1
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Marín MDC, Konno M, Yawo H, Inoue K. Converting a Natural-Light-Driven Outward Proton Pump Rhodopsin into an Artificial Inward Proton Pump. J Am Chem Soc 2023; 145:10938-10942. [PMID: 37083435 DOI: 10.1021/jacs.2c12602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Microbial rhodopsins are a large family of photoreceptive membrane proteins with diverse light-regulated functions. While the most ubiquitous microbial rhodopsins are light-driven outward proton (H+) pumps, new subfamilies of microbial rhodopsins transporting H+ inwardly, i.e., light-driven inward H+ pumps, have been discovered recently. Although structural and spectroscopic studies provide insights into their ion transport mechanisms, the minimum key element(s) that determine the direction of H+ transport have not yet been clarified. Here, we conducted the first functional conversion study by substituting key amino acids in a natural outward H+-pumping rhodopsin (PspR) with those in inward H+-pumping rhodopsins. Consequently, an artificial inward H+ pump was constructed by mutating only three residues of PspR. This result indicates that these residues govern the key processes that discriminate between outward and inward H+ pumps. Spectroscopic studies revealed the presence of an inward H+-accepting residue in the H+ transport pathway and direct H+ uptake from the extracellular solvent. This finding of the simple element for determining H+ transport would provide a new basis for understanding the concept of ion transport not only by microbial rhodopsins but also by other ion-pumping proteins.
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Affiliation(s)
- María Del Carmen Marín
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hiromu Yawo
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
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2
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Halder N, Jana M, Kottekad S, Usharani D, Rath H. Metalloceneincorporated Hybrid Singly N-Methyl N-Confused Calixphyrins: Synthesis, Characterization, Protonation and Deprotonation Studies. Chem Asian J 2022; 17:e202200108. [PMID: 35312224 DOI: 10.1002/asia.202200108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 03/11/2022] [Indexed: 11/09/2022]
Abstract
Rational design and isolation of two hitherto unknown highly stable single conformer of ferrocene incorporated meso-aryl substituted singly N-methyl N-confused-calixphyrins have been achieved in quantitative yields. The solid-state crystal structure reveals the obvious trans-geometry for the meso-protons with the possibility for both the macrocycles to exist either racemic or enantiomer forms. However, thorough solution-state spectroscopic characterization strongly concludes the experimental isolation of a single isomer for both the macrocycles. The drastic modification of UV-vis spectral patterns upon imine pyrrole N protonation and amine pyrrole NH deprotonation of both the calixphyrins could pave way for these macrocycles to act as opto-electronic materials. The conformational preorganization and protonation and deprotonation induced conformational reorganization have been extensively studied by solution state spectroscopic techniques, solid state X-ray crystal structure and in depth DFT level theoretical calculations.
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Affiliation(s)
- Nyancy Halder
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A/2B Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India
| | - Manik Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A/2B Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India
| | - Sanjay Kottekad
- Department of Food Safety and Analytical Quality Control Laboratory Institution, CSIR-Central Food Technological Research Institute, Mysuru, 700020, Karnataka, India
| | - Dandamudi Usharani
- Department of Food Safety and Analytical Quality Control Laboratory Institution, CSIR-Central Food Technological Research Institute, Mysuru, 700020, Karnataka, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh, India
| | - Harapriya Rath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A/2B Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India
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3
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Bondar AN. Mechanisms of long-distance allosteric couplings in proton-binding membrane transporters. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 128:199-239. [PMID: 35034719 DOI: 10.1016/bs.apcsb.2021.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Membrane transporters that use proton binding and proton transfer for function couple local protonation change with changes in protein conformation and water dynamics. Changes of protein conformation might be required to allow transient formation of hydrogen-bond networks that bridge proton donor and acceptor pairs separated by long distances. Inter-helical hydrogen-bond networks adjust rapidly to protonation change, and ensure rapid response of the protein structure and dynamics. Membrane transporters with known three-dimensional structures and proton-binding groups inform on general principles of protonation-coupled protein conformational dynamics. Inter-helical hydrogen bond motifs between proton-binding carboxylate groups and a polar sidechain are observed in unrelated membrane transporters, suggesting common principles of coupling protonation change with protein conformational dynamics.
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Affiliation(s)
- Ana-Nicoleta Bondar
- University of Bucharest, Faculty of Physics, Măgurele, Romania; Forschungszentrum Jülich, Institute of Computational Biomedicine, Jülich, Germany.
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4
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Kikukawa T. Unique Cl - pump rhodopsin with close similarity to H + pump rhodopsin. Biophys Physicobiol 2021; 18:317-326. [PMID: 35087698 PMCID: PMC8756000 DOI: 10.2142/biophysico.bppb-v18.038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/20/2021] [Indexed: 12/01/2022] Open
Abstract
Microbial rhodopsin is a ubiquitous membrane protein in unicellular microorganisms. Similar to animal rhodopsin, this protein consists of seven transmembrane helices and the chromophore retinal. However, unlike animal rhodopsin, microbial rhodopsin acts as not only a photosignal receptor but also a light-activated ion transporter and light-switchable enzyme. In this article, the third Cl- pump microbial rhodopsin will be introduced. The physiological importance of Cl- pumps has not been clarified. Despite this, their mechanisms, especially that of the first Cl- pump halorhodopsin (HR), have been studied to characterize them as model proteins for membrane anion transporters. The third Cl- pump defines a phylogenetic cluster distinct from other microbial rhodopsins. However, this Cl- pump conserves characteristic residues for not only the Cl- pump HR but also the H+ pump bacteriorhodopsin (BR). Reflecting close similarity to BR, the third Cl- pump begins to pump H+ outwardly after single amino acid replacement. This mutation activates several residues that have no roles in the original Cl- pump function but act as important H+ relay residues in the H+ pump mutant. Thus, the third Cl- pump might be the model protein for functional differentiation because this rhodopsin seems to be the Cl- pump occurring immediately after functional differentiation from the BR-type H+ pump.
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Affiliation(s)
- Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Hokkaido 060–0810, Japan
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5
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Functional Mechanism of Cl --Pump Rhodopsin and Its Conversion into H + Pump. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:55-71. [PMID: 33398807 DOI: 10.1007/978-981-15-8763-4_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Cl--pump rhodopsin is the second discovered microbial rhodopsin. Although its physiological role has not been fully clarified, its functional mechanism has been studied as a model for anion transporters. After the success of neural activation by channel rhodopsin, the first Cl--pump halorhodopsin (HR) had become widely used as a neural silencer. The emergence of artificial and natural anion channel rhodopsins lowered the importance of HRs. However, the longer absorption maxima of approximately 585-600 nm for HRs are still advantageous for applications in mammalian brains and collaborations with neural activators possessing shorter absorption maxima. In this chapter, the variation and functional mechanisms of Cl- pumps are summarized. After the discovery of HR, Cl--pump rhodopsins were confined to only extremely halophilic haloarchaea. However, after 2014, two Cl--pump groups were newly discovered in marine and terrestrial bacteria. These Cl- pumps are phylogenetically distinct from HRs and have unique characteristics. In particular, the most recently identified Cl- pump has close similarity with the H+ pump bacteriorhodopsin and was converted into the H+ pump by a single amino acid replacement.
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6
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Besaw JE, Ou WL, Morizumi T, Eger BT, Sanchez Vasquez JD, Chu JHY, Harris A, Brown LS, Miller RJD, Ernst OP. The crystal structures of a chloride-pumping microbial rhodopsin and its proton-pumping mutant illuminate proton transfer determinants. J Biol Chem 2020; 295:14793-14804. [PMID: 32703899 DOI: 10.1074/jbc.ra120.014118] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 07/14/2020] [Indexed: 01/25/2023] Open
Abstract
Microbial rhodopsins are versatile and ubiquitous retinal-binding proteins that function as light-driven ion pumps, light-gated ion channels, and photosensors, with potential utility as optogenetic tools for altering membrane potential in target cells. Insights from crystal structures have been central for understanding proton, sodium, and chloride transport mechanisms of microbial rhodopsins. Two of three known groups of anion pumps, the archaeal halorhodopsins (HRs) and bacterial chloride-pumping rhodopsins, have been structurally characterized. Here we report the structure of a representative of a recently discovered third group consisting of cyanobacterial chloride and sulfate ion-pumping rhodopsins, the Mastigocladopsis repens rhodopsin (MastR). Chloride-pumping MastR contains in its ion transport pathway a unique Thr-Ser-Asp (TSD) motif, which is involved in the binding of a chloride ion. The structure reveals that the chloride-binding mode is more similar to HRs than chloride-pumping rhodopsins, but the overall structure most closely resembles bacteriorhodopsin (BR), an archaeal proton pump. The MastR structure shows a trimer arrangement reminiscent of BR-like proton pumps and shows features at the extracellular side more similar to BR than the other chloride pumps. We further solved the structure of the MastR-T74D mutant, which contains a single amino acid replacement in the TSD motif. We provide insights into why this point mutation can convert the MastR chloride pump into a proton pump but cannot in HRs. Our study points at the importance of precise coordination and exact location of the water molecule in the active center of proton pumps, which serves as a bridge for the key proton transfer.
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Affiliation(s)
- Jessica E Besaw
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Wei-Lin Ou
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Bryan T Eger
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Juan D Sanchez Vasquez
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Jessica H Y Chu
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Harris
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario, Canada
| | - R J Dwayne Miller
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada; Department of Physics, University of Toronto, Toronto, Ontario, Canada
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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7
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Kandori H. Retinal Proteins: Photochemistry and Optogenetics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20190292] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
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8
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Ulrich S, Osypova A, Panzarasa G, Rossi RM, Bruns N, Boesel LF. Pyranine-Modified Amphiphilic Polymer Conetworks as Fluorescent Ratiometric pH Sensors. Macromol Rapid Commun 2019; 40:e1900360. [PMID: 31523877 DOI: 10.1002/marc.201900360] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/21/2019] [Indexed: 01/04/2023]
Abstract
The fluorescent dye 8-hydroxypyrene-1,3,6-trisulfonate (pyranine) combines high photostability with ratiometric pH detection in the physiological range, making it a prime candidate for optical sensors in biomedical applications, such as pH-based chronic wound monitoring. However, pyranine's high water solubility and the difficulty of covalent attachment pose severe limitations in terms of leaching from sensor matrices. Herein, pyranine-modified nanophase-separated amphiphilic polymer conetworks (APCNs) are reported as fluorescent ratiometric pH sensors. The thin, freestanding APCN membranes composed of one hydrophilic and one hydrophobic polymer provide an optically transparent, flexible, and stable ideal matrix that enables contact between dye and aqueous environment. An active ester-based conjugation approach results in a highly homogeneous and stable pyranine modification of the APCN's hydrophilic phase. This concept effectively solves the leaching challenge for pyranine without compromising its functionality, which is demonstrated by ratiometric pH detection in the range of pH 5-9.
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Affiliation(s)
- Sebastian Ulrich
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biomimetic Membranes and Textiles, Lerchenfeldstrasse 5, 9014, St. Gallen, Switzerland.,Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700, Fribourg, Switzerland
| | - Alina Osypova
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biomimetic Membranes and Textiles, Lerchenfeldstrasse 5, 9014, St. Gallen, Switzerland
| | - Guido Panzarasa
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biomimetic Membranes and Textiles, Lerchenfeldstrasse 5, 9014, St. Gallen, Switzerland
| | - René M Rossi
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biomimetic Membranes and Textiles, Lerchenfeldstrasse 5, 9014, St. Gallen, Switzerland
| | - Nico Bruns
- Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, 1700, Fribourg, Switzerland.,Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Luciano F Boesel
- Empa, Swiss Federal Laboratories for Materials Science and Technology, Laboratory for Biomimetic Membranes and Textiles, Lerchenfeldstrasse 5, 9014, St. Gallen, Switzerland
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9
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Mizuno M, Shimoo Y, Kandori H, Mizutani Y. Effect of a bound anion on the structure and dynamics of halorhodopsin from Natronomonas pharaonis. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2019; 6:054703. [PMID: 31673569 PMCID: PMC6811361 DOI: 10.1063/1.5125621] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Abstract
Active ion transport across membranes is vital to maintaining the electrochemical gradients of ions in cells and is mediated by transmembrane proteins. Halorhodopsin (HR) functions as a light-driven inward pump for chloride ions. The protein contains all-trans-retinal bound to a specific lysine residue through a protonated Schiff base. Interaction between the bound chloride ion and the protonated Schiff base is crucial for ion transport because chloride ion movement is driven by the flipping of the protonated Schiff base upon photoisomerization. However, it remains unknown how this interaction evolves in the HR photocycle. Here, we addressed the effect of the bound anion on the structure and dynamics of HR from Natronomonas pharaonis in the early stage of the photocycle. Comparison of the chloride-bound, formate-bound, and anion-depleted forms provided insights into the interaction between the bound anion and the chromophore/protein moiety. In the unphotolyzed state, the bound anion affects the π-conjugation of the polyene chain and the hydrogen bond of the protonated Schiff base of the retinal chromophore. Picosecond time scale measurements showed that the band intensities of the W16 and W18 modes of the tryptophan residues decreased instantaneously upon photoexcitation of the formate-bound form. In contrast, these intensity decreases were delayed for the chloride-bound and anion-depleted forms. These observations suggest the stronger interactions of the bound formate ion with the retinal chromophore and the chromophore pocket. On the nanosecond to microsecond timescales, we found that the interaction between the protonated Schiff base and the bound ion is broken upon formation of the K intermediate and is recovered following translocation of the bound anion toward the protonated Schiff base in the L intermediate. Our results demonstrate that the hydrogen-bonding ability of the bound anion plays an essential role in the ion transport of light-driven anion pumps.
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Affiliation(s)
- Misao Mizuno
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yumi Shimoo
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Aichi 466-8555, Japan
| | - Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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10
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Tsukamoto T, Kikuchi C, Suzuki H, Aizawa T, Kikukawa T, Demura M. Implications for the impairment of the rapid channel closing of Proteomonas sulcata anion channelrhodopsin 1 at high Cl - concentrations. Sci Rep 2018; 8:13445. [PMID: 30194401 PMCID: PMC6128917 DOI: 10.1038/s41598-018-31742-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 08/24/2018] [Indexed: 01/15/2023] Open
Abstract
Natural anion channelrhodopsins (ACRs) have recently received increased attention because of their effectiveness in optogenetic manipulation for neuronal silencing. In this study, we focused on Proteomonas sulcata ACR1 (PsuACR1), which has rapid channel closing kinetics and a rapid recovery to the initial state of its anion channel function that is useful for rapid optogenetic control. To reveal the anion concentration dependency of the channel function, we investigated the photochemical properties of PsuACR1 using spectroscopic techniques. Recombinant PsuACR1 exhibited a Cl− dependent spectral red-shift from 531 nm at 0.1 mM to 535 nm at 1000 mM, suggesting that it binds Cl− in the initial state with a Kd of 5.5 mM. Flash-photolysis experiments revealed that the photocycle was significantly changed at high Cl− concentrations, which led not only to suppression of the accumulation of the M-intermediate involved in the Cl− non-conducting state but also to a drastic change in the equilibrium state of the other photo-intermediates. Because of this, the Cl− conducting state is protracted by one order of magnitude, which implies an impairment of the rapid channel closing of PsuACR1 in the presence of high concentrations of Cl−.
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Affiliation(s)
- Takashi Tsukamoto
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan. .,Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, 001-0021, Japan. .,Division of Macromolecular Functions, Department of Biological Sciences, School of Science, Hokkaido University, Sapporo, 060-0810, Japan. .,Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan.
| | - Chihiro Kikuchi
- Division of Macromolecular Functions, Department of Biological Sciences, School of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Hiromu Suzuki
- Division of Macromolecular Functions, Department of Biological Sciences, School of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Tomoyasu Aizawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan.,Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, 001-0021, Japan.,Division of Macromolecular Functions, Department of Biological Sciences, School of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan.,Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, 001-0021, Japan.,Division of Macromolecular Functions, Department of Biological Sciences, School of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, 060-0810, Japan.,Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, 001-0021, Japan.,Division of Macromolecular Functions, Department of Biological Sciences, School of Science, Hokkaido University, Sapporo, 060-0810, Japan.,Graduate School of Life Science, Hokkaido University, Sapporo, 060-0810, Japan
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11
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Engelhard C, Chizhov I, Siebert F, Engelhard M. Microbial Halorhodopsins: Light-Driven Chloride Pumps. Chem Rev 2018; 118:10629-10645. [DOI: 10.1021/acs.chemrev.7b00715] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | - Igor Chizhov
- Institute for Biophysical Chemistry, Hannover Medical School, OE8830 Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Friedrich Siebert
- Institut für Molekulare Medizin und Zellforschung, Sektion Biophysik, Albert-Ludwigs-Universität Freiburg, Hermann-Herderstr. 9, 79104 Freiburg, Germany
| | - Martin Engelhard
- Max Planck Institute for Molecular Physiology, Otto Hahn Str. 11, 44227 Dortmund, Germany
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12
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Nakajima Y, Tsukamoto T, Kumagai Y, Ogura Y, Hayashi T, Song J, Kikukawa T, Demura M, Kogure K, Sudo Y, Yoshizawa S. Presence of a Haloarchaeal Halorhodopsin-Like Cl - Pump in Marine Bacteria. Microbes Environ 2018; 33:89-97. [PMID: 29553064 PMCID: PMC5877348 DOI: 10.1264/jsme2.me17197] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Light-driven ion-pumping rhodopsins are widely distributed among bacteria, archaea, and eukaryotes in the euphotic zone of the aquatic environment. H+-pumping rhodopsin (proteorhodopsin: PR), Na+-pumping rhodopsin (NaR), and Cl--pumping rhodopsin (ClR) have been found in marine bacteria, which suggests that these genes evolved independently in the ocean. Putative microbial rhodopsin genes were identified in the genome sequences of marine Cytophagia. In the present study, one of these genes was heterologously expressed in Escherichia coli cells and the rhodopsin protein named Rubricoccus marinus halorhodopsin (RmHR) was identified as a light-driven inward Cl- pump. Spectroscopic assays showed that the estimated dissociation constant (Kd,int.) of this rhodopsin was similar to that of haloarchaeal halorhodopsin (HR), while the Cl--transporting photoreaction mechanism of this rhodopsin was similar to that of HR, but different to that of the already-known marine bacterial ClR. This amino acid sequence similarity also suggested that this rhodopsin is similar to haloarchaeal HR and cyanobacterial HRs (e.g., SyHR and MrHR). Additionally, a phylogenetic analysis revealed that retinal biosynthesis pathway genes (blh and crtY) belong to a phylogenetic lineage of haloarchaea, indicating that these marine Cytophagia acquired rhodopsin-related genes from haloarchaea by lateral gene transfer. Based on these results, we concluded that inward Cl--pumping rhodopsin is present in genera of the class Cytophagia and may have the same evolutionary origins as haloarchaeal HR.
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Affiliation(s)
- Yu Nakajima
- Atmosphere and Ocean research Institute (AORI), The University of Tokyo.,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, the University of Tokyo
| | - Takashi Tsukamoto
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | - Yohei Kumagai
- Atmosphere and Ocean research Institute (AORI), The University of Tokyo.,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, the University of Tokyo
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University
| | - Jaeho Song
- Department of Biological Sciences, Inha University
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University.,Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University
| | - Makoto Demura
- Faculty of Advanced Life Science, Hokkaido University.,Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University
| | - Kazuhiro Kogure
- Atmosphere and Ocean research Institute (AORI), The University of Tokyo.,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, the University of Tokyo
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University
| | - Susumu Yoshizawa
- Atmosphere and Ocean research Institute (AORI), The University of Tokyo.,Department of Natural Environmental Studies, Graduate School of Frontier Sciences, the University of Tokyo
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13
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Harris A, Saita M, Resler T, Hughes-Visentin A, Maia R, Pranga-Sellnau F, Bondar AN, Heberle J, Brown LS. Molecular details of the unique mechanism of chloride transport by a cyanobacterial rhodopsin. Phys Chem Chem Phys 2018; 20:3184-3199. [PMID: 29057415 DOI: 10.1039/c7cp06068h] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microbial rhodopsins are well known as versatile and ubiquitous light-driven ion transporters and photosensors. While the proton transport mechanism has been studied in great detail, much less is known about various modes of anion transport. Until recently, only two main groups of light-driven anion pumps were known, archaeal halorhodopsins (HRs) and bacterial chloride pumps (known as ClRs or NTQs). Last year, another group of cyanobacterial anion pumps with a very distinct primary structure was reported. Here, we studied the chloride-transporting photocycle of a representative of this new group, Mastigocladopsis repens rhodopsin (MastR), using time-resolved spectroscopy in the infrared and visible ranges and site-directed mutagenesis. We found that, in accordance with its unique amino acid sequence containing many polar residues in the transmembrane region of the protein, its photocycle features a number of unusual molecular events not known for other anion-pumping rhodopsins. It appears that light-driven chloride ion transfers by MastR are coupled with translocation of protons and water molecules as well as perturbation of several polar sidechains. Of particular interest is transient deprotonation of Asp-85, homologous to the cytoplasmic proton donor of light-driven proton pumps (such as Asp-96 of bacteriorhodopsin), which may serve as a regulatory mechanism.
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Affiliation(s)
- Andrew Harris
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada.
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14
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Nomura Y, Ito S, Teranishi M, Ono H, Inoue K, Kandori H. Low-temperature FTIR spectroscopy provides evidence for protein-bound water molecules in eubacterial light-driven ion pumps. Phys Chem Chem Phys 2018; 20:3165-3171. [DOI: 10.1039/c7cp05674e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The present FTIR study showed that eubacterial light-driven H+, Na+ and Cl− pump rhodopsins contain strongly hydrogen-bonded water molecule, the functional determinant of light-driven proton pump. This explains well the asymmetric functional conversions of light-driven ion pumps.
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Affiliation(s)
- Yurika Nomura
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Shota Ito
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Miwako Teranishi
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Hikaru Ono
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
| | - Keiichi Inoue
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
- OptoBioTechnology Research Center
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry
- Nagoya Institute of Technology
- Showa-ku
- Japan
- OptoBioTechnology Research Center
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15
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Huang H, Yang B, Ge B, Lao J, Zhou S, Huang F. Using self-cleavable ternary fusion pattern for efficient preparation of Bacteriorhodopsin. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.09.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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16
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Kaneko A, Inoue K, Kojima K, Kandori H, Sudo Y. Conversion of microbial rhodopsins: insights into functionally essential elements and rational protein engineering. Biophys Rev 2017; 9:861-876. [PMID: 29178082 DOI: 10.1007/s12551-017-0335-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 11/07/2017] [Indexed: 01/16/2023] Open
Abstract
Technological progress has enabled the successful application of functional conversion to a variety of biological molecules, such as nucleotides and proteins. Such studies have revealed the functionally essential elements of these engineered molecules, which are difficult to characterize at the level of an individual molecule. The functional conversion of biological molecules has also provided a strategy for their rational and atomistic design. The engineered molecules can be used in studies to improve our understanding of their biological functions and to develop protein-based tools. In this review, we introduce the functional conversion of membrane-embedded photoreceptive retinylidene proteins (also called rhodopsins) and discuss these proteins mainly on the basis of results obtained from our own studies. This information provides insights into the molecular mechanism of light-induced protein functions and their use in optogenetics, a technology which involves the use of light to control biological activities.
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Affiliation(s)
- Akimasa Kaneko
- Faculty of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama, 332-0012, Japan
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
- OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 466-8555, Japan
| | - Yuki Sudo
- Faculty of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama, 700-8530, Japan.
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17
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Bondar AN, Smith JC. Protonation-state-Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins. Photochem Photobiol 2017; 93:1336-1344. [DOI: 10.1111/php.12790] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 04/20/2017] [Indexed: 01/27/2023]
Affiliation(s)
- Ana-Nicoleta Bondar
- Theoretical Molecular Biophysics Group; Department of Physics; Freie Universität Berlin; Berlin Germany
| | - Jeremy C. Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics; Oak Ridge TN
- Department of Biochemistry and Cellular and Molecular Biology; University of Tennessee; Knoxville TN
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18
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Dong B, Sánchez-Magraner L, Luecke H. Structure of an Inward Proton-Transporting Anabaena Sensory Rhodopsin Mutant: Mechanistic Insights. Biophys J 2017; 111:963-72. [PMID: 27602724 DOI: 10.1016/j.bpj.2016.04.055] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 04/08/2016] [Accepted: 04/12/2016] [Indexed: 02/03/2023] Open
Abstract
Microbial rhodopsins are light-activated, seven-α-helical, retinylidene transmembrane proteins that have been identified in thousands of organisms across archaea, bacteria, fungi, and algae. Although they share a high degree of sequence identity and thus similarity in structure, many unique functions have been discovered and characterized among them. Some function as outward proton pumps, some as inward chloride pumps, whereas others function as light sensors or ion channels. Unique among the microbial rhodopsins characterized thus far, Anabaena sensory rhodopsin (ASR) is a photochromic sensor that interacts with a soluble 14-kDa cytoplasmic transducer that is encoded on the same operon. The sensor itself stably interconverts between all-trans-15-anti and 13-cis-15-syn retinal forms depending on the wavelength of illumination, although only the former participates in a photocycle with a signaling M intermediate. A mutation in the cytoplasmic half-channel of the protein, replacing Asp217 with Glu (D217E), results in the creation of a light-driven, single-photon, inward proton transporter. We present the 2.3 Å structure of dark-adapted D217E ASR, which reveals significant changes in the water network surrounding Glu217, as well as a shift in the carbon backbone near retinal-binding Lys210, illustrating a possible pathway leading to the protonation of Glu217 in the cytoplasmic half-channel, located 15 Å from the Schiff base. Crystallographic evidence for the protonation of nearby Glu36 is also discussed, which was described previously by Fourier transform infrared spectroscopy analysis. Finally, two histidine residues near the extracellular surface and their possible role in proton uptake are discussed.
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Affiliation(s)
- Bamboo Dong
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California
| | | | - Hartmut Luecke
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California.
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19
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Chen XR, Huang YC, Yi HP, Yang CS. A Unique Light-Driven Proton Transportation Signal in Halorhodopsin from Natronomonas pharaonis. Biophys J 2017; 111:2600-2607. [PMID: 28002736 DOI: 10.1016/j.bpj.2016.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 11/03/2016] [Accepted: 11/07/2016] [Indexed: 11/26/2022] Open
Abstract
Halorhodopsin (HR) is a seven-transmembrane retinylidene protein from haloarchaea that is commonly known to function as a light-driven inward chloride pump. However, previous studies have indicated that despite the general characteristics that most HRs share, HRs from distinct species differ in many aspects. We present indium-tin-oxide-based photocurrent measurements that reveal a light-induced signal generated by proton release that is observed solely in NpHR via purified protein-based assays, demonstrating that indeed HRs are not all identical. We conducted mutagenesis studies on several conserved residues that are considered critical for chloride stability among HRs. Intriguingly, the photocurrent signals were eliminated after specific point mutations. We propose an NpHR light-driven, cytoplasmic-side proton circulation model to explain the unique light-induced photocurrent recorded in NpHR. Notably, the photocurrent and various photocycle intermediates were recorded simultaneously. This approach provides a high-resolution method for further investigations of the proton-assisted chloride translocation mechanism.
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Affiliation(s)
- Xiao-Ru Chen
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Yuan-Chi Huang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Hsiu-Ping Yi
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Chii-Shen Yang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan.
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20
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Crystal structure and functional characterization of a light-driven chloride pump having an NTQ motif. Nat Commun 2016; 7:12677. [PMID: 27554809 PMCID: PMC4999514 DOI: 10.1038/ncomms12677] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 07/20/2016] [Indexed: 02/08/2023] Open
Abstract
A novel light-driven chloride-pumping rhodopsin (ClR) containing an ‘NTQ motif' in its putative ion conduction pathway has been discovered and functionally characterized in a genomic analysis study of a marine bacterium. Here we report the crystal structure of ClR from the flavobacterium Nonlabens marinus S1-08T determined under two conditions at 2.0 and 1.56 Å resolutions. The structures reveal two chloride-binding sites, one around the protonated Schiff base and the other on a cytoplasmic loop. We identify a ‘3 omega motif' formed by three non-consecutive aromatic amino acids that is correlated with the B–C loop orientation. Detailed ClR structural analyses with functional studies in E. coli reveal the chloride ion transduction pathway. Our results help understand the molecular mechanism and physiological role of ClR and provide a structural basis for optogenetic applications. The atypical rhodopsin ClR from flavobacterium Nonlabens marinus is a light-driven chloride-pumping protein. Here, the authors show that ClR crystal structure presents two chloride ion-binding sites, proposing a molecular pathway for ion transport by this light-driven pump.
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21
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Inoue K, Nomura Y, Kandori H. Asymmetric Functional Conversion of Eubacterial Light-driven Ion Pumps. J Biol Chem 2016; 291:9883-93. [PMID: 26929409 DOI: 10.1074/jbc.m116.716498] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Indexed: 12/21/2022] Open
Abstract
In addition to the well-known light-driven outward proton pumps, novel ion-pumping rhodopsins functioning as outward Na(+) and inward Cl(-) pumps have been recently found in eubacteria. They convert light energy into transmembrane electrochemical potential difference, similar to the prototypical archaeal H(+) pump bacteriorhodopsin (BR) and Cl(-) pump halorhodopsin (HR). The H(+), Na(+), and Cl(-) pumps possess the conserved respective DTE, NDQ, and NTQ motifs in the helix C, which likely serve as their functional determinants. To verify this hypothesis, we attempted functional interconversion between selected pumps from each category by mutagenesis. Introduction of the proton-pumping motif resulted in successful Na(+) → H(+) functional conversion. Introduction of the respective characteristic motifs with several additional mutations leads to successful Na(+) → Cl(-) and Cl(-) → H(+) functional conversions, whereas remaining conversions (H(+) → Na(+), H(+) → Cl(-), Cl(-) → Na(+)) were unsuccessful when mutagenesis of 4-6 residues was used. Phylogenetic analysis suggests that a H(+) pump is the common ancestor of all of these rhodopsins, from which Cl(-) pumps emerged followed by Na(+) pumps. We propose that successful functional conversions of these ion pumps are achieved exclusively when mutagenesis reverses the evolutionary amino acid sequence changes. Dependence of the observed functional conversions on the direction of evolution strongly suggests that the essential structural mechanism of an ancestral function is retained even after the gain of a new function during natural evolution, which can be evoked by a few mutations. By contrast, the gain of a new function needs accumulation of multiple mutations, which may not be easily reproduced by limited mutagenesis in vitro.
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Affiliation(s)
- Keiichi Inoue
- From the Department of Frontier Materials and OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan and PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | | | - Hideki Kandori
- From the Department of Frontier Materials and OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan and
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22
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Hasemi T, Kikukawa T, Kamo N, Demura M. Characterization of a Cyanobacterial Chloride-pumping Rhodopsin and Its Conversion into a Proton Pump. J Biol Chem 2015; 291:355-62. [PMID: 26578511 DOI: 10.1074/jbc.m115.688614] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Indexed: 11/06/2022] Open
Abstract
Light-driven ion-pumping rhodopsins are widely distributed in microorganisms and are now classified into the categories of outward H(+) and Na(+) pumps and an inward Cl(-) pump. These different types share a common protein architecture and utilize the photoisomerization of the same chromophore, retinal, to evoke photoreactions. Despite these similarities, successful pump-to-pump conversion had been confined to only the H(+) pump bacteriorhodopsin, which was converted to a Cl(-) pump in 1995 by a single amino acid replacement. In this study we report the first success of the reverse conversion from a Cl(-) pump to a H(+) pump. A novel microbial rhodopsin (MrHR) from the cyanobacterium Mastigocladopsis repens functions as a Cl(-) pump and belongs to a cluster that is far distant from the known Cl(-) pumps. With a single amino acid replacement, MrHR is converted to a H(+) pump in which dissociable residues function almost completely in the H(+) relay reactions. MrHR most likely evolved from a H(+) pump, but it has not yet been highly optimized into a mature Cl(-) pump.
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Affiliation(s)
- Takatoshi Hasemi
- From the Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Takashi Kikukawa
- From the Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Naoki Kamo
- From the Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Makoto Demura
- From the Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
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23
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Aydogan A. Synthesis and characterisation of a calix[4]pyrrole functional polystyrene via ‘click chemistry’ and its use in the extraction of halide anion salts. Supramol Chem 2015. [DOI: 10.1080/10610278.2015.1092538] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Abdullah Aydogan
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
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24
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Gaudana SB, Zarzycki J, Moparthi VK, Kerfeld CA. Bioinformatic analysis of the distribution of inorganic carbon transporters and prospective targets for bioengineering to increase Ci uptake by cyanobacteria. PHOTOSYNTHESIS RESEARCH 2015; 126:99-109. [PMID: 25399051 DOI: 10.1007/s11120-014-0059-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 11/07/2014] [Indexed: 06/04/2023]
Abstract
Cyanobacteria have evolved a carbon-concentrating mechanism (CCM) which has enabled them to inhabit diverse environments encompassing a range of inorganic carbon (Ci: [Formula: see text] and CO2) concentrations. Several uptake systems facilitate inorganic carbon accumulation in the cell, which can in turn be fixed by ribulose 1,5-bisphosphate carboxylase/oxygenase. Here we survey the distribution of genes encoding known Ci uptake systems in cyanobacterial genomes and, using a pfam- and gene context-based approach, identify in the marine (alpha) cyanobacteria a heretofore unrecognized number of putative counterparts to the well-known Ci transporters of beta cyanobacteria. In addition, our analysis shows that there is a huge repertoire of transport systems in cyanobacteria of unknown function, many with homology to characterized Ci transporters. These can be viewed as prospective targets for conversion into ancillary Ci transporters through bioengineering. Increasing intracellular Ci concentration coupled with efforts to increase carbon fixation will be beneficial for the downstream conversion of fixed carbon into value-added products including biofuels. In addition to CCM transporter homologs, we also survey the occurrence of rhodopsin homologs in cyanobacteria, including bacteriorhodopsin, a class of retinal-binding, light-activated proton pumps. Because they are light driven and because of the apparent ease of altering their ion selectivity, we use this as an example of re-purposing an endogenous transporter for the augmentation of Ci uptake by cyanobacteria and potentially chloroplasts.
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Affiliation(s)
- Sandeep B Gaudana
- DOE Plant Research Laboratories, Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA
| | - Jan Zarzycki
- DOE Plant Research Laboratories, Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Vamsi K Moparthi
- Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Cheryl A Kerfeld
- DOE Plant Research Laboratories, Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Road, East Lansing, MI, 48824, USA.
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA.
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25
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Abstract
Rhodopsins are light-sensing proteins used in optogenetics. The word "rhodopsin" originates from the Greek words "rhodo" and "opsis," indicating rose and sight, respectively. Although the classical meaning of rhodopsin is the red-colored pigment in our eyes, the modern meaning of rhodopsin encompasses photoactive proteins containing a retinal chromophore in animals and microbes. Animal and microbial rhodopsins possess 11-cis and all-trans retinal, respectively, to capture light in seven transmembrane α-helices, and photoisomerizations into all-trans and 13-cis forms, respectively, initiate each function. Ion-transporting proteins can be found in microbial rhodopsins, such as light-gated channels and light-driven pumps, which are the main tools in optogenetics. Light-driven pumps, such as archaeal H(+) pump bacteriorhodopsin (BR) and Cl(-) pump halorhodopsin (HR), were discovered in the 1970s, and their mechanism has been extensively studied. On the other hand, different kinds of H(+) and Cl(-) pumps have been found in marine bacteria, such as proteorhodopsin (PR) and Fulvimarina pelagi rhodopsin (FR), respectively. In addition, a light-driven Na(+) pump was found, Krokinobacter eikastus rhodopsin 2 (KR2). These light-driven ion-pumping microbial rhodopsins are classified as DTD, TSA, DTE, NTQ, and NDQ rhodopsins for BR, HR, PR, FR, and KR2, respectively. Recent understanding of ion-pumping microbial rhodopsins is reviewed in this paper.
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Affiliation(s)
- Hideki Kandori
- Department of Frontier Materials and OptoBioTechnology Research Center, Nagoya Institute of Technology Nagoya, Japan
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26
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Halorhodopsin pumps Cl- and bacteriorhodopsin pumps protons by a common mechanism that uses conserved electrostatic interactions. Proc Natl Acad Sci U S A 2014; 111:16377-82. [PMID: 25362051 DOI: 10.1073/pnas.1411119111] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Key mutations differentiate the functions of homologous proteins. One example compares the inward ion pump halorhodopsin (HR) and the outward proton pump bacteriorhodopsin (BR). Of the nine essential buried ionizable residues in BR, six are conserved in HR. However, HR changes three BR acids, D85 in a central cluster of ionizable residues, D96, nearer the intracellular, and E204, nearer the extracellular side of the membrane to the small, neutral amino acids T111, V122, and T230, respectively. In BR, acidic amino acids are stationary anions whose proton affinity is modulated by conformational changes, establishing a sequence of directed binding and release of protons. Multiconformation continuum electrostatics calculations of chloride affinity and residue protonation show that, in reaction intermediates where an acid is ionized in BR, a Cl(-) is bound to HR in a position near the deleted acid. In the HR ground state, Cl(-) binds tightly to the central cluster T111 site and weakly to the extracellular T230 site, recovering the charges on ionized BR-D85 and neutral E204 in BR. Imposing key conformational changes from the BR M intermediate into the HR structure results in the loss of Cl(-) from the central T111 site and the tight binding of Cl(-) to the extracellular T230 site, mirroring the changes that protonate BR-D85 and ionize E204 in BR. The use of a mobile chloride in place of D85 and E204 makes HR more susceptible to the environmental pH and salt concentrations than BR. These studies shed light on how ion transfer mechanisms are controlled through the interplay of protein and ion electrostatics.
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27
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Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown L, Kandori H. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev 2014; 114:126-63. [PMID: 24364740 PMCID: PMC3979449 DOI: 10.1021/cr4003769] [Citation(s) in RCA: 771] [Impact Index Per Article: 77.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Oliver P. Ernst
- Departments
of Biochemistry and Molecular Genetics, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Toronto, Ontario M5S 1A8, Canada
| | - David T. Lodowski
- Center
for Proteomics and Bioinformatics, Case
Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Marcus Elstner
- Institute
for Physical Chemistry, Karlsruhe Institute
of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Peter Hegemann
- Institute
of Biology, Experimental Biophysics, Humboldt-Universität
zu Berlin, Invalidenstrasse
42, 10115 Berlin, Germany
| | - Leonid
S. Brown
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Hideki Kandori
- Department
of Frontier Materials, Nagoya Institute
of Technology, Showa-ku, Nagoya 466-8555, Japan
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28
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Nakanishi T, Kanada S, Murakami M, Ihara K, Kouyama T. Large deformation of helix F during the photoreaction cycle of Pharaonis halorhodopsin in complex with azide. Biophys J 2013; 104:377-85. [PMID: 23442859 DOI: 10.1016/j.bpj.2012.12.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 12/08/2012] [Accepted: 12/11/2012] [Indexed: 02/01/2023] Open
Abstract
Halorhodopsin from Natronomonas pharaonis (pHR), a retinylidene protein that functions as a light-driven chloride ion pump, is converted into a proton pump in the presence of azide ion. To clarify this conversion, we investigated light-induced structural changes in pHR using a C2 crystal that was prepared in the presence of Cl(-) and subsequently soaked in a solution containing azide ion. When the pHR-azide complex was illuminated at pH 9, a profound outward movement (∼4 Å) of the cytoplasmic half of helix F was observed in a subunit with the EF loop facing an open space. This movement created a long water channel between the retinal Schiff base and the cytoplasmic surface, along which a proton could be transported. Meanwhile, the middle moiety of helix C moved inward, leading to shrinkage of the primary anion-binding site (site I), and the azide molecule in site I was expelled out to the extracellular medium. The results suggest that the cytoplasmic half of helix F and the middle moiety of helix C act as different types of valves for active proton transport.
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29
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Thermodynamic parameters of anion binding to halorhodopsin from Natronomonas pharaonis by isothermal titration calorimetry. Biophys Chem 2013; 172:61-7. [DOI: 10.1016/j.bpc.2013.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 01/10/2013] [Accepted: 01/14/2013] [Indexed: 11/21/2022]
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30
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Muroda K, Nakashima K, Shibata M, Demura M, Kandori H. Protein-bound water as the determinant of asymmetric functional conversion between light-driven proton and chloride pumps. Biochemistry 2012; 51:4677-84. [PMID: 22583333 DOI: 10.1021/bi300485r] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Bacteriorhodopsin (BR) and halorhodopsin (HR) are light-driven outward proton and inward chloride pumps, respectively. They have similar protein architecture, being composed of seven-transmembrane helices that bind an all-trans-retinal. BR can be converted into a chloride pump by a single amino acid replacement at position 85, suggesting that BR and HR share a common transport mechanism, and the ionic specificity is determined by the amino acid at that position. However, HR cannot be converted into a proton pump by the corresponding reverse mutation. Here we mutated 6 and 10 amino acids of HR into BR-like, whereas such multiple HR mutants never pump protons. Light-induced Fourier transform infrared spectroscopy revealed that hydrogen bonds of the retinal Schiff base and water are both strong for BR and both weak for HR. Multiple HR mutants exhibit strong hydrogen bonds of the Schiff base, but the hydrogen bond of water is still weak. We concluded that the cause of nonfunctional conversion of HR is the lack of strongly hydrogen-bonded water, the functional determinant of the proton pump.
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Affiliation(s)
- Kosuke Muroda
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan
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Yamada K, Kawanabe A, Yoshizawa S, Inoue K, Kogure K, Kandori H. Anomalous pH Effect of Blue Proteorhodopsin. J Phys Chem Lett 2012; 3:800-804. [PMID: 26286400 DOI: 10.1021/jz3000257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Proteorhodopsin (PR) is a light-driven proton pump found in marine bacteria, and thousands of PRs are classified into blue-absorbing PR (B-PR; λmax ≈ 490 nm) and green-absorbing PR (G-PR; λmax ≈ 525 nm). In this report, we present conversion of B-PR into G-PR using anomalous pH effect. B-PR in LC1-200, marine γ-proteobacteria, absorbs 497 and 513 nm maximally at pH 7 and 4, respectively, whose pH titration was reversible (pKa = 4.8). When pH was lowered from 4, the λmax was further red-shifted (528 nm at pH 2). This is unusual because blue shift occurs by chloride binding in the case of bacteriorhodopsin. Surprisingly, when pH was increased from 2 to 7, the λmax of this B-PR was further red-shifted to 540 nm, indicating that green-absorbing PR (PR540) is created only by changing pH. The present study reports the conformational flexibility of microbial rhodopsins, leading to the switch of absorbing color by a simple pH change.
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Affiliation(s)
- Keisuke Yamada
- †Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Akira Kawanabe
- †Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Susumu Yoshizawa
- ‡Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba 277-8564, Japan
| | - Kentaro Inoue
- ‡Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba 277-8564, Japan
| | - Kazuhiro Kogure
- ‡Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa-shi, Chiba 277-8564, Japan
| | - Hideki Kandori
- †Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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Aydogan A, Akar A. Tri- and Pentacalix[4]pyrroles: Synthesis, Characterization and Their Use in the Extraction of Halide Salts. Chemistry 2012; 18:1999-2005. [DOI: 10.1002/chem.201101605] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 09/21/2011] [Indexed: 11/08/2022]
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Kouyama T, Murakami M. Structural divergence and functional versatility of the rhodopsin superfamily. Photochem Photobiol Sci 2010; 9:1458-65. [PMID: 20931138 DOI: 10.1039/c0pp00236d] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Seven-transmembrane-helix retinylidene proteins, which constitute the rhodopsin superfamily, have been discovered in diverse species, including Archaea, Eubacteria, fungi, algae and animals. Some members of this super-family were specialized to function as light-driven proton pumps, light-driven chloride pumps, photoisomerases, or light-gated ion channels, where the photochemical reactions are self-completed without interactions with other proteins. Other members evolved to acquire the ability to modulate soluble cytoplasmic or membrane-embedded signal transducers. During the last decade, high-resolution crystal structures were reported for ten members of the rhodopsin superfamily; viz., four proton pumps, two chloride pumps, two microbial photosensors and two visual pigments. Comparison of these structures provides us with a hint to elucidate the common structural motif that is utilized to stabilize their tertiary structures as well as unique architectures that are relevant to specific functions.
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Affiliation(s)
- Tsutomu Kouyama
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, 464-8602, Japan.
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The branched photocycle of the slow-cycling channelrhodopsin-2 mutant C128T. J Mol Biol 2010; 398:690-702. [PMID: 20346954 DOI: 10.1016/j.jmb.2010.03.031] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 03/17/2010] [Accepted: 03/18/2010] [Indexed: 11/22/2022]
Abstract
Channelrhodopsins (ChRs) of green algae such as Chlamydomonas are used as neuroscience tools to specifically depolarize cells with light. A crude model of the ChR2 photocycle has been recently established, but details of the photoreactions are widely unknown. Here, we present the photoreactions of a slow-cycling ChR2 mutant (step function rhodopsin), with C128 replaced by threonine and 200-fold extended lifetime of the conducting-state P520. At a late state of the photocycle, a fraction of the proteins branches off into an inactive species, P380, which accumulates during prolonged illumination. At neutral pH, P380 is converted into P353, a species with a characteristic fine-structured spectrum that is interpreted as retroretinyl chromophore. The described branching reactions should be considered, when ChR is used as a neuroscience tool, especially in the case of fluorescence imaging at high light intensities.
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Kouyama T, Kanada S, Takeguchi Y, Narusawa A, Murakami M, Ihara K. Crystal Structure of the Light-Driven Chloride Pump Halorhodopsin from Natronomonas pharaonis. J Mol Biol 2010; 396:564-79. [DOI: 10.1016/j.jmb.2009.11.061] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Revised: 11/21/2009] [Accepted: 11/24/2009] [Indexed: 10/20/2022]
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Finnigan EM, Giordani S, Senge MO, McCabe T. Structural, Spectroscopic, and Anion-Binding Properties of 5,10-Porphodimethenes, An Unusual Class of Calixphyrins. J Phys Chem A 2010; 114:2464-70. [DOI: 10.1021/jp909573m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eimear M. Finnigan
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland, Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin, Dublin 2, Ireland, and Institute for Molecular Medicine, Medicinal Chemistry, Trinity Centre for Health Sciences, Trinity College Dublin, St. James’s Hospital, Dublin 8, Ireland
| | - Silvia Giordani
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland, Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin, Dublin 2, Ireland, and Institute for Molecular Medicine, Medicinal Chemistry, Trinity Centre for Health Sciences, Trinity College Dublin, St. James’s Hospital, Dublin 8, Ireland
| | - Mathias O. Senge
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland, Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin, Dublin 2, Ireland, and Institute for Molecular Medicine, Medicinal Chemistry, Trinity Centre for Health Sciences, Trinity College Dublin, St. James’s Hospital, Dublin 8, Ireland
| | - Tom McCabe
- School of Chemistry, Trinity College Dublin, Dublin 2, Ireland, Centre for Research on Adaptive Nanostructures and Nanodevices (CRANN), Trinity College Dublin, Dublin 2, Ireland, and Institute for Molecular Medicine, Medicinal Chemistry, Trinity Centre for Health Sciences, Trinity College Dublin, St. James’s Hospital, Dublin 8, Ireland
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Maiti TK, Engelhard M, Sheves M. Retinal-protein interactions in halorhodopsin from Natronomonas pharaonis: binding and retinal thermal isomerization catalysis. J Mol Biol 2009; 394:472-84. [PMID: 19766652 DOI: 10.1016/j.jmb.2009.09.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Revised: 09/07/2009] [Accepted: 09/14/2009] [Indexed: 11/29/2022]
Abstract
Halorhodopsin from Natronomonas pharaonis (NpHR) is a member of the retinal protein group and serves as a light-driven chloride pump in which chloride ions are transported through the membrane following light absorption by the retinal chromophore. In this study, we examined two main issues: (1) factors controlling the binding of the retinal chromophore to the NpHR opsin and (2) the ability of the NpHR opsin to catalyze the thermal isomerization of retinal isomers. We have revealed that the reconstitution process of pharaonis HR (NpHR) pigment from its apoprotein and all-trans retinal depends on the pH, and the process has a pK(a) of 5.8+/-0.1. It was proposed that this pK(a) is associated with the pK(a) of the lysine residue that binds the retinal chromophore (Lys256). The pigment formation is regulated by the concentration of sodium chloride, and the maximum yield was observed at 3.7 M NaCl. The low yield of pigment in a lower concentration of NaCl (<3 M) may be due to an altered conformation adopted by the apomembrane, which is not capable of forming the pigment. Unexpectedly and unlike the apomembrane of bacteriorhodopsin, NpHR opsin produces pigments with 11-cis retinal and 9-cis retinal owing to the thermal isomerization of these retinal isomers to all-trans retinal. The isomerization rate depends on the pH, and it is faster at a higher pH. The pK(a) value of the isomerization process is similar to the pK(a) of the binding process of these retinals, which suggests that Lys256 is also involved in the isomerization process. The isomerization is independent of the sodium chloride concentration. However, in the absence of sodium chloride, the apoprotein adopts such a conformation, which does not prevent the isomerization of retinal, but it prevents a covalent bond formation with the lysine residue. The rate and the thermodynamic parameter analysis of the retinal isomerization by NpHR apoprotein led to the conclusion that the apomembrane catalyzes the isomerization via a triplet mechanism.
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Affiliation(s)
- Tushar Kanti Maiti
- Department of Organic Chemistry, The Weizmann Institute of Science, Rehovot, Israel
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Sobotta C, Braun M, Tittor J, Oesterhelt D, Zinth W. Influence of the charge at D85 on the initial steps in the photocycle of bacteriorhodopsin. Biophys J 2009; 97:267-76. [PMID: 19580764 DOI: 10.1016/j.bpj.2009.04.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 03/25/2009] [Accepted: 04/06/2009] [Indexed: 10/20/2022] Open
Abstract
Studies have shown that trans-cis isomerization of retinal is the primary photoreaction in the photocycle of the light-driven proton pump bacteriorhodopsin (BR) from Halobacterium salinarum, as well as in the photocycle of the chloride pump halorhodopsin (HR). The transmembrane proteins HR and BR show extensive structural similarities, but differ in the electrostatic surroundings of the retinal chromophore near the protonated Schiff base. Point mutation of BR of the negatively charged aspartate D85 to a threonine T (D85T) in combination with variation of the pH value and anion concentration is used to study the ultrafast photoisomerization of BR and HR for well-defined electrostatic surroundings of the retinal chromophore. Variations of the pH value and salt concentration allow a switch in the isomerization dynamics of the BR mutant D85T between BR-like and HR-like behaviors. At low salt concentrations or a high pH value (pH 8), the mutant D85T shows a biexponential initial reaction similar to that of HR. The combination of high salt concentration and a low pH value (pH 6) leads to a subpopulation of 25% of the mutant D85T whose stationary and dynamic absorption properties are similar to those of native BR. In this sample, the combination of low pH and high salt concentration reestablishes the electrostatic surroundings originally present in native BR, but only a minor fraction of the D85T molecules have the charge located exactly at the position required for the BR-like fast isomerization reaction. The results suggest that the electrostatics in the native BR protein is optimized by evolution. The accurate location of the fixed charge at the aspartate D85 near the Schiff base in BR is essential for the high efficiency of the primary reaction.
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Affiliation(s)
- Constanze Sobotta
- Lehrstuhl für BioMolekulare Optik, Fakultät für Physik, Ludwig-Maximilians-Universität München, Munich, Germany
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Nakashima K, Nakamura T, Takeuchi S, Shibata M, Demura M, Tahara T, Kandori H. Properties of the Anion-Binding Site of pharaonis Halorhodopsin Studied by Ultrafast Pump−Probe Spectroscopy and Low-Temperature FTIR Spectroscopy. J Phys Chem B 2009; 113:8429-34. [DOI: 10.1021/jp902596k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Keisuke Nakashima
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Takumi Nakamura
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Satoshi Takeuchi
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Mikihiro Shibata
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Makoto Demura
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Tahei Tahara
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, Molecular Spectroscopy Laboratory, Advanced Science Institute (ASI), RIKEN, Hirosawa, Wako 351-0198, Japan, and Department of Biological Sciences, Graduate School of Science, Hokkaido University, Sapporo 060-0812, Japan
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Tamogami J, Kikukawa T, Miyauchi S, Muneyuki E, Kamo N. A Tin Oxide Transparent Electrode Provides the Means for Rapid Time-resolved pH Measurements: Application to Photoinduced Proton Transfer of Bacteriorhodopsin and Proteorhodopsin. Photochem Photobiol 2009; 85:578-89. [DOI: 10.1111/j.1751-1097.2008.00520.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Radu I, Schleeger M, Bolwien C, Heberle J. Time-resolved methods in biophysics. 10. Time-resolved FT-IR difference spectroscopy and the application to membrane proteins. Photochem Photobiol Sci 2009; 8:1517-28. [DOI: 10.1039/b9pp00050j] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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42
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Abstract
In oxygenic photosynthesis, photosystem II (PSII) is the multisubunit membrane protein responsible for the oxidation of water to O2 and the reduction of plastoquinone to plastoquinol. One electron charge separation in the PSII reaction center is coupled to sequential oxidation reactions at the oxygen-evolving complex (OEC), which is composed of four manganese ions and one calcium ion. The sequentially oxidized forms of the OEC are referred to as the S(n) states. S(1) is the dark-adapted state of the OEC. Flash-induced oxygen production oscillates with period four and occurs during the S(3) to S(0) transition. Chloride plays an important, but poorly understood role in photosynthetic water oxidation. Chloride removal is known to block manganese oxidation during the S(2) to S(3) transition. In this work, we have used azide as a probe of proton transfer reactions in PSII. PSII was sulfate-treated to deplete chloride and then treated with azide. Steady state oxygen evolution measurements demonstrate that azide inhibits oxygen evolution in a chloride-dependent manner and that azide is a mixed or noncompetitive inhibitor. This result is consistent with two azide binding sites, one at which azide competes with chloride and one at which azide and chloride do not compete. At pH 7.5, the K(i) for the competing site was estimated as 1 mM, and the K(i)' for the uncompetitive site was estimated as 8 mM. Vibrational spectroscopy was then used to monitor perturbations in the frequency and amplitude of the azide antisymmetric stretching band. These changes were induced by laser-induced charge separation in the PSII reaction center. The results suggest that azide is involved in proton transfer reactions, which occur before manganese oxidation, on the donor side of chloride-depleted PSII.
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43
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Aydogan A, Sessler JL, Akar A, Lynch V. Calix[4]pyrroles with Long Alkyl Chains: Synthesis, Characterization, and Anion Binding Studies. Supramol Chem 2008. [DOI: 10.1080/10610270701429789] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- A. Aydogan
- a Faculty of Science and Letters, Istanbul Technical University, Department of Chemistry , Maslak, 34469, Istanbul, Turkey
| | - J. L. Sessler
- b Institute of Cellular and Molecular Biology, The University of Texas at Austin, Department of Chemistry and Biochemistry , 1 University Station-A5300, Austin, TX, 78712-0165, USA
| | - A. Akar
- a Faculty of Science and Letters, Istanbul Technical University, Department of Chemistry , Maslak, 34469, Istanbul, Turkey
| | - V. Lynch
- b Institute of Cellular and Molecular Biology, The University of Texas at Austin, Department of Chemistry and Biochemistry , 1 University Station-A5300, Austin, TX, 78712-0165, USA
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Muneda N, Shibata M, Demura M, Kandori H. Internal Water Molecules of the Proton-Pumping Halorhodopsin in the Presence of Azide. J Am Chem Soc 2006; 128:6294-5. [PMID: 16683775 DOI: 10.1021/ja060253d] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the FTIR study of rhodopsins, we have so far found that strongly hydrogen-bonded water molecules (O-D stretch at <2400 cm-1) are only present in the proteins exhibiting proton-pumping activity. Halorhodopsin (HR) is a light-driven chloride pump in haloarchaea, which does not possess such water molecules. On the other hand, it is known that addition of azide converts HR into a proton pump. Although the mechanism has not been understood, we observed strongly hydrogen-bonded water molecules in the azide-bound HR of Natronobacterium pharaonis (pHR). This finding is consistent with the previous results, implying that the presence of strongly hydrogen-bonded water molecules is requested for the proton-pumping function of rhodopsins.
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Affiliation(s)
- Norikazu Muneda
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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45
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Brown LS, Jung KH. Bacteriorhodopsin-like proteins of eubacteria and fungi: the extent of conservation of the haloarchaeal proton-pumping mechanism. Photochem Photobiol Sci 2006; 5:538-46. [PMID: 16761082 DOI: 10.1039/b514537f] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A stereotypical image of a retinal-binding proton pump derived from extensive studies of halobacterial ion-transporting and sensory rhodopsins is a fast-cycling protein which possesses two strategically placed carboxylic acids serving as proton donor and acceptor for the retinal Schiff base. We review recent biophysical and bioinformatic data on the novel eubacterial and eucaryotic rhodopsins to analyze the extent of conservation of the haloarchaeal mechanism of transmembrane proton transport. We show that only the most essential elements of the haloarchaeal proton-pumping machinery are conserved universally, and that a mere presence of these elements in primary structures does not guarantee the proton-pumping ability.
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Affiliation(s)
- Leonid S Brown
- Department of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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Magyari K, Simon V, Váró G. The influence of the halide ions on the photochemical reaction cycle of pharaonis halorhodopsin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2006; 82:16-20. [PMID: 16219469 DOI: 10.1016/j.jphotobiol.2005.08.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2005] [Revised: 08/04/2005] [Accepted: 08/08/2005] [Indexed: 11/27/2022]
Abstract
Sodium salt of chloride, bromide and iodide were used to elucidate the effect of the size of the anion on the binding to pharaonis halorhodopsin and its transport during the photocycle of this retinal protein. Spectroscopic titration revealed an apparent strong binding constant of 2 mM for chloride, 0.23 mM for bromide and 5 mM for iodide. In the case of iodide a second, week binding constant of about 10 M could be estimated. This second binding constant was similar to that observed earlier for nitrate. By changing the halide ions, only the transitions in the second half of the photocycle were affected, which contained intermediates N, O, and HR'. The O to HR' transition becomes faster with increasing ion volume, meaning that the ion uptake is accelerated. This effect shows a direct correlation with the ion radius. With increasing ion concentration the N-O-HR' equilibrium changed in such a way that the accumulated O tended to decrease. This tendency was overruled in iodide, by the appearance of the second binding constant. The increasing iodide concentration, up to 100mM decreases the accumulation of the intermediate O, due to kinetic reasons, but at higher ion concentration the amount of O increases, although its decay becomes faster. This effect correlates with the appearance of the second iodide bound to the protein.
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Affiliation(s)
- Klára Magyari
- Department of Physics, University "Babes-Bolyai" Cluj-Napoca, Romania
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47
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Szakács J, Lakatos M, Ganea C, Váró G. Kinetic isotope effects in the photochemical reaction cycle of ion transporting retinal proteins. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2005; 79:145-50. [PMID: 15878119 DOI: 10.1016/j.jphotobiol.2005.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2004] [Revised: 01/05/2005] [Accepted: 01/06/2005] [Indexed: 11/28/2022]
Abstract
The kinetics of the photochemical reaction cycle of the bacteriorhodopsin, pharaonis halorhodopsin and proteorhodopsin were determined in H2O and D2O at low and high pH, to get insight in the proton dependent steps of the transport process. While all the steps of the bacteriorhodopsin photocycle at normal pH exhibited a strong isotope effect, the proton uptake step of the photocycle, measured at high pH, became independent of deuterium exchange, making plausible that this step, at low proton concentration, becomes concentration dependent, not mobility dependent. The proton transporting photocycle of the proteorhodopsin at its normal pH (9.5) shows a marked deuterium effect, while at high pH (12.2) this effect almost totally disappears. It was shown earlier that the proton uptake step of the proteorhodopsin is at the rise of the N form. As the proton concentration decreases with rising pH this step becomes the rate limiting, proton concentration dependent step, hiding all the other isotope dependent components. In the case of halorhodopsin in all the chloride, nitrate and proton transporting conditions the photocycle was not strongly affected by the deuterium exchange. While in the cases of the first two ions this seems normal, the absence of the deuterium effect in the case of the proton transporting photocycle was a puzzle. The only plausible explanation is that in the presence of azide the halorhodopsin transports not the proton, but a negatively charged ion the OH-, the mass and mobility of which is only slightly influenced by the deuterium exchange.
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Affiliation(s)
- Júliánna Szakács
- Department of Biophysics, University of Medicine and Pharmacy, Tg. Mures, Romania
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48
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Bálint Z, Lakatos M, Ganea C, Lanyi JK, Váró G. The nitrate transporting photochemical reaction cycle of the pharaonis halorhodopsin. Biophys J 2004; 86:1655-63. [PMID: 14990493 PMCID: PMC1304001 DOI: 10.1016/s0006-3495(04)74234-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Time-resolved spectroscopy, absorption kinetic and electric signal measurement techniques were used to study the nitrate transporting photocycle of the pharaonis halorhodopsin. The spectral titration reveals two nitrate-binding constants, assigned to two independent binding sites. The high-affinity binding site (K(a) = 11 mM) contributes to the appearance of the nitrate transporting photocycle, whereas the low-affinity constant (having a K(a) of approximately 7 M) slows the last decay process in the photocycle. Although the spectra of the intermediates are not the same as those found in the chloride transporting photocycle, the sequence of the intermediates and the energy diagrams are similar. The differences in spectra and energy levels can be attributed to the difference in the size of the transported chloride or nitrate. Electric signal measurements show that a charge is transferred across the membrane during the photocycle, as expected. A new observation is an apparent release and rebinding of a small fraction of the retinal, inside the retinal pocket, during the photocycle. The release occurs during the N-to-O transition, whereas the rebinding happens in several seconds, well after the other steps of the photocycle are over.
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Affiliation(s)
- Zoltán Bálint
- Institute of Biophysics, Biological Research Center of the Hungarian Academy of Sciences, Szeged, H-6701, Hungary
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Garcia-Viloca M, Nam K, Alhambra C, Gao J. Solvent and Protein Effects on the Vibrational Frequency Shift and Energy Relaxation of the Azide Ligand in Carbonic Anhydrase. J Phys Chem B 2004. [DOI: 10.1021/jp047526g] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mireia Garcia-Viloca
- Department of Chemistry, Supercomputing Institute, and Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455, and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Kwangho Nam
- Department of Chemistry, Supercomputing Institute, and Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455, and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Cristóbal Alhambra
- Department of Chemistry, Supercomputing Institute, and Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455, and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Jiali Gao
- Department of Chemistry, Supercomputing Institute, and Digital Technology Center, University of Minnesota, Minneapolis, Minnesota 55455, and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
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Abstract
The dynamics of proton dissociation from an acidic moiety and its subsequent dispersion in the bulk is regulated by the physical chemical properties of the solvent. The solvent has to provide a potential well to accommodate the discharged proton, screen it from the negative charge of the conjugated base, and provide an efficient mode for the diffusion of the proton to the bulk. On measuring the dynamics of proton dissociation in the time-resolved domain, the kinetic analysis of the reaction can quantitate the properties of the immediate environment. In this review we implement the kinetic analysis for evaluating the properties of small cavities in proteins and the diffusion of protons within narrow channels. On the basis of this analysis,we discuss how the clustering of proton-binding sites on a surface can endow the surface with enhanced capacity to attract protons and to funnel them toward a specific site.
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Affiliation(s)
- M Gutman
- Laser Laboratory for Fast Reactions in Biochemical Systems, Department of Biochemistry, Tel-Aviv University, Tel-Aviv, Israel 69978
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