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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Tomida S, Wada A, Furutani Y. Protonation of Asp116 and distortion of the all-trans retinal chromophore in Krokinobacter eikastus rhodopsin 2 causes a redshift in absorption maximum upon dehydration. Photochem Photobiol Sci 2023; 22:2499-2517. [PMID: 37498510 DOI: 10.1007/s43630-023-00464-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/19/2023] [Indexed: 07/28/2023]
Abstract
Water is usually indispensable for protein function. For ion-pumping rhodopsins, water molecules inside the proteins play an important role in ion transportation. In addition to amino acid residues, water molecules regulate the colors of retinal proteins. It was reported that a sodium-pumping rhodopsin, Krokinobacter eikastus rhodopsin 2 (KR2), showed a color change from red to purple upon dehydration under crystalline conditions. Here, we applied comprehensive visible and IR absorption spectroscopy and resonance Raman spectroscopy to KR2 in liposomes under hydration-controlled conditions. A large increase in the hydrogen-out-of-plane (HOOP) vibration at 947 (H-C11=C12-H Au mode) and moderate increases at 893 (C7-H and C10-H) and 808 (C14-H) cm-1 were observed under dehydrated conditions, which were assigned by using systematically deuterated retinal. Moreover, the Asn variant at Asp116, which functions as a counter ion for the protonated retinal Schiff base (PRSB), caused a large redshift in the absorption maximum and constitutive increase in the HOOP modes under hydrated and dehydrated conditions. The protonation of a counter ion at Asp116 clearly causes a redshift in the absorption maximum as the all-trans retinal chromophore twists upon dehydration. Namely, the results strongly suggested that water molecules are important for maintaining the hydrogen-bonding network at the PRSB and deprotonation state of Asp116 in KR2.
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Affiliation(s)
- Sahoko Tomida
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Akimori Wada
- Laboratory of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Higashinada-ku, Kobe, 658-8558, Japan
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan.
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Ochiai S, Ichikawa Y, Tomida S, Furutani Y. Covalent Bond between the Lys-255 Residue and the Main Chain Is Responsible for Stable Retinal Chromophore Binding and Sodium-Pumping Activity of Krokinobacter Rhodopsin 2. Biochemistry 2023. [PMID: 37243673 DOI: 10.1021/acs.biochem.3c00168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Microbial rhodopsins are light-receptive proteins with various functions triggered by the photoisomerization of the retinal chromophore from the all-trans to 13-cis configuration. A retinal chromophore is covalently bound to a lysine residue in the middle of the seventh transmembrane helix via a protonated Schiff base. Bacteriorhodopsin (BR) variants lacking a covalent bond between the side chain of Lys-216 and the main chain formed purple pigments and exhibited a proton-pumping function. Therefore, the covalent bond linking the lysine residue and the protein backbone is not considered a prerequisite for microbial rhodopsin function. To further examine this hypothesis regarding the role of the covalent bond at the lysine side chain for rhodopsin functions, we investigated K255G and K255A variants of sodium-pumping rhodopsin, Krokinobacter rhodopsin 2 (KR2), with an alkylamine retinal Schiff base (prepared by mixing ethyl- or n-propylamine and retinal (EtSB or nPrSB)). The KR2 K255G variant incorporated nPrSB and EtSB as similarly to the BR variants, whereas the K255A variant did not incorporate these alkylamine Schiff bases. The absorption maximum of K255G + nPrSB was 524-516 nm, which was close to the 526 nm absorption maximum of the wild-type + all-trans retinal (ATR). However, the K255G + nPrSB did not exhibit any ion transport activity. Since the KR2 K255G variant easily released nPrSB during light illumination and did not form an O intermediate, we concluded that a covalent bond at Lys-255 is important for the stable binding of the retinal chromophore and formation of an O intermediate to achieve light-driven Na+ pump function in KR2.
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Affiliation(s)
- Shoha Ochiai
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya 466-8555, Japan
| | - Yuki Ichikawa
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya 466-8555, Japan
| | - Sahoko Tomida
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya 466-8555, Japan
| | - Yuji Furutani
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-Ku, Nagoya 466-8555, Japan
- Optobiotechnology Research Center, Nagoya Institute of Technology, Showa-Ku, Nagoya 466-8555, Japan
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Hososhima S, Abe-Yoshizumi R, Kandori H. Functional assay of light-induced ion-transport by rhodopsins. Methods Enzymol 2022; 679:331-342. [PMID: 36682869 DOI: 10.1016/bs.mie.2022.08.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Microbial rhodopsins are photoreceptive membrane proteins found from diverse microorganisms such as archaea, eubacteria, eukaryotes and viruses. Many microbial rhodopsins possess ion-transport activity by light, such as channels and pumps, and ion-transporting rhodopsins are important tools in optogenetics that control animal behavior by light. Historically, molecular mechanism of rhodopsins has been studied by spectroscopic methods for purified proteins. On the other hand, ion-transport function has to be studied by different methods. This chapter introduces two methods of functional assay of ion-transporting rhodopsins by light. One is a patch clamp method using mammalian cells, and another is an ion-transport assay using pH electrode and microbial cells. These functional assay provides fundamental data of ion-transporting rhodopsins, and thus contributes to evaluation for optogenetic tools.
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Affiliation(s)
- Shoko Hososhima
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
| | - Rei Abe-Yoshizumi
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan.
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Mizutani Y. Concerted Motions and Molecular Function: What Physical Chemistry We Can Learn from Light-Driven Ion-Pumping Rhodopsins. J Phys Chem B 2021; 125:11812-11819. [PMID: 34672596 DOI: 10.1021/acs.jpcb.1c06698] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Transmembrane ion gradients are generated and maintained by ion-pumping proteins in cells. Light-driven ion-pumping rhodopsins are retinal-containing proteins found in archaea, bacteria, and eukarya. Photoisomerization of the retinal chromophore induces structural changes in the protein, allowing the transport of ions in a particular direction. Understanding unidirectional ion transport by ion-pumping rhodopsins is an exciting challenge for biophysical chemistry. Concerted changes in ion-binding affinities of the ion-binding sites in proteins are key to unidirectional ion transport, as is the coupling between the chromophore and the protein moiety to drive the concerted motions regulating ion-binding affinities. The commonality of ion-pumping rhodopsin protein structures and the diversity of their ion-pumping functions suggest universal principles governing ion transport, which would be widely applicable to molecular systems. In this Perspective, I review the insights obtained from previous studies on rhodopsins and discuss future perspectives.
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Affiliation(s)
- Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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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. J Photochem Photobiol B 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Santra M, Seal A, Bhattacharjee K, Chakrabarty S. Structural and dynamical heterogeneity of water trapped inside Na +-pumping KR2 rhodopsin in the dark state. J Chem Phys 2021; 154:215101. [PMID: 34240976 DOI: 10.1063/5.0044904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Photoisomerization in the retinal leads to a channel opening in rhodopsins that triggers translocation or pumping of ions/protons. Crystal structures of rhodopsins contain several structurally conserved water molecules. It has been suggested that water plays an active role in facilitating the ion pumping/translocation process by acting as a lubricant in these systems. In this paper, we systematically investigate the localization, structure, dynamics, and energetics of the water molecules along the channel for the resting/dark state of KR2 rhodopsin. By employing several microseconds long atomistic molecular dynamics simulation of this trans-membrane protein system, we demonstrate the presence of five distinct water containing pockets/cavities separated by gateways controlled by protein side-chains. There exists a strong hydrogen bonded network involving these buried water molecules and functionally important key residues. We present evidence of significant structural and dynamical heterogeneity in the water molecules present in these cavities, with very rare exchange between them. The exchange time scale of such buried water with the bulk has an extremely wide range, from tens of nanoseconds to >1.5 µs. The translational and rotational dynamics of buried water are found to be strongly dependent on the protein cavity size and local interactions with a classic signature of trapped diffusion and rotational anisotropy.
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Affiliation(s)
- Mantu Santra
- School of Chemical and Materials Sciences, Indian Institute of Technology Goa, Ponda, Goa 403401, India
| | - Aniruddha Seal
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, Odisha, India
| | - Kankana Bhattacharjee
- Department of Chemical, Biological & Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, West Bengal, India
| | - Suman Chakrabarty
- Department of Chemical, Biological & Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, West Bengal, India
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Tomida S, Ito S, Mato T, Furutani Y, Inoue K, Kandori H. Infrared spectroscopic analysis on structural changes around the protonated Schiff base upon retinal isomerization in light-driven sodium pump KR2. Biochimica et Biophysica Acta (BBA) - Bioenergetics 2020; 1861:148190. [DOI: 10.1016/j.bbabio.2020.148190] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 01/30/2020] [Accepted: 03/13/2020] [Indexed: 10/24/2022]
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Maliar N, Kovalev K, Baeken C, Balandin T, Astashkin R, Rulev M, Alekseev A, Ilyinsky N, Rogachev A, Chupin V, Dolgikh D, Kirpichnikov M, Gordeliy V. Crystal Structure of the N112A Mutant of the Light-Driven Sodium Pump KR2. Crystals 2020; 10:496. [DOI: 10.3390/cryst10060496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The light-driven sodium pump KR2, found in 2013 in the marine bacteria Krokinobacter eikastus, serves as a model protein for the studies of the sodium-pumping microbial rhodopsins (NaRs). KR2 possesses a unique NDQ (N112, D116, and Q123) set of the amino acid residues in the functionally relevant positions, named the NDQ motif. The N112 was shown to determine the Na+/H+ selectivity and pumping efficiency of the protein. Thus, N112A mutation converts KR2 into an outward proton pump. However, no structural data on the functional conversions of the light-driven sodium pumps are available at the moment. Here we present the crystal structure of the N112A mutant of KR2 in the ground state at the resolution of 2.4 Å. The structure revealed a minor deflection in the central part of the helix C and a double conformation of the L74 residue in the mutant. The organization of the retinal Schiff base and neighboring water molecules is preserved in the ground state of KR2-N112A. The presented data provide structural insights into the effects of the alterations of the characteristic NDQ motif of NaRs. Our findings also demonstrate that for the rational design of the KR2 variants with modified ion selectivity for optogenetic applications, the structures of the intermediate states of both the protein and its functional variants are required.
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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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Skopintsev P, Ehrenberg D, Weinert T, James D, Kar RK, Johnson PJM, Ozerov D, Furrer A, Martiel I, Dworkowski F, Nass K, Knopp G, Cirelli C, Arrell C, Gashi D, Mous S, Wranik M, Gruhl T, Kekilli D, Brünle S, Deupi X, Schertler GFX, Benoit RM, Panneels V, Nogly P, Schapiro I, Milne C, Heberle J, Standfuss J. Femtosecond-to-millisecond structural changes in a light-driven sodium pump. Nature 2020; 583:314-8. [DOI: 10.1038/s41586-020-2307-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 04/16/2020] [Indexed: 01/03/2023]
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15
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Kovalev K, Astashkin R, Gushchin I, Orekhov P, Volkov D, Zinovev E, Marin E, Rulev M, Alekseev A, Royant A, Carpentier P, Vaganova S, Zabelskii D, Baeken C, Sergeev I, Balandin T, Bourenkov G, Carpena X, Boer R, Maliar N, Borshchevskiy V, Büldt G, Bamberg E, Gordeliy V. Molecular mechanism of light-driven sodium pumping. Nat Commun 2020; 11:2137. [PMID: 32358514 PMCID: PMC7195465 DOI: 10.1038/s41467-020-16032-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 04/03/2020] [Indexed: 11/13/2022] Open
Abstract
The light-driven sodium-pumping rhodopsin KR2 from Krokinobacter eikastus is the only non-proton cation active transporter with demonstrated potential for optogenetics. However, the existing structural data on KR2 correspond exclusively to its ground state, and show no sodium inside the protein, which hampers the understanding of sodium-pumping mechanism. Here we present crystal structure of the O-intermediate of the physiologically relevant pentameric form of KR2 at the resolution of 2.1 Å, revealing a sodium ion near the retinal Schiff base, coordinated by N112 and D116 of the characteristic NDQ triad. We also obtained crystal structures of D116N and H30A variants, conducted metadynamics simulations and measured pumping activities of putative pathway mutants to demonstrate that sodium release likely proceeds alongside Q78 towards the structural sodium ion bound between KR2 protomers. Our findings highlight the importance of pentameric assembly for sodium pump function, and may be used for rational engineering of enhanced optogenetic tools.
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Affiliation(s)
- Kirill Kovalev
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institute of Crystallography, RWTH Aachen University, Aachen, Germany
| | - Roman Astashkin
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ivan Gushchin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Philipp Orekhov
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Dmytro Volkov
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Egor Zinovev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Egor Marin
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Maksim Rulev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- European Synchrotron Radiation Facility Grenoble, Grenoble, France
| | - Alexey Alekseev
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Institute of Crystallography, RWTH Aachen University, Aachen, Germany
| | - Antoine Royant
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- European Synchrotron Radiation Facility Grenoble, Grenoble, France
| | - Philippe Carpentier
- European Synchrotron Radiation Facility Grenoble, Grenoble, France
- Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Laboratoire Chimie et Biologie des Métaux (LCBM), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Svetlana Vaganova
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Dmitrii Zabelskii
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Christian Baeken
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Ilya Sergeev
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Taras Balandin
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Gleb Bourenkov
- European Molecular Biology Laboratory, Hamburg unit c/o DESY, Hamburg, Germany
| | - Xavier Carpena
- XALOC beamline, ALBA synchrotron (CELLS), Cerdanyola del Valles, Catalunya, Spain
| | - Roeland Boer
- XALOC beamline, ALBA synchrotron (CELLS), Cerdanyola del Valles, Catalunya, Spain
| | - Nina Maliar
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Valentin Borshchevskiy
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Georg Büldt
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Ernst Bamberg
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France.
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany.
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany.
- Research Center for Molecular Mechanisms of Aging and Age-related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
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16
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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17
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Kovalev K, Polovinkin V, Gushchin I, Alekseev A, Shevchenko V, Borshchevskiy V, Astashkin R, Balandin T, Bratanov D, Vaganova S, Popov A, Chupin V, Büldt G, Bamberg E, Gordeliy V. Structure and mechanisms of sodium-pumping KR2 rhodopsin. Sci Adv 2019; 5:eaav2671. [PMID: 30989112 PMCID: PMC6457933 DOI: 10.1126/sciadv.aav2671] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 02/21/2019] [Indexed: 05/20/2023]
Abstract
Rhodopsins are the most universal biological light-energy transducers and abundant phototrophic mechanisms that evolved on Earth and have a remarkable diversity and potential for biotechnological applications. Recently, the first sodium-pumping rhodopsin KR2 from Krokinobacter eikastus was discovered and characterized. However, the existing structures of KR2 are contradictory, and the mechanism of Na+ pumping is not yet understood. Here, we present a structure of the cationic (non H+) light-driven pump at physiological pH in its pentameric form. We also present 13 atomic structures and functional data on the KR2 and its mutants, including potassium pumps, which show that oligomerization of the microbial rhodopsin is obligatory for its biological function. The studies reveal the structure of KR2 at nonphysiological low pH where it acts as a proton pump. The structure provides new insights into the mechanisms of microbial rhodopsins and opens the way to a rational design of novel cation pumps for optogenetics.
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Affiliation(s)
- Kirill Kovalev
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Vitaly Polovinkin
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
| | - Ivan Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Alexey Alekseev
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Vitaly Shevchenko
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | | | - Roman Astashkin
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Taras Balandin
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
| | - Dmitry Bratanov
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
| | - Svetlana Vaganova
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
| | - Alexander Popov
- European Synchrotron Radiation Facility, 38043 Grenoble, France
| | - Vladimir Chupin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Georg Büldt
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
| | - Ernst Bamberg
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Corresponding author. (V.G.); (E.B.)
| | - Valentin Gordeliy
- Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia
- Corresponding author. (V.G.); (E.B.)
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18
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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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19
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Karasuyama M, Inoue K, Nakamura R, Kandori H, Takeuchi I. Understanding Colour Tuning Rules and Predicting Absorption Wavelengths of Microbial Rhodopsins by Data-Driven Machine-Learning Approach. Sci Rep 2018; 8:15580. [PMID: 30349075 DOI: 10.1038/s41598-018-33984-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 10/07/2018] [Indexed: 11/09/2022] Open
Abstract
The light-dependent ion-transport function of microbial rhodopsin has been widely used in optogenetics for optical control of neural activity. In order to increase the variety of rhodopsin proteins having a wide range of absorption wavelengths, the light absorption properties of various wild-type rhodopsins and their artificially mutated variants were investigated in the literature. Here, we demonstrate that a machine-learning-based (ML-based) data-driven approach is useful for understanding and predicting the light-absorption properties of microbial rhodopsin proteins. We constructed a database of 796 proteins consisting of microbial rhodopsin wildtypes and their variants. We then proposed an ML method that produces a statistical model describing the relationship between amino-acid sequences and absorption wavelengths and demonstrated that the fitted statistical model is useful for understanding colour tuning rules and predicting absorption wavelengths. By applying the ML method to the database, two residues that were not considered in previous studies are newly identified to be important to colour shift.
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20
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Tomida S, Ito S, Inoue K, Kandori H. Hydrogen-bonding network at the cytoplasmic region of a light-driven sodium pump rhodopsin KR2. Biochim Biophys Acta Bioenerg 2018; 1859:684-691. [PMID: 29852143 DOI: 10.1016/j.bbabio.2018.05.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/11/2018] [Accepted: 05/24/2018] [Indexed: 01/15/2023]
Abstract
Light-driven sodium-pumping rhodopsins are able to actively transport sodium ions. Structure/function studies of Krokinobacter eikastus rhodopsin 2 (KR2) identified N61 and G263 at the cytoplasmic surface constituting the "Ion-selectivity filter" for sodium ions, while retinal Schiff base acts as the light "Switch and Gate" for transport of sodium ions. Q123 is located between the two regions, and plays an important role for the pump function, which was implicated by functional, spectroscopic, X-ray crystallographic and computational studies. According to the atomic structure of KR2, Q123 is involved in the hydrogen-bonding network at the cytoplasmic region, together with S64, protein-bound waters, and peptide carbonyl of K255 bound to the chromophore. To gain the detailed structural information around Q123, here we compared light-induced difference Fourier-transform infrared (FTIR) spectra at 77 K between the wild-type (WT) and mutant proteins of KR2, such as Q123A, Q123V, and S64A. The obtained spectra were very similar between WT and these mutants, whereas the observed mutation effects enabled us to identify vibrations of the hydrogen-bonding network at the Q123 and S64 region. This is unique for KR2, not for the corresponding mutations in a light-driven proton-pump bacteriorhodopsin (BR). Hydrogen-bonding alteration is absent for the mutants of KR2, suggesting that proper inter-helical connectivity of helices B, C, and G is important for protein structural changes for sodium-pump function, which is controlled by the region around Q123.
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Affiliation(s)
- Sahoko Tomida
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Shota Ito
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; Frontier Research Institute for Material Science, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
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21
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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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22
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Suomivuori CM, Gamiz-Hernandez AP, Sundholm D, Kaila VRI. Energetics and dynamics of a light-driven sodium-pumping rhodopsin. Proc Natl Acad Sci U S A 2017; 114:7043-8. [PMID: 28611220 DOI: 10.1073/pnas.1703625114] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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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24
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Zhao H, Ma B, Ji L, Li L, Wang H, Chen D. Coexistence of light-driven Na + and H + transport in a microbial rhodopsin from Nonlabens dokdonensis. J Photochem Photobiol B 2017; 172:70-76. [PMID: 28527429 DOI: 10.1016/j.jphotobiol.2017.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 04/06/2017] [Accepted: 05/04/2017] [Indexed: 02/04/2023]
Abstract
Ion pumping microbial rhodopsins are photochemically active membrane proteins, converting light energy into ion-motive-force for ATP synthesis. Nonlabens dokdonensis rhodopsin 2 (NdR2), was recently identified as a light-driven Na+ pump. However, few functional studies on NdR2 have been conducted to elucidate its mechanism of ion transport. By reconstituting NdR2 into liposomes, we proved that NdR2 functions as a light-driven Na+/H+ pump. As Na+ concentration increased, the dominant H+ pump activity switched to the Na+ pump activity at neutral pH. The inversion of pH change by the addition of CCCP at low Na+ further suggested that the transport of Na+ and H+ should coexist in NdR2. By increasing H+ concentration, the affinity for Na+ lowered, which was indicated by an increase in KM from ~31mM at pH ~7.5, to ~74mM at pH ~6.5. These results demonstrated that Na+ transport competed with H+ transport in NdR2, which was confirmed by the dominant H+ pump activity at pH ~5.7. Kinetic experiments using pyranine uncovered a transient H+ uptake, followed by an H+ release at the millisecond time scale in both Na+ and K+ solutions. Therefore, these NdR2 results may provide functional and kinetic insights into the ion transport mechanism in light-driven Na+ pumps.
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Affiliation(s)
- Hongshen Zhao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baofu Ma
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liangliang Ji
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Longjie Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huanhuan Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Deliang Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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