1
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Podoliak E, Lamm GHU, Marin E, Schellbach AV, Fedotov DA, Stetsenko A, Asido M, Maliar N, Bourenkov G, Balandin T, Baeken C, Astashkin R, Schneider TR, Bateman A, Wachtveitl J, Schapiro I, Busskamp V, Guskov A, Gordeliy V, Alekseev A, Kovalev K. A subgroup of light-driven sodium pumps with an additional Schiff base counterion. Nat Commun 2024; 15:3119. [PMID: 38600129 PMCID: PMC11006869 DOI: 10.1038/s41467-024-47469-0] [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: 10/12/2023] [Accepted: 04/01/2024] [Indexed: 04/12/2024] Open
Abstract
Light-driven sodium pumps (NaRs) are unique ion-transporting microbial rhodopsins. The major group of NaRs is characterized by an NDQ motif and has two aspartic acid residues in the central region essential for sodium transport. Here we identify a subgroup of the NDQ rhodopsins bearing an additional glutamic acid residue in the close vicinity to the retinal Schiff base. We thoroughly characterize a member of this subgroup, namely the protein ErNaR from Erythrobacter sp. HL-111 and show that the additional glutamic acid results in almost complete loss of pH sensitivity for sodium-pumping activity, which is in contrast to previously studied NaRs. ErNaR is capable of transporting sodium efficiently even at acidic pH levels. X-ray crystallography and single particle cryo-electron microscopy reveal that the additional glutamic acid residue mediates the connection between the other two Schiff base counterions and strongly interacts with the aspartic acid of the characteristic NDQ motif. Hence, it reduces its pKa. Our findings shed light on a subgroup of NaRs and might serve as a basis for their rational optimization for optogenetics.
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Affiliation(s)
- E Podoliak
- Department of Ophthalmology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - G H U Lamm
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - E Marin
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - A V Schellbach
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
- School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - D A Fedotov
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - A Stetsenko
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - M Asido
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - N Maliar
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - G Bourenkov
- European Molecular Biology Laboratory, EMBL Hamburg c/o DESY, 22607, Hamburg, Germany
| | - T Balandin
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - C Baeken
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - R Astashkin
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - T R Schneider
- European Molecular Biology Laboratory, EMBL Hamburg c/o DESY, 22607, Hamburg, Germany
| | - A Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - J Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - I Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - V Busskamp
- Department of Ophthalmology, University Hospital Bonn, Medical Faculty, Bonn, Germany
| | - A Guskov
- Groningen Institute for Biomolecular Sciences and Biotechnology, University of Groningen, 9747AG, Groningen, the Netherlands
| | - V Gordeliy
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - A Alekseev
- University Medical Center Göttingen, Institute for Auditory Neuroscience and InnerEarLab, Robert-Koch-Str. 40, 37075, Göttingen, Germany.
- Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
| | - K Kovalev
- European Molecular Biology Laboratory, EMBL Hamburg c/o DESY, 22607, Hamburg, Germany.
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2
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Fujisawa T, Kinoue K, Seike R, Kikukawa T, Unno M. Configurational Changes of Retinal Schiff Base during Membrane Na + Transport by a Sodium Pumping Rhodopsin. J Phys Chem Lett 2024; 15:1993-1998. [PMID: 38349321 DOI: 10.1021/acs.jpclett.3c03435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Microbial rhodopsins are photoreceptors containing the retinal Schiff base chromophore and are ubiquitous among microorganisms. The Schiff base configuration of the chromophore, 15-anti (C═N trans) or 15-syn (C═N cis), is structurally important for their functions, such as membrane ion transport, because this configuration dictates the orientation of the positively charged NH group that interacts with substrate ions. The 15-anti/syn configuration is thus essential for elucidating the ion-transport mechanisms in microbial rhodopsins. Here, we identified the Schiff base configuration during the photoreaction of a sodium pumping rhodopsin from Indibacter alkaliphilus using Raman spectroscopy. We found that the unique configurational change from the 13-cis, 15-anti to all-trans, 15-syn form occurs between the photointermediates termed O1 and O2, which accomplish the Na+ uptake and release, respectively. This isomerization is considered to give rise to the highly irreversible O1 → O2 step that is crucial for unidirectional Na+ transport.
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Affiliation(s)
- Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Kouta Kinoue
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Ryouhei Seike
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
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3
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Mei Y, Shen Y. Cation-π Interactions Greatly Influence Ion Transportability of the Light-Driven Sodium Pump KR2: A Molecular Dynamics Study. J Chem Inf Model 2024; 64:974-982. [PMID: 38237560 DOI: 10.1021/acs.jcim.3c01883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2024]
Abstract
Krokinobacter eikastus rhodopsin 2 (KR2) is a typical light-driven sodium pump. Although wild-type KR2 exhibits high Na+ selectivity, mutagenesis performed on the residues constituting the entrance enables permeation of K+ and Cs+, while the underlying mechanism remains elusive. This study presents a comprehensive molecular dynamics investigation, including force field optimization, metadynamics, and alchemical free energy methods, to explore the N61L/G263F mutant of KR2, which exhibits transportability for K+ and Cs+. The introduced Phe263 residue can directly promote ion binding at the entrance through cation-π interactions, while the N61L mutation can enhance ion binding at Phe46 by relieving steric hindrance. These results suggest that cation-π interactions may significantly influence the ion transportability and selectivity of KR2, which can provide important insights for protein engineering and the design of artificial ion transporters.
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Affiliation(s)
- Yunhao Mei
- School of Chemistry, IGCME, Sun Yat-sen University, Guangzhou 510006, China
| | - Yong Shen
- School of Chemistry, IGCME, Sun Yat-sen University, Guangzhou 510006, China
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4
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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: 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: 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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5
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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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6
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González-Viegas M, Kar RK, Miller AF, Mroginski MA. Non-covalent interactions that tune the reactivities of the flavins in bifurcating electron transferring flavoprotein. J Biol Chem 2023:104762. [PMID: 37119850 DOI: 10.1016/j.jbc.2023.104762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/20/2023] [Accepted: 04/25/2023] [Indexed: 05/01/2023] Open
Abstract
Bifurcating electron transferring flavoproteins (Bf-ETFs) tune chemically identical flavins to two contrasting roles. To understand how, we used hybrid quantum mechanical molecular mechanical calculations to characterize non-covalent interactions applied to each flavin by the protein. Our computations replicated the differences between the reactivities of the flavins: the electron transferring flavin (ETflavin) was calculated to stabilize anionic semiquinone (ASQ) as needed to execute its single-electron transfers, whereas the Bf flavin (Bfflavin) was found to disfavor the ASQ state more than does free flavin and to be less susceptible to reduction. The stability of ETflavin ASQ was attributed in part to H-bond donation to the flavin O2 from a nearby His side chain, via comparison of models employing different tautomers of His. This H-bond between O2 and the ET site was uniquely strong in the ASQ state, whereas reduction of ETflavin to the anionic hydroquinone (AHQ) was associated with side chain reorientation, backbone displacement and reorganization of its H-bond network including a Tyr from the other domain and subunit of the ETF. The Bf site was less responsive overall, but formation of the Bfflavin AHQ allowed a nearby Arg side chain to adopt an alternative rotamer that can H-bond to the Bfflavin O4. This would stabilize the anionic Bfflavin and rationalize effects of mutation at this position. Thus, our computations provide insights on states and conformations that have not been possible to characterize experimentally, offering explanations for observed residue conservation and raising possibilities that can now be tested.
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Affiliation(s)
- María González-Viegas
- Department of Chemistry, Technische Universität - Berlin, Berlin, Germany; Department of Physics, Freie Universität Berlin, Berlin, Germany
| | - Rajiv K Kar
- Department of Chemistry, Technische Universität - Berlin, Berlin, Germany
| | - Anne-Frances Miller
- Department of Chemistry, Technische Universität - Berlin, Berlin, Germany; Department of Chemistry, University of Kentucky, Lexington KY, U.S.A..
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7
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Furutani Y, Yang CS. Ion-transporting mechanism in microbial rhodopsins: Mini-review relating to the session 5 at the 19th International Conference on Retinal Proteins. Biophys Physicobiol 2023; 20:e201005. [PMID: 38362333 PMCID: PMC10865854 DOI: 10.2142/biophysico.bppb-v20.s005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Affiliation(s)
- Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Aichi 466-8555, Japan
| | - Chii-Shen Yang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
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8
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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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9
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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: 3] [Impact Index Per Article: 3.0] [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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10
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Tsujimura M, Chiba Y, Saito K, Ishikita H. Proton transfer and conformational changes along the hydrogen bond network in heliorhodopsin. Commun Biol 2022; 5:1336. [PMID: 36474019 PMCID: PMC9726877 DOI: 10.1038/s42003-022-04311-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Heliorhodopsin releases a proton from the Schiff base during the L-state to M-state transition but not toward the protein bulk surface. Here we investigate proton transfer and induced structural changes along the H-bond network in heliorhodopsin using a quantum mechanical/molecular mechanical approach and molecular dynamics simulations. Light-induced proton transfer could occur from the Schiff base toward Glu107, reorienting Ser76, followed by subsequent proton transfer toward His80. His80 protonation induces the reorientation of Trp246 on the extracellular surface, originating from the electrostatic interaction that propagates along the transmembrane H-bond network [His80…His23…H2O[H23/Q26]…Gln26…Trp246] over a distance of 15 Å. Furthermore, it induces structural fluctuation on the intracellular side in the H-bond network [His80…Asn16…Tyr92…Glu230…Arg104…Glu149], opening the inner cavity at the Tyr92 moiety. These may be a basis of how light-induced proton transfer causes conformational changes during the M-state to O-state transition.
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Affiliation(s)
- Masaki Tsujimura
- grid.26999.3d0000 0001 2151 536XDepartment of Advanced Interdisciplinary Studies, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904 Japan
| | - Yoshihiro Chiba
- grid.26999.3d0000 0001 2151 536XDepartment of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 Japan
| | - Keisuke Saito
- grid.26999.3d0000 0001 2151 536XDepartment of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 Japan ,grid.26999.3d0000 0001 2151 536XResearch Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904 Japan
| | - Hiroshi Ishikita
- grid.26999.3d0000 0001 2151 536XDepartment of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654 Japan ,grid.26999.3d0000 0001 2151 536XResearch Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904 Japan
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11
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Fujisawa T, Kinoue K, Seike R, Kikukawa T, Unno M. Reisomerization of retinal represents a molecular switch mediating Na + uptake and release by a bacterial sodium-pumping rhodopsin. J Biol Chem 2022; 298:102366. [PMID: 35963435 PMCID: PMC9483557 DOI: 10.1016/j.jbc.2022.102366] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 11/27/2022] Open
Abstract
Sodium-pumping rhodopsins (NaRs) are membrane transporters that utilize light energy to pump Na+ across the cellular membrane. Within the NaRs, the retinal Schiff base chromophore absorbs light, and a photochemically induced transient state, referred to as the “O intermediate”, performs both the uptake and release of Na+. However, the structure of the O intermediate remains unclear. Here, we used time-resolved cryo-Raman spectroscopy under preresonance conditions to study the structure of the retinal chromophore in the O intermediate of an NaR from the bacterium Indibacter alkaliphilus. We observed two O intermediates, termed O1 and O2, having distinct chromophore structures. We show O1 displays a distorted 13-cis chromophore, while O2 contains a distorted all-trans structure. This finding indicated that the uptake and release of Na+ are achieved not by a single O intermediate but by two sequential O intermediates that are toggled via isomerization of the retinal chromophore. These results provide crucial structural insight into the unidirectional Na+ transport mediated by the chromophore-binding pocket of NaRs.
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Affiliation(s)
- Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan.
| | - Kouta Kinoue
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Ryouhei Seike
- Department of Chemistry and Applied Chemistry, Faculty 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, Sappo-ro 060-0810, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan.
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12
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Mandal M, Saito K, Ishikita H. Release of a Proton and Formation of a Low-Barrier Hydrogen Bond between Tyrosine D and D2-His189 in Photosystem II. ACS PHYSICAL CHEMISTRY AU 2022; 2:423-429. [PMID: 36855688 PMCID: PMC9955220 DOI: 10.1021/acsphyschemau.2c00019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In photosystem II (PSII), the second-lowest oxidation state (S1) of the oxygen-evolving Mn4CaO5 cluster is the most stable, as the radical form of the redox-active D2-Tyr160 is considered to be a candidate that accepts an electron from the lowest oxidation state (S0) in the dark. Using quantum mechanical/molecular mechanical calculations, we investigated the redox potential (E m) of TyrD and its H-bond partner, D2-His189. The potential energy profile indicates that the release of a proton from the TyrD...D2-His189 pair leads to the formation of a low-barrier H-bond. The E m depends on the H+ position along the low-barrier H-bond, e.g., 680 mV when the H+ is at the D2-His189 moiety and 800 mV when the H+ is at the TyrD moiety, which can explain why TyrD mediates both the S0 to S1 oxidation and the S2 to S1 reduction.
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Affiliation(s)
- Manoj Mandal
- Department
of Chemical, Biological & Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, West Bengal, India
| | - Keisuke Saito
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan,Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Hiroshi Ishikita
- Research
Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan,Department
of Applied Chemistry, The University of
Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan,. Tel: +81-3-5452-5056. Fax: +81-3-5452-5083
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13
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Absorption wavelength along chromophore low-barrier hydrogen bonds. iScience 2022; 25:104247. [PMID: 35521532 PMCID: PMC9062252 DOI: 10.1016/j.isci.2022.104247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 03/18/2022] [Accepted: 04/07/2022] [Indexed: 11/22/2022] Open
Abstract
In low-barrier hydrogen bonds (H-bonds), the pKa values for the H-bond donor and acceptor moieties are nearly equal, whereas the redox potential values depend on the H+ position. Spectroscopic details of low-barrier H-bonds remain unclear. Here, we report the absorption wavelength along low-barrier H-bonds in protein environments, using a quantum mechanical/molecular mechanical approach. Low-barrier H-bonds form between Glu46 and p-coumaric acid (pCA) in the intermediate pRCW state of photoactive yellow protein and between Asp116 and the retinal Schiff base in the intermediate M-state of the sodium-pumping rhodopsin KR2. The H+ displacement of only ∼0.4 Å, which does not easily occur without low-barrier H-bonds, is responsible for the ∼50 nm-shift in the absorption wavelength. This may be a basis of how photoreceptor proteins have evolved to proceed photocycles using abundant protons. The low-barrier H-bond formation is a prerequisite for proton transfer How the absorption wavelength changes as H+ moves is an open question The H+ displacement of ∼0.4 Å leads to the absorption wavelength shift of ∼50 nm The localization of the molecular orbitals plays a key role in the wavelength shift
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14
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Tsuneishi T, Takahashi M, Tsujimura M, Kojima K, Ishikita H, Takeuchi Y, Sudo Y. Exploring the Retinal Binding Cavity of Archaerhodopsin-3 by Replacing the Retinal Chromophore With a Dimethyl Phenylated Derivative. Front Mol Biosci 2022; 8:794948. [PMID: 34988122 PMCID: PMC8721008 DOI: 10.3389/fmolb.2021.794948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
Rhodopsins act as photoreceptors with their chromophore retinal (vitamin-A aldehyde) and they regulate light-dependent biological functions. Archaerhodopsin-3 (AR3) is an outward proton pump that has been widely utilized as a tool for optogenetics, a method for controlling cellular activity by light. To characterize the retinal binding cavity of AR3, we synthesized a dimethyl phenylated retinal derivative, (2E,4E,6E,8E)-9-(2,6-Dimethylphenyl)-3,7-dimethylnona-2,4,6,8-tetraenal (DMP-retinal). QM/MM calculations suggested that DMP-retinal can be incorporated into the opsin of AR3 (archaeopsin-3, AO3). Thus, we introduced DMP-retinal into AO3 to obtain the non-natural holoprotein (AO3-DMP) and compared some molecular properties with those of AO3 with the natural A1-retinal (AO3-A1) or AR3. Light-induced pH change measurements revealed that AO3-DMP maintained slow outward proton pumping. Noteworthy, AO3-DMP had several significant changes in its molecular properties compared with AO3-A1 as follows; 1) spectroscopic measurements revealed that the absorption maximum was shifted from 556 to 508 nm and QM/MM calculations showed that the blue-shift was due to the significant increase in the HOMO-LUMO energy gap of the chromophore with the contribution of some residues around the chromophore, 2) time-resolved spectroscopic measurements revealed the photocycling rate was significantly decreased, and 3) kinetical spectroscopic measurements revealed the sensitivity of the chromophore binding Schiff base to attack by hydroxylamine was significantly increased. The QM/MM calculations show that a cavity space is present at the aromatic ring moiety in the AO3-DMP structure whereas it is absent at the corresponding β-ionone ring moiety in the AO3-A1 structure. We discuss these alterations of the difference in interaction between the natural A1-retinal and the DMP-retinal with binding cavity residues.
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Affiliation(s)
- Taichi Tsuneishi
- Laboratory of Biophysical Chemistry, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Masataka Takahashi
- Laboratory of Synthetic and Medicinal Chemistry, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Masaki Tsujimura
- Department of Applied Chemistry, The University of Tokyo, Tokyo, Japan
| | - Keiichi Kojima
- Laboratory of Biophysical Chemistry, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, Tokyo, Japan.,Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Yasuo Takeuchi
- Laboratory of Synthetic and Medicinal Chemistry, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
| | - Yuki Sudo
- Laboratory of Biophysical Chemistry, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan
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15
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Cho SG, Shim JG, Choun K, Meas S, Kang KW, Kim JH, Cho HS, Jung KH. Discovery of a new light-driven Li +/Na +-pumping rhodopsin with DTG motif. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 223:112285. [PMID: 34411952 DOI: 10.1016/j.jphotobiol.2021.112285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 07/31/2021] [Accepted: 08/10/2021] [Indexed: 11/17/2022]
Abstract
Microbial pumping rhodopsin is a seven-transmembrane retinal binding protein, which is light-driven ion pump with a functional key motif. Ion-pumping with the key motif and charged amino acids in the rhodopsin is biochemically important. The rhodopsins with DTG motif have been discovered in various eubacteria, and they function as H+ pump. Especially, the DTG motif rhodopsins transported H+ despite the replacement of a proton donor by Gly. We investigated Methylobacterium populi rhodopsin (MpR) in one of the DTG motif rhodopsin clades. To determine which ions the MpR transport, we tested with various monovalent ion solutions and determined that MpR transports Li+/Na+. By replacing the three negatively charged residues residues which are located in helix B, Glu32, Glu33, and Asp35, we concluded that the residues play a critical role in the transport of Li+/Na+. The MpR E33Q transported H+ in place of Li+/Na+, suggesting that Glu33 is a Li+/Na+ binding site on the cytoplasmic side. Gly93 in MpR was replaced by Asp to convert from the Li+/Na+ pump to the H+ pump, resulting in MpR G93D transporting H+. Dissociation constant (Kd) values of Na+ for MpR WT and E33Q were determined to be 4.0 and 72.5 mM, respectively. These results indicated the mechanism by which MpR E33Q transports H+. Up to now, various ion-pumping rhodopsins have been discovered, and Li+/Na+-pumping rhodopsins were only found in the NDQ motif in NaR. Here, we report a new light-driven Na+ pump MpR and have determined the important residues required for Li+/Na+-pumping different from previously known NaR.
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Affiliation(s)
- Shin-Gyu Cho
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Jin-Gon Shim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Kimleng Choun
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Seanghun Meas
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea; Department of Biology, Faculty of Science, Royal University of Phnom Penh, Phnom Penh 12000, Cambodia
| | - Kun-Wook Kang
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Ji-Hyun Kim
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Hyun-Suk Cho
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea
| | - Kwang-Hwan Jung
- Department of Life Science and Institute of Biological Interfaces, Sogang University, Seoul 04107, Republic of Korea.
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