
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17
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Inoue K. Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:89-126. [PMID: 33398809 DOI: 10.1007/978-981-15-8763-4_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ion-transporting microbial rhodopsins are widely used as major molecular tools in optogenetics. They are categorized into light-gated ion channels and light-driven ion pumps. While the former passively transport various types of cations and anions in a light-dependent manner, light-driven ion pumps actively transport specific ions, such as H+, Na+, Cl-, against electrophysiological potential by using light energy. Since the ion transport by these pumps induces hyperpolarization of membrane potential and inhibit neural firing, light-driven ion-pumping rhodopsins are mostly applied as inhibitory optogenetics tools. Recent progress in genome and metagenome sequencing identified more than several thousands of ion-pumping rhodopsins from a wide variety of microbes, and functional characterization studies has been revealing many new types of light-driven ion pumps one after another. Since light-gated channels were reviewed in other chapters in this book, here the rapid progress in functional characterization, molecular mechanism study, and optogenetic application of ion-pumping rhodopsins were reviewed.
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Affiliation(s)
- Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Chiba, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama, Japan.
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18
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Eberhardt P, Slavov C, Sörmann J, Bamann C, Braun M, Wachtveitl J. Temperature Dependence of the Krokinobacter rhodopsin 2 Kinetics. Biophys J 2020; 120:568-575. [PMID: 33347887 DOI: 10.1016/j.bpj.2020.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 11/13/2020] [Accepted: 12/07/2020] [Indexed: 11/16/2022] Open
Abstract
We investigated the temperature-dependent kinetics of the light-driven Na+ pump Krokinobacter rhodopsin 2 (KR2) at Na+-pumping conditions. The recorded microsecond flash photolysis data were subjected to detailed global target analysis, employing Eyring constraints and spectral decomposition. The analysis resulted in the kinetic rates, the composition of the different photocycle equilibria, and the spectra of the involved photointermediates. Our results show that with the temperature increase (from 10 to 40°C), the overall photocycle duration is accelerated by a factor of 6, with the L-to-M transition exhibiting an impressive 40-fold increase. It follows from the analysis that in KR2 the chromophore and the protein scaffold are more kinetically decoupled than in other microbial rhodopsins. We link this effect to the rigidity of the retinal protein environment. This kinetic decoupling should be considered in future studies and could potentially be exploited for fine-tuning biotechnological applications.
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Affiliation(s)
- Peter Eberhardt
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Chavdar Slavov
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Janina Sörmann
- Department of Biophysical Chemistry, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Christian Bamann
- Department of Biophysical Chemistry, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Markus Braun
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
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19
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Artes Vivancos JM, van Stokkum IHM, Saccon F, Hontani Y, Kloz M, Ruban A, van Grondelle R, Kennis JTM. Unraveling the Excited-State Dynamics and Light-Harvesting Functions of Xanthophylls in Light-Harvesting Complex II Using Femtosecond Stimulated Raman Spectroscopy. J Am Chem Soc 2020; 142:17346-17355. [PMID: 32878439 PMCID: PMC7564077 DOI: 10.1021/jacs.0c04619] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Photosynthesis
in plants starts with the capture of photons by
light-harvesting complexes (LHCs). Structural biology and spectroscopy
approaches have led to a map of the architecture and energy transfer
pathways between LHC pigments. Still, controversies remain regarding
the role of specific carotenoids in light-harvesting and photoprotection,
obligating the need for high-resolution techniques capable of identifying
excited-state signatures and molecular identities of the various pigments
in photosynthetic systems. Here we demonstrate the successful application
of femtosecond stimulated Raman spectroscopy (FSRS) to a multichromophoric
biological complex, trimers of LHCII. We demonstrate the application
of global and target analysis (GTA) to FSRS data and utilize it to
quantify excitation migration in LHCII trimers. This powerful combination
of techniques allows us to obtain valuable insights into structural,
electronic, and dynamic information from the carotenoids of LHCII
trimers. We report spectral and dynamical information on ground- and
excited-state vibrational modes of the different pigments, resolving
the vibrational relaxation of the carotenoids and the pathways of
energy transfer to chlorophylls. The lifetimes and spectral characteristics
obtained for the S1 state confirm that lutein 2 has a distorted conformation
in LHCII and that the lutein 2 S1 state does not transfer to chlorophylls,
while lutein 1 is the only carotenoid whose S1 state plays a significant
energy-harvesting role. No appreciable energy transfer takes place
from lutein 1 to lutein 2, contradicting recent proposals regarding
the functions of the various carotenoids (Son et al. Chem.2019, 5 (3), 575–584). Also, our results demonstrate that FSRS can be used in combination
with GTA to simultaneously study the electronic and vibrational landscapes
in LHCs and pave the way for in-depth studies of photoprotective conformations
in photosynthetic systems.
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Affiliation(s)
- Juan M Artes Vivancos
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands.,Department of Chemistry, Kennedy College of Science, University of Massachusetts-Lowell, One University Avenue, Lowell, Massachusetts 01854, United States
| | - Ivo H M van Stokkum
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Francesco Saccon
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road/E1 4NS London, U.K
| | - Yusaku Hontani
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Miroslav Kloz
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Alexander Ruban
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road/E1 4NS London, U.K
| | - Rienk van Grondelle
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - John T M Kennis
- Department of Physics and Astronomy and LaserLaB, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
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20
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Hontani Y, Broser M, Luck M, Weißenborn J, Kloz M, Hegemann P, Kennis JTM. Dual Photoisomerization on Distinct Potential Energy Surfaces in a UV-Absorbing Rhodopsin. J Am Chem Soc 2020; 142:11464-11473. [PMID: 32475117 PMCID: PMC7315636 DOI: 10.1021/jacs.0c03229] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
UV-absorbing rhodopsins are essential
for UV vision and sensing
in all kingdoms of life. Unlike the well-known visible-absorbing rhodopsins,
which bind a protonated retinal Schiff base for light absorption,
UV-absorbing rhodopsins bind an unprotonated retinal Schiff base.
Thus far, the photoreaction dynamics and mechanisms of UV-absorbing
rhodopsins have remained essentially unknown. Here, we report the
complete excited- and ground-state dynamics of the UV form of histidine
kinase rhodopsin 1 (HKR1) from eukaryotic algae, using femtosecond
stimulated Raman spectroscopy (FSRS) and transient absorption spectroscopy,
covering time scales from femtoseconds to milliseconds. We found that
energy-level ordering is inverted with respect to visible-absorbing
rhodopsins, with an optically forbidden low-lying S1 excited
state that has Ag– symmetry and a higher-lying UV-absorbing
S2 state of Bu+ symmetry. UV-photoexcitation
to the S2 state elicits a unique dual-isomerization reaction:
first, C13=C14 cis–trans isomerization occurs during S2–S1 evolution
in <100 fs. This very fast reaction features the remarkable property
that the newly formed isomer appears in the excited state rather than
in the ground state. Second, C15=N16 anti–syn isomerization occurs on the S1–S0 evolution to the ground state in 4.8 ps. We detected two
ground-state unprotonated retinal photoproducts, 13-trans/15-anti (all-trans) and 13-cis/15-syn, after relaxation to the ground
state. These isomers become protonated in 58 μs and 3.2 ms,
respectively, resulting in formation of the blue-absorbing form of
HKR1. Our results constitute a benchmark of UV-induced photochemistry
of animal and microbial rhodopsins.
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Affiliation(s)
- Yusaku Hontani
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan, Amsterdam 1081 HV, The Netherlands
| | - Matthias Broser
- Institut für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Meike Luck
- Institut für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Jörn Weißenborn
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan, Amsterdam 1081 HV, The Netherlands
| | - Miroslav Kloz
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan, Amsterdam 1081 HV, The Netherlands.,ELI-Beamlines, Institute of Physics, Na Slovance 2, 182 21 Praha 8, Czech Republic
| | - Peter Hegemann
- Institut für Biologie, Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - John T M Kennis
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, De Boelelaan, Amsterdam 1081 HV, The Netherlands
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21
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Kwon SK, Jun SH, Kim JF. Omega Rhodopsins: A Versatile Class of Microbial Rhodopsins. J Microbiol Biotechnol 2020; 30:633-641. [PMID: 32482928 PMCID: PMC9728251 DOI: 10.4014/jmb.1912.12010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 03/27/2020] [Indexed: 12/15/2022]
Abstract
Microbial rhodopsins are a superfamily of photoactive membrane proteins with covalently bound retinal cofactor. Isomerization of the retinal chromophore upon absorption of a photon triggers conformational changes of the protein to function as ion pumps or sensors. After the discovery of proteorhodopsin in an uncultivated γ-proteobacterium, light-activated proton pumps have been widely detected among marine bacteria and, together with chlorophyll-based photosynthesis, are considered as an important axis responsible for primary production in the biosphere. Rhodopsins and related proteins show a high level of phylogenetic diversity; we focus on a specific class of bacterial rhodopsins containing the 3 omega motif. This motif forms a stack of three nonconsecutive aromatic amino acids that correlates with the B-C loop orientation, and is shared among the phylogenetically close ion pumps such as the NDQ motif-containing sodium-pumping rhodopsin, the NTQ motif-containing chloride-pumping rhodopsin, and some proton-pumping rhodopsins including xanthorhodopsin. Here, we reviewed the recent research progress on these omega rhodopsins, and speculated on their evolutionary origin of functional diversity..
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Affiliation(s)
- Soon-Kyeong Kwon
- Division of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Sung-Hoon Jun
- Electron Microscopy Research Center, Korea Basic Science Institute, Cheongju 8119, Republic of Korea
| | - Jihyun F. Kim
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seoul 0722, Republic of Korea
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22
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Femtosecond-to-millisecond structural changes in a light-driven sodium pump. Nature 2020; 583:314-318. [DOI: 10.1038/s41586-020-2307-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/16/2020] [Indexed: 01/03/2023]
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23
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Fang C, Tang L. Mapping Structural Dynamics of Proteins with Femtosecond Stimulated Raman Spectroscopy. Annu Rev Phys Chem 2020; 71:239-265. [PMID: 32075503 DOI: 10.1146/annurev-physchem-071119-040154] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The structure-function relationships of biomolecules have captured the interest and imagination of the scientific community and general public since the field of structural biology emerged to enable the molecular understanding of life processes. Proteins that play numerous functional roles in cellular processes have remained in the forefront of research, inspiring new characterization techniques. In this review, we present key theoretical concepts and recent experimental strategies using femtosecond stimulated Raman spectroscopy (FSRS) to map the structural dynamics of proteins, highlighting the flexible chromophores on ultrafast timescales. In particular, wavelength-tunable FSRS exploits dynamic resonance conditions to track transient-species-dependent vibrational motions, enabling rational design to alter functions. Various ways of capturing excited-state chromophore structural snapshots in the time and/or frequency domains are discussed. Continuous development of experimental methodologies, synergistic correlation with theoretical modeling, and the expansion to other nonequilibrium, photoswitchable, and controllable protein systems will greatly advance the chemical, physical, and biological sciences.
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Affiliation(s)
- Chong Fang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA;
| | - Longteng Tang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA;
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24
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Abstract
This is a review of relevant Raman spectroscopy (RS) techniques and their use in structural biology, biophysics, cells, and tissues imaging towards development of various medical diagnostic tools, drug design, and other medical applications. Classical and contemporary structural studies of different water-soluble and membrane proteins, DNA, RNA, and their interactions and behavior in different systems were analyzed in terms of applicability of RS techniques and their complementarity to other corresponding methods. We show that RS is a powerful method that links the fundamental structural biology and its medical applications in cancer, cardiovascular, neurodegenerative, atherosclerotic, and other diseases. In particular, the key roles of RS in modern technologies of structure-based drug design are the detection and imaging of membrane protein microcrystals with the help of coherent anti-Stokes Raman scattering (CARS), which would help to further the development of protein structural crystallography and would result in a number of novel high-resolution structures of membrane proteins—drug targets; and, structural studies of photoactive membrane proteins (rhodopsins, photoreceptors, etc.) for the development of new optogenetic tools. Physical background and biomedical applications of spontaneous, stimulated, resonant, and surface- and tip-enhanced RS are also discussed. All of these techniques have been extensively developed during recent several decades. A number of interesting applications of CARS, resonant, and surface-enhanced Raman spectroscopy methods are also discussed.
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25
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Otomo A, Mizuno M, Inoue K, Kandori H, Mizutani Y. Allosteric Communication with the Retinal Chromophore upon Ion Binding in a Light-Driven Sodium Ion-Pumping Rhodopsin. Biochemistry 2020; 59:520-529. [PMID: 31887021 DOI: 10.1021/acs.biochem.9b01062] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Krokinobacter rhodopsin 2 (KR2) serves as a light-driven sodium ion pump in the presence of sodium ion and works as a proton pump in the presence of larger monovalent cations such as potassium ion, rubidium ion, and cesium ion. Recent crystallographic studies revealed that KR2 forms a pentamer and possesses an ion binding site at the subunit interface. It is assumed that sodium ion bound at this binding site is not transported but contributes to the thermal stability. Because KR2 can convert its function in response to coexisting cation species, this ion binding site is likely to be involved in ion transport selectively. However, how sodium ion binding affects the structure of the retinal chromophore, which plays a crucial role in ion transport, remains poorly understood. Here, we observed the structure of the retinal chromophore under a wide range of cation concentrations using visible absorption and resonance Raman spectroscopy. We discovered that the hydrogen bond formed between the Schiff base of the retinal chromophore and its counterion, Asp116, is weakened upon binding of sodium ion. This allosteric communication between the Schiff base and the ion binding site at the subunit interface likely increases the apparent efficiency of sodium ion transport. In addition, this study demonstrates the significance of sodium ion binding: even though sodium ion is not transported, binding regulates the structure around the Schiff base and stabilizes the oligomeric structure.
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Affiliation(s)
- Akihiro Otomo
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo , Kashiwa 277-8581 , Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry , Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555 , Japan.,OptoBio Technology Research Center , Nagoya Institute of Technology , Showa-Ku, Nagoya 466-8555 , Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science , Osaka University , 1-1 Machikaneyama , Toyonaka , Osaka 560-0043 , Japan
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26
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Buhrke D, Hildebrandt P. Probing Structure and Reaction Dynamics of Proteins Using Time-Resolved Resonance Raman Spectroscopy. Chem Rev 2019; 120:3577-3630. [PMID: 31814387 DOI: 10.1021/acs.chemrev.9b00429] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The mechanistic understanding of protein functions requires insight into the structural and reaction dynamics. To elucidate these processes, a variety of experimental approaches are employed. Among them, time-resolved (TR) resonance Raman (RR) is a particularly versatile tool to probe processes of proteins harboring cofactors with electronic transitions in the visible range, such as retinal or heme proteins. TR RR spectroscopy offers the advantage of simultaneously providing molecular structure and kinetic information. The various TR RR spectroscopic methods can cover a wide dynamic range down to the femtosecond time regime and have been employed in monitoring photoinduced reaction cascades, ligand binding and dissociation, electron transfer, enzymatic reactions, and protein un- and refolding. In this account, we review the achievements of TR RR spectroscopy of nearly 50 years of research in this field, which also illustrates how the role of TR RR spectroscopy in molecular life science has changed from the beginning until now. We outline the various methodological approaches and developments and point out current limitations and potential perspectives.
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Affiliation(s)
- David Buhrke
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für Chemie, Sekr. PC14, Straße des 17, Juni 135, D-10623 Berlin, Germany
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27
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Asido M, Eberhardt P, Kriebel CN, Braun M, Glaubitz C, Wachtveitl J. Time-resolved IR spectroscopy reveals mechanistic details of ion transport in the sodium pump Krokinobacter eikastus rhodopsin 2. Phys Chem Chem Phys 2019; 21:4461-4471. [PMID: 30734791 DOI: 10.1039/c8cp07418f] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a comparative study on the structural dynamics of the light-driven sodium pump Krokinobacter eikastus rhodopsin 2 wild type under sodium and proton pumping conditions by means of time-resolved IR spectroscopy. The kinetics of KR2 under sodium pumping conditions exhibits a sequential character, whereas the kinetics of KR2 under proton pumping conditions involves several equilibrium states. The sodium translocation itself is characterized by major conformational changes of the protein backbone, such as distortions of the α-helices and probably of the ECL1 domain, indicated by distinct marker bands in the amide I region. Carbonyl stretch modes of specific amino acid residues helped to elucidate structural changes in the retinal Schiff base moiety, including the protonation and deprotonation of D116, which is crucial for a deeper understanding of the mechanistic features in the photocycle of KR2.
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Affiliation(s)
- Marvin Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue Straße 7, 60438 Frankfurt am Main, Germany.
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28
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Hontani Y, Ganapathy S, Frehan S, Kloz M, de Grip WJ, Kennis JTM. Photoreaction Dynamics of Red-Shifting Retinal Analogues Reconstituted in Proteorhodopsin. J Phys Chem B 2019; 123:4242-4250. [PMID: 30998011 PMCID: PMC6526469 DOI: 10.1021/acs.jpcb.9b01136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Microbial rhodopsins
constitute a key protein family in optobiotechnological
applications such as optogenetics and voltage imaging. Spectral tuning
of rhodopsins into the deep-red and near-infrared spectral regions
is of great demand in such applications because more bathochromic
light into the near-infrared range penetrates deeper in living tissue.
Recently, retinal analogues have been successfully used in ion transporting
and fluorescent rhodopsins to achieve red-shifted absorption, activity,
and emission properties. Understanding their photochemical mechanism
is essential for further design of appropriate retinal analogues but
is yet only poorly understood for most retinal analogue pigments.
Here, we report the photoreaction dynamics of red-shifted analogue
pigments of the proton pump proteorhodopsin (PR) containing A2 (all-trans-3,4-dehydroretinal), MOA2 (all-trans-3-methoxy-3,4-dehydroretinal), or DMAR (all-trans-3-dimethylamino-16-nor-1,2,3,4-didehydroretinal), utilizing femto-
to submillisecond transient absorption spectroscopy. We found that
the A2 analogue photoisomerizes in 1.4, 3.0, and/or 13 ps upon 510
nm light illumination, which is comparable to the native retinal (A1)
in PR. On the other hand, the deprotonation of the A2 pigment Schiff
base was observed with a dominant time constant of 67 μs, which
is significantly slower than the A1 pigment. In the MOA2 pigment,
no isomerization or photoproduct formation was detected upon 520 nm
excitation, implying that all the excited molecules returned to the
initial ground state in 2.0 and 4.2 ps. The DMAR pigment showed very
slow excited state dynamics similar to the previously studied MMAR
pigment, but only very little photoproduct was formed. The low efficiency
of the photoproduct formation likely is the reason why DMAR analogue
pigments of PR showed very weak proton pumping activity.
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Affiliation(s)
- Yusaku Hontani
- Department of Physics and Astronomy , Vrije Universiteit , Amsterdam 1081 HV , The Netherlands
| | - Srividya Ganapathy
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories , Leiden University , Leiden 2300 RA , The Netherlands
| | - Sean Frehan
- Department of Physics and Astronomy , Vrije Universiteit , Amsterdam 1081 HV , The Netherlands
| | - Miroslav Kloz
- ELI-Beamlines , Institute of Physics , Na Slovance 2 , Praha 8 182 21 , Czech Republic
| | - Willem J de Grip
- Department of Biophysical Organic Chemistry, Leiden Institute of Chemistry, Gorlaeus Laboratories , Leiden University , Leiden 2300 RA , The Netherlands.,Department of Biochemistry , Radboud University Medical Center , Nijmegen 6500 HB , The Netherlands
| | - John T M Kennis
- Department of Physics and Astronomy , Vrije Universiteit , Amsterdam 1081 HV , The Netherlands
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29
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Nishimura N, Mizuno M, Kandori H, Mizutani Y. Distortion and a Strong Hydrogen Bond in the Retinal Chromophore Enable Sodium-Ion Transport by the Sodium-Ion Pump KR2. J Phys Chem B 2019; 123:3430-3440. [DOI: 10.1021/acs.jpcb.9b00928] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nao Nishimura
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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30
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Kaur J, Kriebel CN, Eberhardt P, Jakdetchai O, Leeder AJ, Weber I, Brown LJ, Brown RC, Becker-Baldus J, Bamann C, Wachtveitl J, Glaubitz C. Solid-state NMR analysis of the sodium pump Krokinobacter rhodopsin 2 and its H30A mutant. J Struct Biol 2019; 206:55-65. [DOI: 10.1016/j.jsb.2018.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/05/2018] [Accepted: 06/02/2018] [Indexed: 12/26/2022]
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31
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Miyahara T, Nakatsuji H. Light-Driven Proton, Sodium Ion, and Chloride Ion Transfer Mechanisms in Rhodopsins: SAC-CI Study. J Phys Chem A 2019; 123:1766-1784. [DOI: 10.1021/acs.jpca.8b10203] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Tomoo Miyahara
- Quantum Chemistry Research Institute, Kyoto Technoscience Center 16, 14 Yoshida Kawara-machi, Sakyou-ku, Kyoto 606-8305, Japan
| | - Hiroshi Nakatsuji
- Quantum Chemistry Research Institute, Kyoto Technoscience Center 16, 14 Yoshida Kawara-machi, Sakyou-ku, Kyoto 606-8305, Japan
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32
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Konold PE, van Stokkum IHM, Muzzopappa F, Wilson A, Groot ML, Kirilovsky D, Kennis JTM. Photoactivation Mechanism, Timing of Protein Secondary Structure Dynamics and Carotenoid Translocation in the Orange Carotenoid Protein. J Am Chem Soc 2019; 141:520-530. [PMID: 30511841 PMCID: PMC6331140 DOI: 10.1021/jacs.8b11373] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Indexed: 01/10/2023]
Abstract
The orange carotenoid protein (OCP) is a two-domain photoactive protein that noncovalently binds an echinenone (ECN) carotenoid and mediates photoprotection in cyanobacteria. In the dark, OCP assumes an orange, inactive state known as OCPO; blue light illumination results in the red active state, known as OCPR. The OCPR state is characterized by large-scale structural changes that involve dissociation and separation of C-terminal and N-terminal domains accompanied by carotenoid translocation into the N-terminal domain. The mechanistic and dynamic-structural relations between photon absorption and formation of the OCPR state have remained largely unknown. Here, we employ a combination of time-resolved UV-visible and (polarized) mid-infrared spectroscopy to assess the electronic and structural dynamics of the carotenoid and the protein secondary structure, from femtoseconds to 0.5 ms. We identify a hereto unidentified carotenoid excited state in OCP, the so-called S* state, which we propose to play a key role in breaking conserved hydrogen-bond interactions between carotenoid and aromatic amino acids in the binding pocket. We arrive at a comprehensive reaction model where the hydrogen-bond rupture with conserved aromatic side chains at the carotenoid β1-ring in picoseconds occurs at a low yield of <1%, whereby the β1-ring retains a trans configuration with respect to the conjugated π-electron chain. This event initiates structural changes at the N-terminal domain in 1 μs, which allow the carotenoid to translocate into the N-terminal domain in 10 μs. We identified infrared signatures of helical elements that dock on the C-terminal domain β-sheet in the dark and unfold in the light to allow domain separation. These helical elements do not move within the experimental range of 0.5 ms, indicating that domain separation occurs on longer time scales, lagging carotenoid translocation by at least 2 decades of time.
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Affiliation(s)
- Patrick E. Konold
- Department of Physics
and Astronomy, Faculty of Sciences, Vrije
Universiteit, De Boelelaan
1081, 1081HV Amsterdam, The Netherlands
| | - Ivo H. M. van Stokkum
- Department of Physics
and Astronomy, Faculty of Sciences, Vrije
Universiteit, De Boelelaan
1081, 1081HV Amsterdam, The Netherlands
| | - Fernando Muzzopappa
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Universite Paris-Sud,
Universite Paris-Saclay, 91198 Gif-sur-Yvette, France
- Institut Joliot, Commissariat a l’Energie
Atomique (CEA), 91191 Gif-sur-Yvette, France
| | - Adjélé Wilson
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Universite Paris-Sud,
Universite Paris-Saclay, 91198 Gif-sur-Yvette, France
- Institut Joliot, Commissariat a l’Energie
Atomique (CEA), 91191 Gif-sur-Yvette, France
| | - Marie-Louise Groot
- Department of Physics
and Astronomy, Faculty of Sciences, Vrije
Universiteit, De Boelelaan
1081, 1081HV Amsterdam, The Netherlands
| | - Diana Kirilovsky
- Institute for Integrative Biology of the
Cell (I2BC), CEA, CNRS, Universite Paris-Sud,
Universite Paris-Saclay, 91198 Gif-sur-Yvette, France
- Institut Joliot, Commissariat a l’Energie
Atomique (CEA), 91191 Gif-sur-Yvette, France
| | - John T. M. Kennis
- Department of Physics
and Astronomy, Faculty of Sciences, Vrije
Universiteit, De Boelelaan
1081, 1081HV Amsterdam, The Netherlands
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33
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Hontani Y, Ganapathy S, Frehan S, Kloz M, de Grip WJ, Kennis JTM. Strong pH-Dependent Near-Infrared Fluorescence in a Microbial Rhodopsin Reconstituted with a Red-Shifting Retinal Analogue. J Phys Chem Lett 2018; 9:6469-6474. [PMID: 30376338 PMCID: PMC6240888 DOI: 10.1021/acs.jpclett.8b02780] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 10/30/2018] [Indexed: 06/08/2023]
Abstract
Near-infrared (NIR)-driven rhodopsins are of great interest in optogenetics and other optobiotechnological developments such as artificial photosynthesis and deep-tissue voltage imaging. Here we report that the proton pump proteorhodopsin (PR) containing a NIR-active retinal analogue (PR:MMAR) exhibits intense NIR fluorescence at a quantum yield of 3.3%. This is 130 times higher than native PR ( Lenz , M. O. ; Biophys J. 2006 , 91 , 255 - 262 ) and 3-8 times higher than the QuasAr and PROPS voltage sensors ( Kralj , J. ; Science 2011 , 333 , 345 - 348 ; Hochbaum , D. R. ; Nat. Methods 2014 , 11 , 825 - 833 ). The NIR fluorescence strongly depends on the pH in the range of 6-8.5, suggesting potential application of MMAR-binding proteins as ultrasensitive NIR-driven pH and/or voltage sensors. Femtosecond transient absorption spectroscopy showed that upon near-IR excitation, PR:MMAR features an unusually long fluorescence lifetime of 310 ps and the absence of isomerized photoproducts, consistent with the high fluorescence quantum yield. Stimulated Raman analysis indicates that the NIR-absorbing species develops upon protonation of a conserved aspartate, which promotes charge delocalization and bond length leveling due to an additional methylamino group in MMAR, in essence providing a secondary protonated Schiff base. This results in much smaller bond length alteration along the conjugated backbone, thereby conferring significant single-bond character to the C13═C14 bond and structural deformation of the chromophore, which interferes with photoinduced isomerization and extends the lifetime for fluorescence. Hence, our studies allow for a molecular understanding of the relation between absorption/emission wavelength, isomerization, and fluorescence in PR:MMAR. As acidification enhances the resonance state, this explains the strong pH dependence of the NIR emission.
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Affiliation(s)
- Yusaku Hontani
- Department
of Physics and Astronomy, Vrije Universiteit, Amsterdam 1081 HV, The Netherlands
| | - Srividya Ganapathy
- Department
of Biophysical Organic Chemistry, Leiden Institute of
Chemistry, Gorlaeus Laboratories, Leiden University, Leiden 2300 RA, The Netherlands
| | - Sean Frehan
- Department
of Physics and Astronomy, Vrije Universiteit, Amsterdam 1081 HV, The Netherlands
| | - Miroslav Kloz
- Department
of Physics and Astronomy, Vrije Universiteit, Amsterdam 1081 HV, The Netherlands
- ELI-Beamlines,
Institute of Physics, Na Slovance 2, 182 21 Praha 8, Czech Republic
| | - Willem J. de Grip
- Department
of Biophysical Organic Chemistry, Leiden Institute of
Chemistry, Gorlaeus Laboratories, Leiden University, Leiden 2300 RA, The Netherlands
- Department
of Biochemistry, Radboud University Medical
Center, Nijmegen 6500 HB, The Netherlands
| | - John T. M. Kennis
- Department
of Physics and Astronomy, Vrije Universiteit, Amsterdam 1081 HV, The Netherlands
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34
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Inoue K, Tahara S, Kato Y, Takeuchi S, Tahara T, Kandori H. Spectroscopic Study of Proton-Transfer Mechanism of Inward Proton-Pump Rhodopsin, Parvularcula oceani Xenorhodopsin. J Phys Chem B 2018; 122:6453-6461. [DOI: 10.1021/acs.jpcb.8b01279] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Keiichi Inoue
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Shinya Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | | | - Satoshi Takeuchi
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
| | - Tahei Tahara
- Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
- Ultrafast Spectroscopy Research Team, RIKEN Center for Advanced Photonics (RAP), RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan
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35
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Tahara S, Takeuchi S, Abe-Yoshizumi R, Inoue K, Ohtani H, Kandori H, Tahara T. Origin of the Reactive and Nonreactive Excited States in the Primary Reaction of Rhodopsins: pH Dependence of Femtosecond Absorption of Light-Driven Sodium Ion Pump Rhodopsin KR2. J Phys Chem B 2018; 122:4784-4792. [DOI: 10.1021/acs.jpcb.8b01934] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | | | | | - Keiichi Inoue
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Hiroyuki Ohtani
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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36
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Shigeta A, Ito S, Kaneko R, Tomida S, Inoue K, Kandori H, Kawamura I. Long-distance perturbation on Schiff base-counterion interactions by His30 and the extracellular Na +-binding site in Krokinobacter rhodopsin 2. Phys Chem Chem Phys 2018. [PMID: 29537054 DOI: 10.1039/c8cp00626a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Krokinobacter rhodopsin 2 (KR2), a light-driven Na+ pump, is a dual-functional protein, pumping protons in the absence of Na+ when K+ or larger alkali metal ions are present. A specific mutation in helix A near the extracellular Na+ binding site, H30A, eliminates its proton pumping ability. We induced structural changes in H30A by altering the alkali metal ion bound at the extracellular binding site, and observed a strong electrostatic interaction between the Schiff base and counterion and torsion around the Schiff base as revealed by solid-state nuclear magnetic resonance (NMR) and Fourier transform infrared (FTIR) spectroscopies. The strong interaction when His30 was absent and no ion bound at the extracellular binding site disabled retinal reisomerization, as was shown with flash-photolysis, forming a small amount of only a K-like intermediate. This revealed why H30A lacks the proton pumping function. Long-distance perturbation of the binding site and Schiff base revealed that a non-transported ion binding at the extracellular site is essential for pumping.
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Affiliation(s)
- Arisu Shigeta
- Graduate School of Engineering, Yokohama National University, Hodogaya-ku, Yokohama 240-8501, Japan.
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37
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Hontani Y, Kloz M, Polívka T, Shukla MK, Sobotka R, Kennis JTM. Molecular Origin of Photoprotection in Cyanobacteria Probed by Watermarked Femtosecond Stimulated Raman Spectroscopy. J Phys Chem Lett 2018; 9:1788-1792. [PMID: 29569927 PMCID: PMC5942868 DOI: 10.1021/acs.jpclett.8b00663] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Photoprotection is fundamental in photosynthesis to avoid oxidative photodamage upon excess light exposure. Excited chlorophylls (Chl) are quenched by carotenoids, but the precise molecular origin remains controversial. The cyanobacterial HliC protein belongs to the Hlip family ancestral to plant light-harvesting complexes, and binds Chl a and β-carotene in 2:1 ratio. We analyzed HliC by watermarked femtosecond stimulated Raman spectroscopy to follow the time evolution of its vibrational modes. We observed a 2 ps rise of the C═C stretch band of the 2Ag- (S1) state of β-carotene upon Chl a excitation, demonstrating energy transfer quenching and fast excess-energy dissipation. We detected two distinct β-carotene conformers by the C═C stretch frequency of the 2Ag- (S1) state, but only the β-carotene whose 2Ag- energy level is significantly lowered and has a lower C═C stretch frequency is involved in quenching. It implies that the low carotenoid S1 energy that results from specific pigment-protein or pigment-pigment interactions is the key property for creating a dissipative energy channel. We conclude that watermarked femtosecond stimulated Raman spectroscopy constitutes a promising experimental method to assess energy transfer and quenching mechanisms in oxygenic photosynthesis.
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Affiliation(s)
- Yusaku Hontani
- Department
of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
| | - Miroslav Kloz
- Department
of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
- ELI-Beamlines, Institute of Physics, Na Slovance 2, 182 21 Praha 8, Czech Republic
| | - Tomáš Polívka
- Institute
of Physics and Biophysics, Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic
| | - Mahendra K. Shukla
- Centre
Algatech, Institute of Microbiology, Academy
of Sciences of the Czech Republic, Třeboň, 379 81, Czech Republic
| | - Roman Sobotka
- Centre
Algatech, Institute of Microbiology, Academy
of Sciences of the Czech Republic, Třeboň, 379 81, Czech Republic
| | - John T. M. Kennis
- Department
of Physics and Astronomy, Vrije Universiteit, De Boelelaan 1081, 1081 HV Amsterdam, The Netherlands
- E-mail:
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Kandori H, Inoue K, Tsunoda SP. Light-Driven Sodium-Pumping Rhodopsin: A New Concept of Active Transport. Chem Rev 2018. [DOI: 10.1021/acs.chemrev.7b00548] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | - Keiichi Inoue
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Satoshi P. Tsunoda
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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Chen HF, Inoue K, Ono H, Abe-Yoshizumi R, Wada A, Kandori H. Time-resolved FTIR study of light-driven sodium pump rhodopsins. Phys Chem Chem Phys 2018; 20:17694-17704. [DOI: 10.1039/c8cp02599a] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Light-driven sodium ion pump rhodopsin (NaR) is a new functional class of microbial rhodopsin. Present step-scan time-resolved FTIR spectroscopy revealed that the K, L and O intermediates of NaRs contain 13-cis retinal with similar distortion.
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Affiliation(s)
- Hui-Fen Chen
- Department of Medicinal and Applied Chemistry
- Kaohsiung Medical University
- Kaohsiung
- Taiwan
- Department of Life Science and Applied Chemistry
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- OptoBioTechnology Research Center
| | - Hikaru Ono
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
| | - Akimori Wada
- Laboratory of Organic Chemistry for Life Science
- Kobe Pharmaceutical University
- Kobe 658-8558
- Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Nagoya 466-8555
- Japan
- OptoBioTechnology Research Center
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40
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Hall CR, Heisler IA, Jones GA, Frost JE, Gil AA, Tonge PJ, Meech SR. Femtosecond stimulated Raman study of the photoactive flavoprotein AppABLUF. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.03.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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41
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Abstract
Channelrhodopsin (ChR) is a key protein of the optogenetic toolkit. C1C2, a functional chimeric protein of Chlamydomonas reinhardtii ChR1 and ChR2, is the only ChR whose crystal structure has been solved, and thus uniquely suitable for structure-based analysis. We report C1C2 photoreaction dynamics with ultrafast transient absorption and multi-pulse spectroscopy combined with target analysis and structure-based hybrid quantum mechanics/molecular mechanics calculations. Two relaxation pathways exist on the excited (S1) state through two conical intersections CI1 and CI2, that are reached via clockwise and counter-clockwise rotations: (i) the C13=C14 isomerization path with 450 fs via CI1 and (ii) a relaxation path to the initial ground state with 2.0 ps and 11 ps via CI2, depending on the hydrogen-bonding network, hence indicating active-site structural heterogeneity. The presence of the additional conical intersection CI2 rationalizes the relatively low quantum yield of photoisomerization (30 ± 3%), reported here. Furthermore, we show the photoreaction dynamics from picoseconds to seconds, characterizing the complete photocycle of C1C2.
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42
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Abstract
The conversion of light energy into ion gradients across biological membranes is one of the most fundamental reactions in primary biological energy transduction. Recently, the structure of the first light-activated Na+ pump, Krokinobacter eikastus rhodopsin 2 (KR2), was resolved at atomic resolution [Kato HE, et al. (2015) Nature 521:48-53]. To elucidate its molecular mechanism for Na+ pumping, we perform here extensive classical and quantum molecular dynamics (MD) simulations of transient photocycle states. Our simulations show how the dynamics of key residues regulate water and ion access between the bulk and the buried light-triggered retinal site. We identify putative Na+ binding sites and show how protonation and conformational changes gate the ion through these sites toward the extracellular side. We further show by correlated ab initio quantum chemical calculations that the obtained putative photocycle intermediates are in close agreement with experimental transient optical spectroscopic data. The combined results of the ion translocation and gating mechanisms in KR2 may provide a basis for the rational design of novel light-driven ion pumps with optogenetic applications.
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43
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From Gene to Function: Cell-Free Electrophysiological and Optical Analysis of Ion Pumps in Nanodiscs. Biophys J 2017; 113:1331-1341. [PMID: 28450130 DOI: 10.1016/j.bpj.2017.03.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/14/2017] [Accepted: 03/27/2017] [Indexed: 12/15/2022] Open
Abstract
Nanodiscs that hold a lipid bilayer surrounded by a boundary of scaffold proteins have emerged as a powerful tool for membrane protein solubilization and analysis. By combining nanodiscs and cell-free expression technologies, even completely detergent-free membrane protein characterization protocols can be designed. Nanodiscs are compatible with various techniques, and due to their bilayer environment and increased stability, they are often superior to detergent micelles or liposomes for membrane protein solubilization. However, transport assays in nanodiscs have not been conducted so far, due to limitations of the two-dimensional nature of nanodisc membranes that offers no compartmentalization. Here, we study Krokinobacter eikastus rhodopsin-2 (KR2), a microbial light-driven sodium or proton pump, with noncovalent mass-spectrometric, electrophysiological, and flash photolysis measurements after its cotranslational insertion into nanodiscs. We demonstrate the feasibility of adsorbing nanodiscs containing KR2 to an artificial bilayer. This allows us to record light-induced capacitive currents that reflect KR2's ion transport activity. The solid-supported membrane assay with nanodisc samples provides reliable control over the ionic condition and information of the relative ion activity of this promiscuous pump. Our strategy is complemented with flash photolysis data, where the lifetimes of different photointermediates were determined at different ionic conditions. The advantage of using identical samples to three complementary approaches allows for a comprehensive comparability. The cell-free synthesis in combination with nanodiscs provides a defined hydrophobic lipid environment minimizing the detergent dependence often seen in assays with membrane proteins. KR2 is a promising tool for optogenetics, thus directed engineering to modify ion selectivity can be highly beneficial. Our approach, using the fast generation of functional ion pumps incorporated into nanodiscs and their subsequent analysis by several biophysical techniques, can serve as a versatile screening and engineering platform. This may open new avenues for the study of ion pumps and similar electrogenic targets.
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Kajimoto K, Kikukawa T, Nakashima H, Yamaryo H, Saito Y, Fujisawa T, Demura M, Unno M. Transient Resonance Raman Spectroscopy of a Light-Driven Sodium-Ion-Pump Rhodopsin from Indibacter alkaliphilus. J Phys Chem B 2017; 121:4431-4437. [DOI: 10.1021/acs.jpcb.7b02421] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kousuke Kajimoto
- Department
of Chemistry and Applied Chemistry, Graduate School of Science and
Engineering, Saga University, Saga 840-8502, Japan
| | - Takashi Kikukawa
- Faculty
of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Global
Station for Soft Matter, Global Institution for Collaborative Research
and Education, Hokkaido University, Sapporo 060-0810, Japan
| | - Hiroki Nakashima
- Department
of Chemistry and Applied Chemistry, Graduate School of Science and
Engineering, Saga University, Saga 840-8502, Japan
| | - Haruki Yamaryo
- Department
of Chemistry and Applied Chemistry, Graduate School of Science and
Engineering, Saga University, Saga 840-8502, Japan
| | - Yuta Saito
- Faculty
of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Tomotsumi Fujisawa
- Department
of Chemistry and Applied Chemistry, Graduate School of Science and
Engineering, Saga University, Saga 840-8502, Japan
| | - Makoto Demura
- Faculty
of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
- Global
Station for Soft Matter, Global Institution for Collaborative Research
and Education, Hokkaido University, Sapporo 060-0810, Japan
| | - Masashi Unno
- Department
of Chemistry and Applied Chemistry, Graduate School of Science and
Engineering, Saga University, Saga 840-8502, Japan
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45
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Hontani Y, Broser M, Silapetere A, Krause BS, Hegemann P, Kennis JTM. The femtosecond-to-second photochemistry of red-shifted fast-closing anion channelrhodopsin PsACR1. Phys Chem Chem Phys 2017; 19:30402-30409. [DOI: 10.1039/c7cp06414d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Femtosecond-to-second complete photocycle model of anion channelrhodopsin PsACR1.
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Affiliation(s)
- Yusaku Hontani
- Department of Physics and Astronomy
- Vrije Universiteit Amsterdam
- Amsterdam 1081 HV, De Boelelaan
- The Netherlands
| | - Matthias Broser
- Institut für Biologie
- Experimentelle Biophysik
- Humboldt-Universität zu Berlin
- D-10115 Berlin
- Germany
| | - Arita Silapetere
- Institut für Biologie
- Experimentelle Biophysik
- Humboldt-Universität zu Berlin
- D-10115 Berlin
- Germany
| | - Benjamin S. Krause
- Institut für Biologie
- Experimentelle Biophysik
- Humboldt-Universität zu Berlin
- D-10115 Berlin
- Germany
| | - Peter Hegemann
- Institut für Biologie
- Experimentelle Biophysik
- Humboldt-Universität zu Berlin
- D-10115 Berlin
- Germany
| | - John T. M. Kennis
- Department of Physics and Astronomy
- Vrije Universiteit Amsterdam
- Amsterdam 1081 HV, De Boelelaan
- The Netherlands
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