1
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Bertalan É, Konno M, Del Carmen Marín M, Bagherzadeh R, Nagata T, Brown L, Inoue K, Bondar AN. Hydrogen-Bonding and Hydrophobic Interaction Networks as Structural Determinants of Microbial Rhodopsin Function. J Phys Chem B 2024; 128:7407-7426. [PMID: 39024507 DOI: 10.1021/acs.jpcb.4c02946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Microbial pump rhodopsins are highly versatile light-driven membrane proteins that couple protein conformational dynamics with ion translocation across the cell membranes. Understanding how microbial pump rhodopsins use specific amino acid residues at key functional sites to control ion selectivity and ion pumping direction is of general interest for membrane transporters, and could guide site-directed mutagenesis for optogenetics applications. To enable direct comparisons between proteins with different sequences we implement, for the first time, a unique numbering scheme for the microbial pump rhodopsin residues, NS-mrho. We use NS-mrho to show that distinct microbial pump rhodopsins typically have hydrogen-bond networks that are less conserved than anticipated from the amino acid residue conservation, whereas their hydrophobic interaction networks are largely conserved. To illustrate the role of the hydrogen-bond networks as structural elements that determine the functionality of microbial pump rhodopsins, we performed experiments, atomic-level simulations, and hydrogen bond network analyses on GR, the outward proton pump from Gloeobacter violaceus, and KR2, the outward sodium pump from Krokinobacter eikastus. The experiments indicate that multiple mutations that recover KR2 amino acid residues in GR not only fail to convert it into a sodium pump, but completely inactivate GR by abolishing photoisomerization of the retinal chromophore. This observation could be attributed to the drastically altered hydrogen-bond interaction network identified with simulations and network analyses. Taken together, our findings suggest that functional specificity could be encoded in the collective hydrogen-bond network of microbial pump rhodopsins.
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Affiliation(s)
- Éva Bertalan
- Department of Mathematics and Natural Sciences, RWTH Aachen University, Templergraben 59, 52062 Aachen, Germany
| | - Masae Konno
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa 277-8581, Chiba, Japan
| | - María Del Carmen Marín
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa 277-8581, Chiba, Japan
| | - Reza Bagherzadeh
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa 277-8581, Chiba, Japan
| | - Takashi Nagata
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa 277-8581, Chiba, Japan
| | - Leonid Brown
- Department of Physics, University of Guelph, 488 Gordon Street, Guelph, Ontario N1G 2W1, Canada
| | - Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, 5-1-5 Kashiwano-ha, Kashiwa 277-8581, Chiba, Japan
| | - Ana-Nicoleta Bondar
- Institute of Computational Biomedicine, Forschungszentrum Jülich, IAS-5/INM-9, Wilhelm-Johnen Straße, 5428 Jülich, Germany
- Faculty of Physics, University of Bucharest, Atomiştilor 405, 077125 Măgurele, Romania
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2
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Giani M, Pire C, Martínez-Espinosa RM. Bacterioruberin: Biosynthesis, Antioxidant Activity, and Therapeutic Applications in Cancer and Immune Pathologies. Mar Drugs 2024; 22:167. [PMID: 38667784 PMCID: PMC11051356 DOI: 10.3390/md22040167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 04/28/2024] Open
Abstract
Halophilic archaea, also termed haloarchaea, are a group of moderate and extreme halophilic microorganisms that constitute the major microbial populations in hypersaline environments. In these ecosystems, mainly aquatic, haloarchaea are constantly exposed to ionic and oxidative stress due to saturated salt concentrations and high incidences of UV radiation (mainly in summer). To survive under these harsh conditions, haloarchaea have developed molecular adaptations including hyperpigmentation. Regarding pigmentation, haloarchaeal species mainly synthesise the rare C50 carotenoid called bacterioruberin (BR) and its derivatives, monoanhydrobacterioruberin and bisanhydrobacterioruberin. Due to their colours and extraordinary antioxidant properties, BR and its derivatives have been the aim of research in several research groups all over the world during the last decade. This review aims to summarise the most relevant characteristics of BR and its derivatives as well as describe their reported antitumoral, immunomodulatory, and antioxidant biological activities. Based on their biological activities, these carotenoids can be considered promising natural biomolecules that could be used as tools to design new strategies and/or pharmaceutical formulas to fight against cancer, promote immunomodulation, or preserve skin health, among other potential uses.
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Affiliation(s)
- Micaela Giani
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (M.G.); (C.P.)
| | - Carmen Pire
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (M.G.); (C.P.)
- Biochemistry and Molecular Biology and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain
| | - Rosa María Martínez-Espinosa
- Multidisciplinary Institute for Environmental Studies “Ramón Margalef”, University of Alicante, Ap. 99, E-03080 Alicante, Spain; (M.G.); (C.P.)
- Biochemistry and Molecular Biology and Edaphology and Agricultural Chemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain
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3
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Morilla MJ, Ghosal K, Romero EL. More Than Pigments: The Potential of Astaxanthin and Bacterioruberin-Based Nanomedicines. Pharmaceutics 2023; 15:1828. [PMID: 37514016 PMCID: PMC10385456 DOI: 10.3390/pharmaceutics15071828] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/18/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
Carotenoids are natural products regulated by the food sector, currently used as feed dyes and as antioxidants in dietary supplements and composing functional foods for human consumption. Of the nearly one thousand carotenoids described to date, only retinoids, derived from beta carotene, have the status of a drug and are regulated by the pharmaceutical sector. In this review, we address a novel field: the transformation of xanthophylls, particularly the highly marketed astaxanthin and the practically unknown bacterioruberin, in therapeutic agents by altering their pharmacokinetics, biodistribution, and pharmacodynamics through their formulation as nanomedicines. The antioxidant activity of xanthophylls is mediated by routes different from those of the classical oral anti-inflammatory drugs such as corticosteroids and non-steroidal anti-inflammatory drugs (NSAIDs): remarkably, xanthophylls lack therapeutic activity but also lack toxicity. Formulated as nanomedicines, xanthophylls gain therapeutic activity by mechanisms other than increased bioavailability. Loaded into ad hoc tailored nanoparticles to protect their structure throughout storage and during gastrointestinal transit or skin penetration, xanthophylls can be targeted and delivered to selected inflamed cell groups, achieving a massive intracellular concentration after endocytosis of small doses of formulation. Most first reports showing the activities of oral and topical anti-inflammatory xanthophyll-based nanomedicines against chronic diseases such as inflammatory bowel disease, psoriasis, atopic dermatitis, and dry eye disease emerged between 2020 and 2023. Here we discuss in detail their preclinical performance, mostly targeted vesicular and polymeric nanoparticles, on cellular models and in vivo. The results, although preliminary, are auspicious enough to speculate upon their potential use for oral or topical administration in the treatment of chronic inflammatory diseases.
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Affiliation(s)
- Maria Jose Morilla
- Nanomedicine Research and Development Centre (NARD), Science and Technology Department, National University of Quilmes, Roque Saenz Peña 352, Bernal 1876, Argentina
| | - Kajal Ghosal
- Department of Pharmaceutical Technology, Jadavpur University, 188, Raja Subodh Chandra Mallick Rd., Jadavpur, Kolkata 700032, West Bengal, India
| | - Eder Lilia Romero
- Nanomedicine Research and Development Centre (NARD), Science and Technology Department, National University of Quilmes, Roque Saenz Peña 352, Bernal 1876, Argentina
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4
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Archaea Carotenoids: Natural Pigments with Unexplored Innovative Potential. Mar Drugs 2022; 20:md20080524. [PMID: 36005527 PMCID: PMC9410494 DOI: 10.3390/md20080524] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/21/2022] [Accepted: 08/11/2022] [Indexed: 11/29/2022] Open
Abstract
For more than 40 years, marine microorganisms have raised great interest because of their major ecological function and their numerous applications for biotechnology and pharmacology. Particularly, Archaea represent a resource of great potential for the identification of new metabolites because of their adaptation to extreme environmental conditions and their original metabolic pathways, allowing the synthesis of unique biomolecules. Studies on archaeal carotenoids are still relatively scarce and only a few works have focused on their industrial scale production and their biotechnological and pharmacological properties, while the societal demand for these bioactive pigments is growing. This article aims to provide a comprehensive review of the current knowledge on carotenoid metabolism in Archaea and the potential applications of these pigments in biotechnology and medicine. After reviewing the ecology and classification of these microorganisms, as well as their unique cellular and biochemical characteristics, this paper highlights the most recent data concerning carotenoid metabolism in Archaea, the biological properties of these pigments, and biotechnological considerations for their production at industrial scale.
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5
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Kouyama T, Ihara K. Two substates in the O intermediate of the light-driven proton pump archaerhodopsin-2. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183919. [PMID: 35304864 DOI: 10.1016/j.bbamem.2022.183919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 02/16/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
The proton pumping cycle of archaerhodopsin-2 (aR2) was investigated over a wide pH range and at different salt concentrations. We have found that two substates, which are spectroscopically and kinetically distinguishable, occur in the O intermediate. The first O-intermediate (O1) absorbs maximumly at ~580 nm, whereas the late O-intermediate (O2) absorbs maximumly at 605 nm. At neutral pH, O1 is in rapid equilibrium with the N intermediate. When the medium pH is increased, O1 becomes less stable than N and, in proportion to the amount of O1 in the dynamic equilibrium between N and O1, the formation rate of O2 decreases. By contrast, the decay rate of O2 increases ~100 folds when the pH of a low-salt membrane suspension is increased from 5.5 to 7.5 or when the salt concentration is increased to 2 M KCl. Together with our recent study on two substates in the O intermediate of bacteriorhodopsin (bR), the present study suggests that the thermally activated re-isomerization of the retinylidene chromophore into the initial all-trans configuration takes place in the O1-to-O2 transition; that is, O1 contains a distorted 13-cis chromophore. It is also found that the pKa value of the key ionizable residue (Asp101aR2, Asp96bR) in the proton uptake channel is elevated in the O1 state of aR2 as compared to the O1 state of bR. This implies that the structural property of O1 in the aR2 photocycle can be investigated over a wide pH range.
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Affiliation(s)
- Tsutomu Kouyama
- Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan.
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Nagoya 464-8602, Japan
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6
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Hoskin CEG, Schild VR, Vinals J, Bayley H. Parallel transmission in a synthetic nerve. Nat Chem 2022; 14:650-657. [PMID: 35449216 DOI: 10.1038/s41557-022-00916-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 02/21/2022] [Indexed: 01/19/2023]
Abstract
Bioelectronic devices that are tetherless and soft are promising developments in medicine, robotics and chemical computing. Here, we describe bioinspired synthetic neurons, composed entirely of soft, flexible biomaterials, capable of rapid electrochemical signal transmission over centimetre distances. Like natural cells, our synthetic neurons release neurotransmitters from their terminals, which initiate downstream reactions. The components of the neurons are nanolitre aqueous droplets and hydrogel fibres, connected through lipid bilayers. Transmission is powered at these interfaces by light-driven proton pumps and mediated by ion-conducting protein pores. By bundling multiple neurons into a synthetic nerve, we have shown that distinct signals can propagate simultaneously along parallel axons, thereby transmitting spatiotemporal information. Synthetic nerves might play roles in next-generation implants, soft machines and computing devices.
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Affiliation(s)
- Charlotte E G Hoskin
- Chemistry Department, Oxford University, Oxford, UK.,Doctoral Training Centre, Oxford University, Oxford, UK
| | | | - Javier Vinals
- Biochemistry Department, Oxford University, Oxford, UK
| | - Hagan Bayley
- Chemistry Department, Oxford University, Oxford, UK.
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7
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Kishi KE, Kim YS, Fukuda M, Inoue M, Kusakizako T, Wang PY, Ramakrishnan C, Byrne EFX, Thadhani E, Paggi JM, Matsui TE, Yamashita K, Nagata T, Konno M, Quirin S, Lo M, Benster T, Uemura T, Liu K, Shibata M, Nomura N, Iwata S, Nureki O, Dror RO, Inoue K, Deisseroth K, Kato HE. Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine. Cell 2022; 185:672-689.e23. [PMID: 35114111 PMCID: PMC7612760 DOI: 10.1016/j.cell.2022.01.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 12/13/2021] [Accepted: 01/11/2022] [Indexed: 12/24/2022]
Abstract
ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, exhibits puzzling properties (large photocurrents, red-shifted spectrum, and extreme light sensitivity) that have created new opportunities in optogenetics. ChRmine and its homologs function as ion channels but, by primary sequence, more closely resemble ion pump rhodopsins; mechanisms for passive channel conduction in this family have remained mysterious. Here, we present the 2.0 Å resolution cryo-EM structure of ChRmine, revealing architectural features atypical for channelrhodopsins: trimeric assembly, a short transmembrane-helix 3, a twisting extracellular-loop 1, large vestibules within the monomer, and an opening at the trimer interface. We applied this structure to design three proteins (rsChRmine and hsChRmine, conferring further red-shifted and high-speed properties, respectively, and frChRmine, combining faster and more red-shifted performance) suitable for fundamental neuroscience opportunities. These results illuminate the conduction and gating of pump-like channelrhodopsins and point the way toward further structure-guided creation of channelrhodopsins for applications across biology.
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Affiliation(s)
- Koichiro E Kishi
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Masahiro Fukuda
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Masatoshi Inoue
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Peter Y Wang
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Eamon F X Byrne
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Elina Thadhani
- Department of Bioengineering, Stanford University, Stanford, CA, USA; Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Joseph M Paggi
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Toshiki E Matsui
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan
| | - Keitaro Yamashita
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Takashi Nagata
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Masae Konno
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Sean Quirin
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Maisie Lo
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Tyler Benster
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Tomoko Uemura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Sakyo, Japan
| | - Kehong Liu
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Sakyo, Japan
| | - Mikihiro Shibata
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma, Kanazawa, Japan; High-Speed AFM for Biological Application Unit, Institute for Frontier Science Initiative, Kanazawa University, Kakuma, Kanazawa, Japan
| | - Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Sakyo, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Sakyo, Japan; RIKEN SPring-8 Center, Kouto, Sayo-cho, Sayo-gun, Hyogo, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA; Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Keiichi Inoue
- Institute for Solid State Physics, The University of Tokyo, Kashiwa, Japan
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA; CNC Program, Stanford University, Palo Alto, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
| | - Hideaki E Kato
- Komaba Institute for Science, The University of Tokyo, Meguro, Tokyo, Japan; Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo, Japan; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan; FOREST, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.
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8
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Abstract
Microbial rhodopsins are light-sensitive transmembrane proteins, evolutionary adapted by various organisms like archaea, bacteria, simple eukaryote, and viruses to utilize solar energy for their survival. A complete understanding of functional mechanisms of these proteins is not possible without the knowledge of their high-resolution structures, which can be primarily obtained by X-ray crystallography. This technique, however, requires high-quality crystals, growing of which is a great challenge especially in case of membrane proteins. In this chapter, we summarize methods applied for crystallization of microbial rhodopsins with the emphasis on crystallization in lipidic mesophases, also known as in meso approach. In particular, we describe in detail the methods of crystallization using lipidic cubic phase to grow both large crystals optimized for traditional crystallographic data collection and microcrystals for serial crystallography.
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Affiliation(s)
- Kirill Kovalev
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
- Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, Jülich, Germany
- JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
- Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany
| | - Roman Astashkin
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Valentin Gordeliy
- Institut de Biologie Structurale (IBS), Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA, USA.
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9
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Fujimoto KJ. Electronic Couplings and Electrostatic Interactions Behind the Light Absorption of Retinal Proteins. Front Mol Biosci 2021; 8:752700. [PMID: 34604313 PMCID: PMC8480471 DOI: 10.3389/fmolb.2021.752700] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/02/2021] [Indexed: 11/13/2022] Open
Abstract
The photo-functional chromophore retinal exhibits a wide variety of optical absorption properties depending on its intermolecular interactions with surrounding proteins and other chromophores. By utilizing these properties, microbial and animal rhodopsins express biological functions such as ion-transport and signal transduction. In this review, we present the molecular mechanisms underlying light absorption in rhodopsins, as revealed by quantum chemical calculations. Here, symmetry-adapted cluster-configuration interaction (SAC-CI), combined quantum mechanical and molecular mechanical (QM/MM), and transition-density-fragment interaction (TDFI) methods are used to describe the electronic structure of the retinal, the surrounding protein environment, and the electronic coupling between chromophores, respectively. These computational approaches provide successful reproductions of experimentally observed absorption and circular dichroism (CD) spectra, as well as insights into the mechanisms of unique optical properties in terms of chromophore-protein electrostatic interactions and chromophore-chromophore electronic couplings. On the basis of the molecular mechanisms revealed in these studies, we also discuss strategies for artificial design of the optical absorption properties of rhodopsins.
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Affiliation(s)
- Kazuhiro J Fujimoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan
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10
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Bada Juarez JF, Judge PJ, Adam S, Axford D, Vinals J, Birch J, Kwan TOC, Hoi KK, Yen HY, Vial A, Milhiet PE, Robinson CV, Schapiro I, Moraes I, Watts A. Structures of the archaerhodopsin-3 transporter reveal that disordering of internal water networks underpins receptor sensitization. Nat Commun 2021; 12:629. [PMID: 33504778 PMCID: PMC7840839 DOI: 10.1038/s41467-020-20596-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022] Open
Abstract
Many transmembrane receptors have a desensitized state, in which they are unable to respond to external stimuli. The family of microbial rhodopsin proteins includes one such group of receptors, whose inactive or dark-adapted (DA) state is established in the prolonged absence of light. Here, we present high-resolution crystal structures of the ground (light-adapted) and DA states of Archaerhodopsin-3 (AR3), solved to 1.1 Å and 1.3 Å resolution respectively. We observe significant differences between the two states in the dynamics of water molecules that are coupled via H-bonds to the retinal Schiff Base. Supporting QM/MM calculations reveal how the DA state permits a thermodynamic equilibrium between retinal isomers to be established, and how this same change is prevented in the ground state in the absence of light. We suggest that the different arrangement of internal water networks in AR3 is responsible for the faster photocycle kinetics compared to homologs.
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Affiliation(s)
- Juan F Bada Juarez
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK
| | - Peter J Judge
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK
| | - Suliman Adam
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
| | - Javier Vinals
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK
| | - James Birch
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
| | - Tristan O C Kwan
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK
- National Physical Laboratory, Hampton Road, Teddington, London, TW11 0LW, UK
| | - Kin Kuan Hoi
- Chemistry Research Laboratory, Oxford University, Mansfield Road, Oxford, OX1 3TA, UK
| | - Hsin-Yung Yen
- OMass Therapeutics, The Schrodinger Building, Oxford Science Park, Oxford, OX4 4GE, UK
| | - Anthony Vial
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, University of Montpellier, Montpellier, France
| | - Pierre-Emmanuel Milhiet
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, University of Montpellier, Montpellier, France
| | - Carol V Robinson
- Chemistry Research Laboratory, Oxford University, Mansfield Road, Oxford, OX1 3TA, UK
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics Research, Institute of Chemistry, Hebrew University of Jerusalem, Jerusalem, 9190401, Israel
| | - Isabel Moraes
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, OX11 0FA, UK.
- National Physical Laboratory, Hampton Road, Teddington, London, TW11 0LW, UK.
| | - Anthony Watts
- Biochemistry Department, Oxford University, South Parks Road, Oxford, OX1 3QU, UK.
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11
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Moopantakath J, Imchen M, Siddhardha B, Kumavath R. 16s rRNA metagenomic analysis reveals predominance of Crtl and CruF genes in Arabian Sea coast of India. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 743:140699. [PMID: 32679495 DOI: 10.1016/j.scitotenv.2020.140699] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/25/2020] [Accepted: 07/01/2020] [Indexed: 06/11/2023]
Abstract
Microbial communities perform crucial biogeochemical cycles in distinct ecosystems. Halophilic microbial communities are enriched in the saline areas. Hence, haloarchaea have been primarily studied in salterns and marine biosystems with the aim to harness haloarcheal carotenoids biosynthesis. In this study, sediment from several distinct biosystems (mangrove, seashore, estuary, river, lake, salt pan and island) across the Arabian coastal region of India were collected and analyzed though 16s rRNA metagenomic and whole genome approach to elucidated the dominant representative genre, haloarcheal diversity, and the prevalence of Crtl and CruF genes. We found that the microbial diversity in mangrove sediment (794 OTUs) was highest and lowest in lake and river (558-560 OTUs). Moreover, the bacterial domain dominated in all biosystems (96.00-99.45%). Top 10 abundant genera were involved in biochemical cycles such as sulfur, methane, ammonia, hydrocarbon degradation, and antibiotics production. The Archaea was mainly composed of Haloarchaea, Methanobacteria, Methanococci, Methanomicrobia and Crenarchaeota. Carotenoid gene, Crtl, was observed in a major portion (abundance 60%; diversity 45%) of microbial community. Interestingly, we found that all species under haloarcheal class that were represented in fresh as well as marine biosystems encodes CruF gene (bacterioruberin carotenoid). Our study demonstrates the high microbial diversity in various ecosystems, enrichment of Crtl gene, and also shows that Crtl and CruF genes are highly abundant in haloarcheal genera. The finding of ecosystems specific Crtl and CruF encoding genera opens up a promising area in bioprospecting the carotenoid derivatives from the wide range of natural biosystems.
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Affiliation(s)
- Jamseel Moopantakath
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod 671320, Kerala, India
| | - Madangchanok Imchen
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod 671320, Kerala, India
| | - Busi Siddhardha
- Department of Microbiology, School of Life Sciences, Pondicherry University, Puducherry 605014, India
| | - Ranjith Kumavath
- Department of Genomic Science, Central University of Kerala, Tejaswini Hills, Periya, Kasaragod 671320, Kerala, India.
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12
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Yun JH, Park JH, Jin Z, Ohki M, Wang Y, Lupala CS, Liu H, Park SY, Lee W. Structure-Based Functional Modification Study of a Cyanobacterial Chloride Pump for Transporting Multiple Anions. J Mol Biol 2020; 432:5273-5286. [PMID: 32721401 DOI: 10.1016/j.jmb.2020.07.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 11/16/2022]
Abstract
Understanding the structure and functional mechanisms of cyanobacterial halorhodopsin has become increasingly important, given the report that Synechocystis halorhodopsin (SyHR), a homolog of the cyanobacterial halorhodopsin from Mastigocladopsis repens (MrHR), can take up divalent ions, such as SO42-, as well as chloride ions. Here, the crystal structure of MrHR, containing a unique "TSD" chloride ion conduction motif, was determined as a homotrimer at a resolution of 1.9 Å. The detailed structure of MrHR revealed a unique trimeric topology of the light-driven chloride pump, with peculiar coordination of two water molecules and hydrogen-mediated bonds near the TSD motif, as well as a short B-C loop. Structural and functional analyses of MrHR revealed key residues responsible for the anion selectivity of cyanobacterial halorhodopsin and the involvement of two chloride ion-binding sites in the ion conduction pathway. Alanine mutant of Asn63, Pro118, and Glu182 locating in the anion inlet induce multifunctional uptake of chloride, nitrate, and sulfate ions. Moreover, the structure of N63A/P118A provides information on how SyHR promotes divalent ion transport. Our findings significantly advance the structural understanding of microbial rhodopsins with different motifs. They also provide insight into the general structural framework underlying the molecular mechanisms of the cyanobacterial chloride pump containing SyHR, the only molecule known to transport both sulfate and chloride ions.
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Affiliation(s)
- Ji-Hye Yun
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, 50 Yonsei-ro, Seoul 03722, Republic of Korea
| | - Jae-Hyun Park
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, 50 Yonsei-ro, Seoul 03722, Republic of Korea
| | - Zeyu Jin
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, 50 Yonsei-ro, Seoul 03722, Republic of Korea
| | - Mio Ohki
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Yang Wang
- Complex Systems Division, Beijing Computational Science Research Center, 10 E. Xibeiwang Rd., Haidian District, Beijing 100193, China
| | - Cecylia Severin Lupala
- Complex Systems Division, Beijing Computational Science Research Center, 10 E. Xibeiwang Rd., Haidian District, Beijing 100193, China
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Center, 10 E. Xibeiwang Rd., Haidian District, Beijing 100193, China; Department of Physics, Beijing Normal University, Haidian, Beijing, 100875, China
| | - Sam-Yong Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan.
| | - Weontae Lee
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, 50 Yonsei-ro, Seoul 03722, Republic of Korea.
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13
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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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14
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Salvador-Castell M, Tourte M, Oger PM. In Search for the Membrane Regulators of Archaea. Int J Mol Sci 2019; 20:E4434. [PMID: 31505830 PMCID: PMC6770870 DOI: 10.3390/ijms20184434] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 09/04/2019] [Accepted: 09/06/2019] [Indexed: 11/23/2022] Open
Abstract
Membrane regulators such as sterols and hopanoids play a major role in the physiological and physicochemical adaptation of the different plasmic membranes in Eukarya and Bacteria. They are key to the functionalization and the spatialization of the membrane, and therefore indispensable for the cell cycle. No archaeon has been found to be able to synthesize sterols or hopanoids to date. They also lack homologs of the genes responsible for the synthesis of these membrane regulators. Due to their divergent membrane lipid composition, the question whether archaea require membrane regulators, and if so, what is their nature, remains open. In this review, we review evidence for the existence of membrane regulators in Archaea, and propose tentative location and biological functions. It is likely that no membrane regulator is shared by all archaea, but that they may use different polyterpenes, such as carotenoids, polyprenols, quinones and apolar polyisoprenoids, in response to specific stressors or physiological needs.
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Affiliation(s)
- Marta Salvador-Castell
- Université de Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France.
- Université de Lyon, INSA de Lyon, UMR 5240, F-69621 Villeurbanne, France.
| | - Maxime Tourte
- Université de Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France.
- Université de Lyon, INSA de Lyon, UMR 5240, F-69621 Villeurbanne, France.
| | - Philippe M Oger
- Université de Lyon, CNRS, UMR 5240, F-69621 Villeurbanne, France.
- Université de Lyon, INSA de Lyon, UMR 5240, F-69621 Villeurbanne, France.
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15
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Giani M, Garbayo I, Vílchez C, Martínez-Espinosa RM. Haloarchaeal Carotenoids: Healthy Novel Compounds from Extreme Environments. Mar Drugs 2019; 17:md17090524. [PMID: 31500208 PMCID: PMC6780574 DOI: 10.3390/md17090524] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/02/2019] [Accepted: 09/02/2019] [Indexed: 01/08/2023] Open
Abstract
Haloarchaea are halophilic microorganisms belonging to the archaea domain that inhabit salty environments (mainly soils and water) all over the world. Most of the genera included in this group can produce carotenoids at significant concentrations (even wild-type strains). The major carotenoid produced by the cells is bacterioruberin (and its derivatives), which is only produced by this kind of microbes and few bacteria, like Micrococcus roseus. Nevertheless, the understanding of carotenoid metabolism in haloarchaea, its regulation, and the roles of carotenoid derivatives in this group of extreme microorganisms remains mostly unrevealed. Besides, potential biotechnological uses of haloarchaeal pigments are poorly explored. This work summarises what it has been described so far about carotenoids from haloarchaea and their production at mid- and large-scale, paying special attention to the most recent findings on the potential uses of haloarchaeal pigments in biomedicine.
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Affiliation(s)
- Micaela Giani
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain.
| | - Inés Garbayo
- Algal Biotechnology Group, University of Huelva and Marine International Campus of Excellence (CEIMAR), CIDERTA and Faculty of Sciences, 21071 Huelva, Spain.
| | - Carlos Vílchez
- Algal Biotechnology Group, University of Huelva and Marine International Campus of Excellence (CEIMAR), CIDERTA and Faculty of Sciences, 21071 Huelva, Spain.
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain.
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16
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Morizumi T, Ou WL, Van Eps N, Inoue K, Kandori H, Brown LS, Ernst OP. X-ray Crystallographic Structure and Oligomerization of Gloeobacter Rhodopsin. Sci Rep 2019; 9:11283. [PMID: 31375689 PMCID: PMC6677831 DOI: 10.1038/s41598-019-47445-5] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/24/2019] [Indexed: 01/27/2023] Open
Abstract
Gloeobacter rhodopsin (GR) is a cyanobacterial proton pump which can be potentially applied to optogenetics. We solved the crystal structure of GR and found that it has overall similarity to the homologous proton pump from Salinibacter ruber, xanthorhodopsin (XR). We identified distinct structural characteristics of GR’s hydrogen bonding network in the transmembrane domain as well as the displacement of extracellular sides of the transmembrane helices relative to those of XR. Employing Raman spectroscopy and flash-photolysis, we found that GR in the crystals exists in a state which displays retinal conformation and photochemical cycle similar to the functional form observed in lipids. Based on the crystal structure of GR, we selected a site for spin labeling to determine GR’s oligomerization state using double electron–electron resonance (DEER) spectroscopy and demonstrated the pH-dependent pentamer formation of GR. Determination of the structure of GR as well as its pentamerizing propensity enabled us to reveal the role of structural motifs (extended helices, 3-omega motif and flipped B-C loop) commonly found among light-driven bacterial pumps in oligomer formation. Here we propose a new concept to classify these pumps based on the relationship between their oligomerization propensities and these structural determinants.
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Affiliation(s)
- Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Wei-Lin Ou
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Ned Van Eps
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Keiichi Inoue
- The Institute for Solid State Physics, University of Tokyo, Kashiwa, Chiba, 277-8581, Japan
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, 464-8555, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, 464-8555, Japan
| | - Leonid S Brown
- Department of Physics, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada. .,Department of Molecular Genetics, University of Toronto, Ontario, M5S 1A8, Canada.
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17
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Wickstrand C, Nogly P, Nango E, Iwata S, Standfuss J, Neutze R. Bacteriorhodopsin: Structural Insights Revealed Using X-Ray Lasers and Synchrotron Radiation. Annu Rev Biochem 2019; 88:59-83. [DOI: 10.1146/annurev-biochem-013118-111327] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Directional transport of protons across an energy transducing membrane—proton pumping—is ubiquitous in biology. Bacteriorhodopsin (bR) is a light-driven proton pump that is activated by a buried all- trans retinal chromophore being photoisomerized to a 13- cis conformation. The mechanism by which photoisomerization initiates directional proton transport against a proton concentration gradient has been studied by a myriad of biochemical, biophysical, and structural techniques. X-ray free electron lasers (XFELs) have created new opportunities to probe the structural dynamics of bR at room temperature on timescales from femtoseconds to milliseconds using time-resolved serial femtosecond crystallography (TR-SFX). Wereview these recent developments and highlight where XFEL studies reveal new details concerning the structural mechanism of retinal photoisomerization and proton pumping. We also discuss the extent to which these insights were anticipated by earlier intermediate trapping studies using synchrotron radiation. TR-SFX will open up the field for dynamical studies of other proteins that are not naturally light-sensitive.
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Affiliation(s)
- Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
| | - Przemyslaw Nogly
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Eriko Nango
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - So Iwata
- RIKEN SPring-8 Center, Hyogo 679-5148, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Jörg Standfuss
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-40530 Gothenburg, Sweden
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18
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Geng X, Dai G, Chao L, Wen D, Kikukawa T, Iwasa T. Two Consecutive Polar Amino Acids at the End of Helix E are Important for Fast Turnover of the Archaerhodopsin Photocycle. Photochem Photobiol 2018; 95:980-989. [PMID: 30548616 DOI: 10.1111/php.13072] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/09/2018] [Indexed: 11/27/2022]
Abstract
Archaerhodopsins (ARs) is one of the members of microbial rhodopsins. Threonine 164 (T164) and serine 165 (S165) residues of the AR from Halorubrum sp. ejinoor (HeAR) are fully conserved in ARs, although they are far from the proton transfer channel and the retinal Schiff base, and are likely involved in a hydrogen-bonding network at the end of the Helix E where most microbial rhodopsins assume a "bent structure". In the present work, T164 and/or S165 were replaced with an alanine (A), and the photocycles of the mutants were analyzed with flash photolysis. The amino acid replacements caused profound changes to the photocycle of HeAR including prolonged photocycle, accelerated decay of M intermediate and appearance of additional two intermediates which were evident in T164A- and T164A/S165A-HeAR photocyles. These results suggest that although T164 and S165 are located at the far end of the photoactive center, these two amino acid residues are important for maintaining the fast turnover of the HeAR photocycle. The underlying molecular mechanisms are discussed in relation to hydrogen-bonding networks involving these two amino acids. Present study may arouse our interests to explore the functional role of the well-conserved "bent structure" in different types of microbial rhodopsin.
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Affiliation(s)
- Xiong Geng
- Division of Engineering, Muroran Institute of Technology, Muroran, Japan
| | - Gang Dai
- College of Chemistry and Environmental Science, Inner Mongolia Normal University, Hohhot, China
| | - Luomeng Chao
- College of Animal Science and Technology, Inner Mongolia University for The Nationalities, Tong Liao, China
| | - Durige Wen
- Division of Engineering, Muroran Institute of Technology, Muroran, Japan
| | - Takashi Kikukawa
- Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.,Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Tatsuo Iwasa
- Division of Engineering, Muroran Institute of Technology, Muroran, Japan
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19
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Sun C, Ding X, Cui H, Yang Y, Chen S, Watts A, Zhao X. In Situ Study of the Function of Bacterioruberin in the Dual-Chromophore Photoreceptor Archaerhodopsin-4. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803195] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chao Sun
- Department of Physics; East China Normal University; Shanghai 200062 P. R. China
| | - Xiaoyan Ding
- Department of Physics; East China Normal University; Shanghai 200062 P. R. China
- Department of Biochemistry and Molecular Biology; Penn State College of Medicine; Hershey PA 17033-0850 USA
| | - Haolin Cui
- Department of Physics; East China Normal University; Shanghai 200062 P. R. China
| | - Yanan Yang
- Department of Physics; East China Normal University; Shanghai 200062 P. R. China
| | - Sijin Chen
- Department of Physics; East China Normal University; Shanghai 200062 P. R. China
| | - Anthony Watts
- Department of Biochemistry; University of Oxford; Oxford OX1 3QU UK
| | - Xin Zhao
- Department of Physics; East China Normal University; Shanghai 200062 P. R. China
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20
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Sun C, Ding X, Cui H, Yang Y, Chen S, Watts A, Zhao X. In Situ Study of the Function of Bacterioruberin in the Dual-Chromophore Photoreceptor Archaerhodopsin-4. Angew Chem Int Ed Engl 2018; 57:8937-8941. [PMID: 29781190 DOI: 10.1002/anie.201803195] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Indexed: 11/11/2022]
Abstract
While certain archaeal ion pumps have been shown to contain two chromophores, retinal and the carotenoid bacterioruberin, the functions of bacterioruberin have not been well explored. To address this research gap, recombinant archaerhodopsin-4 (aR4), either with retinal only or with both retinal and bacterioruberin chromophores, was successfully expressed together with endogenous lipids in H. salinarum L33 and MPK409 respectively. In situ solid-state NMR, supported by molecular spectroscopy and functional assays, revealed for the first time that the retinal thermal equilibrium in the dark-adapted state is modulated by bacterioruberin binding through a cluster of aromatic residues on helix E. Bacterioruberin not only stabilizes the protein trimeric structure but also affects the photocycle kinetics and the ATP formation rate. These new insights may be generalized to other receptors and proteins in which metastable thermal equilibria and functions are perturbed by ligand binding.
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Affiliation(s)
- Chao Sun
- Department of Physics, East China Normal University, Shanghai, 200062, P. R. China
| | - Xiaoyan Ding
- Department of Physics, East China Normal University, Shanghai, 200062, P. R. China.,Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, 17033-0850, USA
| | - Haolin Cui
- Department of Physics, East China Normal University, Shanghai, 200062, P. R. China
| | - Yanan Yang
- Department of Physics, East China Normal University, Shanghai, 200062, P. R. China
| | - Sijin Chen
- Department of Physics, East China Normal University, Shanghai, 200062, P. R. China
| | - Anthony Watts
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Xin Zhao
- Department of Physics, East China Normal University, Shanghai, 200062, P. R. China
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21
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Oren A, Hirschberg J, Mann V, Jehlička J. Effects of nicotine on the biosynthesis of carotenoids in halophilic Archaea (class Halobacteria): an HPLC and Raman spectroscopy study. Extremophiles 2018; 22:359-366. [PMID: 29335805 DOI: 10.1007/s00792-018-0995-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 01/02/2018] [Indexed: 12/23/2022]
Abstract
Nicotine has a profound influence on the carotenoid metabolism in halophilic Archaea of the class Halobacteria. In a study of Halobacterium salinarum, Haloarcula marismortui and Halorubrum sodomense, using different analytical techniques to monitor the production of different carotenoids as a function of the presence of nicotine, we showed that the formation of α-bacterioruberin was inhibited in all. In Hbt. salinarum, addition of nicotine led to a significant change in the color of the culture due to the accumulation of lycopene, in addition to the formation of bisanhydrobacterioruberin which does not differ in color from α-bacterioruberin. Very little or no lycopene was formed in Har. marismortui and in Hrr. sodomense; instead bisanhydrobacterioruberin was the only major carotenoid found in nicotine-amended cultures. The findings are discussed in the framework of the recently elucidated biochemical pathway for the formation of the different carotenoid pigments encountered in the Halobacteria.
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Affiliation(s)
- Aharon Oren
- Department of Plant and Environmental Sciences, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, 9190401, Jerusalem, Israel.
| | - Joseph Hirschberg
- Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, 9190401, Jerusalem, Israel
| | - Varda Mann
- Department of Genetics, Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, 9190401, Jerusalem, Israel
| | - Jan Jehlička
- Institute of Geochemistry, Mineralogy and Mineral Resources, Charles University, Albertov 6, 12843, Prague, Czech Republic
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22
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Abstract
Microbial rhodopsins (MRs) are a large family of photoactive membrane proteins, found in microorganisms belonging to all kingdoms of life, with new members being constantly discovered. Among the MRs are light-driven proton, cation and anion pumps, light-gated cation and anion channels, and various photoreceptors. Due to their abundance and amenability to studies, MRs served as model systems for a great variety of biophysical techniques, and recently found a great application as optogenetic tools. While the basic aspects of microbial rhodopsins functioning have been known for some time, there is still a plenty of unanswered questions. This chapter presents and summarizes the available knowledge, focusing on the functional and structural studies.
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Affiliation(s)
- Ivan Gushchin
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
| | - Valentin Gordeliy
- Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.
- University of Grenoble Alpes, CEA, CNRS, IBS, Grenoble, France.
- Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Jülich, Jülich, Germany.
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23
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Optogenetic Tools for Subcellular Applications in Neuroscience. Neuron 2017; 96:572-603. [PMID: 29096074 DOI: 10.1016/j.neuron.2017.09.047] [Citation(s) in RCA: 217] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/30/2017] [Accepted: 09/26/2017] [Indexed: 12/21/2022]
Abstract
The ability to study cellular physiology using photosensitive, genetically encoded molecules has profoundly transformed neuroscience. The modern optogenetic toolbox includes fluorescent sensors to visualize signaling events in living cells and optogenetic actuators enabling manipulation of numerous cellular activities. Most optogenetic tools are not targeted to specific subcellular compartments but are localized with limited discrimination throughout the cell. Therefore, optogenetic activation often does not reflect context-dependent effects of highly localized intracellular signaling events. Subcellular targeting is required to achieve more specific optogenetic readouts and photomanipulation. Here we first provide a detailed overview of the available optogenetic tools with a focus on optogenetic actuators. Second, we review established strategies for targeting these tools to specific subcellular compartments. Finally, we discuss useful tools and targeting strategies that are currently missing from the optogenetics repertoire and provide suggestions for novel subcellular optogenetic applications.
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24
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Chen Q, Arents J, Ganapathy S, de Grip WJ, Hellingwerf KJ. Functional Expression of Gloeobacter Rhodopsin inSynechocystissp. PCC6803. Photochem Photobiol 2017; 93:772-781. [DOI: 10.1111/php.12745] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/07/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Que Chen
- Molecular Microbial Physiology; Swammerdam Institute for Life Sciences; University of Amsterdam; Amsterdam The Netherlands
| | - Jos Arents
- Molecular Microbial Physiology; Swammerdam Institute for Life Sciences; University of Amsterdam; Amsterdam The Netherlands
| | - Srividya Ganapathy
- Biophysical Organic Chemistry; Leiden Institute of Chemistry; Leiden University; Leiden The Netherlands
| | - Willem J. de Grip
- Biophysical Organic Chemistry; Leiden Institute of Chemistry; Leiden University; Leiden The Netherlands
| | - Klaas J. Hellingwerf
- Molecular Microbial Physiology; Swammerdam Institute for Life Sciences; University of Amsterdam; Amsterdam The Netherlands
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25
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Gdor I, Mani-Hazan M, Friedman N, Sheves M, Ruhman S. Membrane Independence of Ultrafast Photochemistry in Pharaonis Halorhodopsin: Testing the Role of Bacterioruberin. J Phys Chem B 2017; 121:2319-2325. [PMID: 28230358 DOI: 10.1021/acs.jpcb.6b12698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ultrafast photochemistry of pharaonis halorhodopsin (p-HR) in the intact membrane of Natronomonas pharaonis has been studied by photoselective femtosecond pump-hyperspectral probe spectroscopy with high time resolution. Two variants of this sample were studied, one with wild-type retinal prosthetic groups and another after shifting the retinal absorption deep into the blue range by reducing the Schiff base linkage, and the results were compared to a previous study on detergent-solubilized p-HR. This comparison shows that retinal photoisomerization dynamics is identical in the membrane and in the solubilized sample. Selective photoexcitation of bacterioruberin, which is associated with the protein in the native membrane, in wild-type and reduced samples, demonstrates conclusively that unlike the carotenoids associated with some bacterial retinal proteins the carrotenoid in p-HR does not act as a light-harvesting antenna.
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Affiliation(s)
- Itay Gdor
- Institute of Chemistry, the Hebrew University , Jerusalem 91904, Israel
| | - Maya Mani-Hazan
- Department of Organic Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Noga Friedman
- Department of Organic Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Mordechai Sheves
- Department of Organic Chemistry, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Sanford Ruhman
- Institute of Chemistry, the Hebrew University , Jerusalem 91904, Israel
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Kato HE, Inoue K, Kandori H, Nureki O. The light-driven sodium ion pump: A new player in rhodopsin research. Bioessays 2016; 38:1274-1282. [PMID: 27859420 DOI: 10.1002/bies.201600065] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Rhodopsins are one of the most studied photoreceptor protein families, and ion-translocating rhodopsins, both pumps and channels, have recently attracted broad attention because of the development of optogenetics. Recently, a new functional class of ion-pumping rhodopsins, an outward Na+ pump, was discovered, and following structural and functional studies enable us to compare three functionally different ion-pumping rhodopsins: outward proton pump, inward Cl- pump, and outward Na+ pump. Here, we review the current knowledge on structure-function relationships in these three light-driven pumps, mainly focusing on Na+ pumps. A structural and functional comparison reveals both unique and conserved features of these ion pumps, and enhances our understanding about how the structurally similar microbial rhodopsins acquired such diverse functions. We also discuss some unresolved questions and future perspectives in research of ion-pumping rhodopsins, including optogenetics application and engineering of novel rhodopsins.
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Affiliation(s)
- Hideaki E Kato
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan.,OptoBioTechnology Research Center, Nagoya Institute of Technology, Nagoya, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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27
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Gushchin I, Shevchenko V, Polovinkin V, Borshchevskiy V, Buslaev P, Bamberg E, Gordeliy V. Structure of the light-driven sodium pump KR2 and its implications for optogenetics. FEBS J 2015; 283:1232-8. [DOI: 10.1111/febs.13585] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 10/22/2015] [Accepted: 10/30/2015] [Indexed: 01/27/2023]
Affiliation(s)
- Ivan Gushchin
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
| | - Vitaly Shevchenko
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
| | - Vitaly Polovinkin
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
- Institut de Biologie Structurale; Université Grenoble Alpes; France
- Institut de Biologie Structurale; Centre National de la Recherche Scientifique; Grenoble France
- Institut de Biologie Structurale; Direction des Sciences du Vivant; Commissariat à l'Énergie Atomique; Grenoble France
| | - Valentin Borshchevskiy
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
| | - Pavel Buslaev
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
| | - Ernst Bamberg
- Max Planck Institute of Biophysics; Frankfurt am Main Germany
| | - Valentin Gordeliy
- Institute of Complex Systems (ICS); ICS-6: Structural Biochemistry; Research Centre Jülich; Germany
- Moscow Institute of Physics and Technology; Dolgoprudniy Russia
- Institut de Biologie Structurale; Université Grenoble Alpes; France
- Institut de Biologie Structurale; Centre National de la Recherche Scientifique; Grenoble France
- Institut de Biologie Structurale; Direction des Sciences du Vivant; Commissariat à l'Énergie Atomique; Grenoble France
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28
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Optogenetic acidification of synaptic vesicles and lysosomes. Nat Neurosci 2015; 18:1845-1852. [PMID: 26551543 PMCID: PMC4869830 DOI: 10.1038/nn.4161] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/08/2015] [Indexed: 12/12/2022]
Abstract
Acidification is required for the function of many intracellular organelles, but methods
to acutely manipulate their intraluminal pH have not been available. Here we
present a targeting strategy to selectively express the light-driven proton pump
Arch3 on synaptic vesicles. Our new tool, pHoenix, can functionally replace
endogenous proton pumps, enabling optogenetic control of vesicular acidification
and neurotransmitter accumulation. Under physiological conditions, glutamatergic
vesicles are nearly full, as additional vesicle acidification with pHoenix only
slightly increased the quantal size. By contrast, we found that incompletely
filled vesicles exhibited a lower release probability than full vesicles,
suggesting preferential exocytosis of vesicles with high transmitter content.
Our subcellular targeting approach can be transferred to other organelles, as
demonstrated for a pHoenix variant that allows light-activated acidification of
lysosomes.
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Furuse M, Tamogami J, Hosaka T, Kikukawa T, Shinya N, Hato M, Ohsawa N, Kim SY, Jung KH, Demura M, Miyauchi S, Kamo N, Shimono K, Kimura-Someya T, Yokoyama S, Shirouzu M. Structural basis for the slow photocycle and late proton release in Acetabularia rhodopsin I from the marine plant Acetabularia acetabulum. ACTA ACUST UNITED AC 2015; 71:2203-16. [DOI: 10.1107/s1399004715015722] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 08/21/2015] [Indexed: 11/10/2022]
Abstract
Although many crystal structures of microbial rhodopsins have been solved, those with sufficient resolution to identify the functional water molecules are very limited. In this study, the Acetabularia rhodopsin I (ARI) protein derived from the marine alga A. acetabulum was synthesized on a large scale by the Escherichia coli cell-free membrane-protein production method, and crystal structures of ARI were determined at the second highest (1.52–1.80 Å) resolution for a microbial rhodopsin, following bacteriorhodopsin (BR). Examinations of the photochemical properties of ARI revealed that the photocycle of ARI is slower than that of BR and that its proton-transfer reactions are different from those of BR. In the present structures, a large cavity containing numerous water molecules exists on the extracellular side of ARI, explaining the relatively low pK
a of Glu206ARI, which cannot function as an initial proton-releasing residue at any pH. An interhelical hydrogen bond exists between Leu97ARI and Tyr221ARI on the cytoplasmic side, which facilitates the slow photocycle and regulates the pK
a of Asp100ARI, a potential proton donor to the Schiff base, in the dark state.
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Hsu MF, Fu HY, Cai CJ, Yi HP, Yang CS, Wang AHJ. Structural and Functional Studies of a Newly Grouped Haloquadratum walsbyi Bacteriorhodopsin Reveal the Acid-resistant Light-driven Proton Pumping Activity. J Biol Chem 2015; 290:29567-77. [PMID: 26483542 PMCID: PMC4705956 DOI: 10.1074/jbc.m115.685065] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Indexed: 11/23/2022] Open
Abstract
Retinal bound light-driven proton pumps are widespread in eukaryotic and prokaryotic organisms. Among these pumps, bacteriorhodopsin (BR) proteins cooperate with ATP synthase to convert captured solar energy into a biologically consumable form, ATP. In an acidic environment or when pumped-out protons accumulate in the extracellular region, the maximum absorbance of BR proteins shifts markedly to the longer wavelengths. These conditions affect the light-driven proton pumping functional exertion as well. In this study, wild-type crystal structure of a BR with optical stability under wide pH range from a square halophilic archaeon, Haloquadratum walsbyi (HwBR), was solved in two crystal forms. One crystal form, refined to 1.85 Å resolution, contains a trimer in the asymmetric unit, whereas another contains an antiparallel dimer was refined at 2.58 Å. HwBR could not be classified into any existing subgroup of archaeal BR proteins based on the protein sequence phylogenetic tree, and it showed unique absorption spectral stability when exposed to low pH values. All structures showed a unique hydrogen-bonding network between Arg82 and Thr201, linking the BC and FG loops to shield the retinal-binding pocket in the interior from the extracellular environment. This result was supported by R82E mutation that attenuated the optical stability. The negatively charged cytoplasmic side and the Arg82–Thr201 hydrogen bond may play an important role in the proton translocation trend in HwBR under acidic conditions. Our findings have unveiled a strategy adopted by BR proteins to solidify their defenses against unfavorable environments and maintain their optical properties associated with proton pumping.
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Affiliation(s)
- Min-Feng Hsu
- From the Institute of Biological Chemistry and Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 11529 and
| | - Hsu-Yuan Fu
- the Department of Biochemical Science and Technology, College of Life Science, Yen Tjing Ling Industrial Research Institute, and
| | - Chun-Jie Cai
- the Department of Biochemical Science and Technology, College of Life Science
| | - Hsiu-Pin Yi
- the Department of Biochemical Science and Technology, College of Life Science
| | - Chii-Shen Yang
- the Department of Biochemical Science and Technology, College of Life Science, Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Andrew H-J Wang
- From the Institute of Biological Chemistry and Core Facilities for Protein Structural Analysis, Academia Sinica, Taipei 11529 and
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31
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Dai G, Kikukawa T, Ihara K, Iwasa T. Microbial rhodopsins of Halorubrum species isolated from Ejinoor salt lake in Inner Mongolia of China. Photochem Photobiol Sci 2015; 14:1974-82. [PMID: 26328780 DOI: 10.1039/c5pp00161g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Microbial rhodopsins are photoactive proteins that use a retinal molecule as the photoactive center. Because of structural simplicity and functional diversity, microbial rhodopsins have been an excellent model system for structural biology. In this study, a halophilic archaea that has three microbial rhodopsin-type genes in its genome was isolated from Ejinoor salt lake in Inner Mongolia of China. A sequence of 16S rRNA showed that the strain belongs to Halorubrum genus and named Halorubrum sp. ejinoor (He). The translated amino acid sequences of its microbial rhodopsin-type genes suggest that they are homologs of archaerhodopsin (HeAR), halorhodopsin (HeHR) and sensory rhodopsin II (HeSRII). The mRNAs of three types of genes were detected by RT-PCR and their amounts were investigated by Real-Time RT-PCR. The amount of mRNA of HeSRII was the smallest and the amounts of of HeAR and HeHR were 30 times and 10 times greater than that of HeSRII. The results of light-induced pH changes suggested the presence of a light-driven proton pump and a light-driven chloride ion pump in the membrane vesicles of He. Flash induced absorbance changes of the He membrane fraction indicated that HeAR and HeHR are photoactive and undergo their own photocycles. This study revealed that three microbial rhodopsin-type genes are all expressed in the strain and at least two of them, HeAR and HeHR, are photochemically and physiologically active like BR and HR of Halobacterium salinarum, respectively. To our knowledge, this is the first report of physiological activity of HR-homolog of Halorubrum species.
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Rodrigo-Baños M, Garbayo I, Vílchez C, Bonete MJ, Martínez-Espinosa RM. Carotenoids from Haloarchaea and Their Potential in Biotechnology. Mar Drugs 2015; 13:5508-32. [PMID: 26308012 PMCID: PMC4584337 DOI: 10.3390/md13095508] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/02/2015] [Accepted: 08/10/2015] [Indexed: 12/02/2022] Open
Abstract
The production of pigments by halophilic archaea has been analysed during the last half a century. The main reasons that sustains this research are: (i) many haloarchaeal species possess high carotenoids production availability; (ii) downstream processes related to carotenoid isolation from haloarchaea is relatively quick, easy and cheap; (iii) carotenoids production by haloarchaea can be improved by genetic modification or even by modifying several cultivation aspects such as nutrition, growth pH, temperature, etc.; (iv) carotenoids are needed to support plant and animal life and human well-being; and (v) carotenoids are compounds highly demanded by pharmaceutical, cosmetic and food markets. Several studies about carotenoid production by haloarchaea have been reported so far, most of them focused on pigments isolation or carotenoids production under different culture conditions. However, the understanding of carotenoid metabolism, regulation, and roles of carotenoid derivatives in this group of extreme microorganisms remains mostly unrevealed. The uses of those haloarchaeal pigments have also been poorly explored. This work summarises what has been described so far about carotenoids production by haloarchaea and their potential uses in biotechnology and biomedicine. In particular, new scientific evidence of improved carotenoid production by one of the better known haloarchaeon (Haloferax mediterranei) is also discussed.
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Affiliation(s)
- Montserrat Rodrigo-Baños
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain.
| | - Inés Garbayo
- Algal Biotechnology Group, University of Huelva and Marine International Campus of Excellence (CEIMAR), CIDERTA and Faculty of Sciences, 21071 Huelva, Spain.
| | - Carlos Vílchez
- Algal Biotechnology Group, University of Huelva and Marine International Campus of Excellence (CEIMAR), CIDERTA and Faculty of Sciences, 21071 Huelva, Spain.
| | - María José Bonete
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain.
| | - Rosa María Martínez-Espinosa
- Biochemistry and Molecular Biology Division, Agrochemistry and Biochemistry Department, Faculty of Sciences, University of Alicante, Ap. 99, E-03080 Alicante, Spain.
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Hoffmann A, Kovermann M, Oberwinkler T, Siedler F, Cortina NS, Balbach J, Oesterhelt D. Novel sulfated phosphoglycolipids from Natronomonas moolapensis. Chem Phys Lipids 2015; 191:8-15. [PMID: 26134137 DOI: 10.1016/j.chemphyslip.2015.06.004] [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] [Received: 10/30/2014] [Revised: 06/22/2015] [Accepted: 06/23/2015] [Indexed: 01/09/2023]
Abstract
Polar lipid pattern determination is often used for the taxonomic classification of halophilic Archaea in addition to a genomic characterization. During the analysis of polar lipid extracts from the recently described haloarchaeon Natrononomonas moolapensis, an unknown glycolipid was detected. Fragmentation patterns observed from preliminary mass spectrometric analysis initially suggested the presence of a sulfo-hexosyl-phosphatidylglycerol. However, by NMR spectroscopy and enzymatic assays the existence of two isomeric molecules with different hexoses (1-(6-sulfo-d-glcp/galf-β1,2-glycero)-phospho-2,3-diphytanylglycerol) could be shown. The structural origin from phosphatidylglycerol distinguishes these glycolipids within Archaea, because all other characterized haloarchaeal glycolipids consist of diphytanylglycerol directly linked to an oligoglycosyl moiety. Now the door is open to investigate the physical and functional consequences of these architectural differences of the head groups.
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Affiliation(s)
- Andreas Hoffmann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Michael Kovermann
- Institute of Physics, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 7, 06120 Halle, Germany; Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Tanja Oberwinkler
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Frank Siedler
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Niña Socorro Cortina
- Institute of Organic Chemistry and Chemical Biology, Goethe University, Max-von-Laue-Str. 15, 60438 Frankfurt, Germany
| | - Jochen Balbach
- Institute of Physics, Martin Luther University Halle-Wittenberg, Betty-Heimann-Str. 7, 06120 Halle, Germany
| | - Dieter Oesterhelt
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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Novel expression and characterization of a light driven proton pump archaerhodopsin 4 in a Halobacterium salinarum strain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:390-398. [DOI: 10.1016/j.bbabio.2014.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 12/22/2014] [Accepted: 12/25/2014] [Indexed: 11/19/2022]
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Shevchenko V, Gushchin I, Polovinkin V, Round E, Borshchevskiy V, Utrobin P, Popov A, Balandin T, Büldt G, Gordeliy V. Crystal structure of Escherichia coli-expressed Haloarcula marismortui bacteriorhodopsin I in the trimeric form. PLoS One 2014; 9:e112873. [PMID: 25479443 PMCID: PMC4257550 DOI: 10.1371/journal.pone.0112873] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 10/17/2014] [Indexed: 12/02/2022] Open
Abstract
Bacteriorhodopsins are a large family of seven-helical transmembrane proteins that function as light-driven proton pumps. Here, we present the crystal structure of a new member of the family, Haloarcula marismortui bacteriorhodopsin I (HmBRI) D94N mutant, at the resolution of 2.5 Å. While the HmBRI retinal-binding pocket and proton donor site are similar to those of other archaeal proton pumps, its proton release region is extended and contains additional water molecules. The protein's fold is reinforced by three novel inter-helical hydrogen bonds, two of which result from double substitutions relative to Halobacterium salinarum bacteriorhodopsin and other similar proteins. Despite the expression in Escherichia coli and consequent absence of native lipids, the protein assembles as a trimer in crystals. The unique extended loop between the helices D and E of HmBRI makes contacts with the adjacent protomer and appears to stabilize the interface. Many lipidic hydrophobic tail groups are discernible in the membrane region, and their positions are similar to those of archaeal isoprenoid lipids in the crystals of other proton pumps, isolated from native or native-like sources. All these features might explain the HmBRI properties and establish the protein as a novel model for the microbial rhodopsin proton pumping studies.
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Affiliation(s)
- Vitaly Shevchenko
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
| | - Ivan Gushchin
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Vitaly Polovinkin
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
| | - Ekaterina Round
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
| | - Valentin Borshchevskiy
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
| | - Petr Utrobin
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
| | | | - Taras Balandin
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
| | - Georg Büldt
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
| | - Valentin Gordeliy
- Institute of Complex Systems (ICS-6) Structural Biochemistry, Research Centre Jülich GmbH, Jülich, Germany
- Laboratory for advanced studies of membrane proteins, Moscow institute of physics and technology, Dolgoprudniy, Russia
- Univ. Grenoble Alpes, IBS, Grenoble, France
- CNRS, IBS, Grenoble, France
- CEA, IBS, Grenoble, France
- European Synchrotron Radiation Facility, Grenoble, France
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Kouyama T, Fujii R, Kanada S, Nakanishi T, Chan SK, Murakami M. Structure of archaerhodopsin-2 at 1.8 Å resolution. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2692-701. [PMID: 25286853 PMCID: PMC4188009 DOI: 10.1107/s1399004714017313] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Accepted: 07/28/2014] [Indexed: 11/10/2022]
Abstract
Archaerhodopsin-2 (aR2), the sole protein found in the claret membrane of Halorubrum sp. Aus-2, functions as a light-driven proton pump. In this study, structural analysis of aR2 was performed using a novel three-dimensional crystal prepared by the successive fusion of claret membranes. The crystal is made up of stacked membranes, in each of which aR2 trimers are arranged on a hexagonal lattice. This lattice structure resembles that found in the purple membrane of H. salinarum, except that lipid molecules trapped within the trimeric structure are not distributed with perfect threefold symmetry. Nonetheless, diffraction data at 1.8 Å resolution provide accurate structural information about functionally important residues. It is shown that two glutamates in the proton-release channel form a paired structure that is maintained by a low-barrier hydrogen bond. Although the structure of the proton-release pathway is highly conserved among proton-pumping archaeal rhodopsins, aR2 possesses the following peculiar structural features: (i) the motional freedom of the tryptophan residue that makes contact with the C13 methyl group of retinal is restricted, affecting the formation/decay kinetics of the L state, and (ii) the N-terminal polypeptide folds into an Ω-loop, which may play a role in organizing the higher-order structure.
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Affiliation(s)
- Tsutomu Kouyama
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
- RIKEN Harima Institute/SPring-8, 1-1-1 Kouto, Mikazuki, Sayo, Hyogo, Japan
| | - Ryudo Fujii
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Soun Kanada
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Taichi Nakanishi
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Siu Kit Chan
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Midori Murakami
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
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Chan SK, Kitajima-Ihara T, Fujii R, Gotoh T, Murakami M, Ihara K, Kouyama T. Crystal structure of Cruxrhodopsin-3 from Haloarcula vallismortis. PLoS One 2014; 9:e108362. [PMID: 25268964 PMCID: PMC4182453 DOI: 10.1371/journal.pone.0108362] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 08/26/2014] [Indexed: 01/09/2023] Open
Abstract
Cruxrhodopsin-3 (cR3), a retinylidene protein found in the claret membrane of Haloarcula vallismortis, functions as a light-driven proton pump. In this study, the membrane fusion method was applied to crystallize cR3 into a crystal belonging to space group P321. Diffraction data at 2.1 Å resolution show that cR3 forms a trimeric assembly with bacterioruberin bound to the crevice between neighboring subunits. Although the structure of the proton-release pathway is conserved among proton-pumping archaeal rhodopsins, cR3 possesses the following peculiar structural features: 1) The DE loop is long enough to interact with a neighboring subunit, strengthening the trimeric assembly; 2) Three positive charges are distributed at the cytoplasmic end of helix F, affecting the higher order structure of cR3; 3) The cytoplasmic vicinity of retinal is more rigid in cR3 than in bacteriorhodopsin, affecting the early reaction step in the proton-pumping cycle; 4) the cytoplasmic part of helix E is greatly bent, influencing the proton uptake process. Meanwhile, it was observed that the photobleaching of retinal, which scarcely occurred in the membrane state, became significant when the trimeric assembly of cR3 was dissociated into monomers in the presence of an excess amount of detergent. On the basis of these observations, we discuss structural factors affecting the photostabilities of ion-pumping rhodopsins.
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Affiliation(s)
- Siu Kit Chan
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | | | - Ryudoh Fujii
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Toshiaki Gotoh
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Midori Murakami
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Nagoya, Japan
| | - Tsutomu Kouyama
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan
- RIKEN Harima Institute/SPring-8, Mikazuki, Sayo, Hyogo, Japan
- * E-mail:
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Wickstrand C, Dods R, Royant A, Neutze R. Bacteriorhodopsin: Would the real structural intermediates please stand up? Biochim Biophys Acta Gen Subj 2014; 1850:536-53. [PMID: 24918316 DOI: 10.1016/j.bbagen.2014.05.021] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/23/2014] [Accepted: 05/29/2014] [Indexed: 11/18/2022]
Abstract
BACKGROUND Bacteriorhodopsin (bR) is the simplest known light driven proton pump and has been heavily studied using structural methods: eighty four X-ray diffraction, six electron diffraction and three NMR structures of bR are deposited within the protein data bank. Twenty one X-ray structures report light induced structural changes and changes induced by mutation, changes in pH, thermal annealing or X-ray induced photo-reduction have also been examined. SCOPE OF REVIEW We argue that light-induced structural changes that are replicated across several studies by independent research groups are those most likely to represent what is happening in reality. We present both internal distance matrix analyses that sort deposited bR structures into hierarchal trees, and difference Fourier analysis of deposited X-ray diffraction data. MAJOR CONCLUSIONS An internal distance matrix analysis separates most wild-type bR structures according to their different crystal forms, indicating how the protein's structure is influenced by crystallization conditions. A similar analysis clusters eleven studies of illuminated bR crystals as one branch of a hierarchal tree with reproducible movements of the extracellular portion of helix C towards helix G, and of the cytoplasmic portion of helix F away from helices A, B and G. All crystallographic data deposited for illuminated crystals show negative difference density on a water molecule (Wat402) that forms H-bonds to the retinal Schiff Base and two aspartate residues (Asp85, Asp212) in the bR resting state. Other recurring difference density features indicated reproducible side-chain, backbone and water molecule displacements. X-ray induced radiation damage also disorders Wat402 but acts via cleaving the head-groups of Asp85 and Asp212. GENERAL SIGNIFICANCE A remarkable level of agreement exists when deposited structures and crystallographic observations are viewed as a whole. From this agreement a unified picture of the structural mechanism of light-induced proton pumping by bR emerges. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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Affiliation(s)
- Cecilia Wickstrand
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Robert Dods
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden
| | - Antoine Royant
- Univ. Grenoble Alpes, IBS, F-38044 Grenoble, France; CNRS, IBS, F-38044 Grenoble, France; CEA, IBS, F-38044 Grenoble, France; European Synchrotron Radiation Facility, F-38043 Grenoble, France.
| | - Richard Neutze
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, SE-40530 Gothenburg, Sweden.
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39
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Álvarez R, Vaz B, Gronemeyer H, de Lera ÁR. Functions, therapeutic applications, and synthesis of retinoids and carotenoids. Chem Rev 2013; 114:1-125. [PMID: 24266866 DOI: 10.1021/cr400126u] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rosana Álvarez
- Departamento de Química Orgánica, Centro de Investigación Biomédica (CINBIO), and Instituto de Investigación Biomédica de Vigo (IBIV), Universidade de Vigo , 36310 Vigo, Spain
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40
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Zhang J, Mizuno K, Murata Y, Koide H, Murakami M, Ihara K, Kouyama T. Crystal structure of deltarhodopsin-3 from Haloterrigena thermotolerans. Proteins 2013; 81:1585-92. [DOI: 10.1002/prot.24316] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 03/25/2013] [Accepted: 04/03/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Jin Zhang
- Department of Physics; Graduate School of Science; Nagoya University; Nagoya Japan
| | - Katsuhide Mizuno
- Department of Physics; Graduate School of Science; Nagoya University; Nagoya Japan
| | - Yuki Murata
- Department of Physics; Graduate School of Science; Nagoya University; Nagoya Japan
| | - Hideaki Koide
- Department of Physics; Graduate School of Science; Nagoya University; Nagoya Japan
| | - Midori Murakami
- Department of Physics; Graduate School of Science; Nagoya University; Nagoya Japan
| | - Kunio Ihara
- Center for Gene Research; Nagoya University; Nagoya Japan
| | - Tsutomu Kouyama
- Department of Physics; Graduate School of Science; Nagoya University; Nagoya Japan
- RIKEN Harima Institute/SPring-8, 1-1-1; Kouto Mikazuki, Sayo, Hyogo Japan
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41
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Brown LS. Eubacterial rhodopsins - unique photosensors and diverse ion pumps. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:553-61. [PMID: 23748216 DOI: 10.1016/j.bbabio.2013.05.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Revised: 05/27/2013] [Accepted: 05/29/2013] [Indexed: 10/26/2022]
Abstract
Since the discovery of proteorhodopsins, the ubiquitous marine light-driven proton pumps of eubacteria, a large number of other eubacterial rhodopsins with diverse structures and functions have been characterized. Here, we review the body of knowledge accumulated on the four major groups of eubacterial rhodopsins, with the focus on their biophysical characterization. We discuss advances and controversies on the unique eubacterial sensory rhodopsins (as represented by Anabaena sensory rhodopsin), proton-pumping proteorhodopsins and xanthorhodopsins, as well as novel non-proton ion pumps. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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Affiliation(s)
- Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Ontario N1G 2W1, Canada.
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42
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LIGHT-DRIVEN PROTON PUMPS OF ARCHAERHODOPSIN AND BACTERIORHODOPSIN AND POLYMER-MATRIX COMPOSITE MATERIALS OF THOSE FUNCTIONAL PROTEINS. ACTA POLYM SIN 2012. [DOI: 10.3724/sp.j.1105.2012.12051] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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43
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Homotrimer formation and dissociation of pharaonis halorhodopsin in detergent system. Biophys J 2012; 102:2906-15. [PMID: 22735541 DOI: 10.1016/j.bpj.2012.05.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 05/06/2012] [Accepted: 05/08/2012] [Indexed: 12/13/2022] Open
Abstract
Halorhodopsin from NpHR is a light-driven Cl(-) pump that forms a trimeric NpHR-bacterioruberin complex in the native membrane. In the case of NpHR expressed in Escherichia coli cell, NpHR forms a robust homotrimer in a detergent DDM solution. To identify the important residue for the homotrimer formation, we carried out mutation experiments on the aromatic amino acids expected to be located at the molecular interface. The results revealed that Phe(150) was essential to form and stabilize the NpHR trimer in the DDM solution. Further analyses for examining the structural significance of Phe(150) showed the dissociation of the trimer in F150A (dimer) and F150W (monomer) mutants. Only the F150Y mutant exhibited dissociation into monomers in an ionic strength-dependent manner. These results indicated that spatial positions and interactions between F150-aromatic side chains were crucial to homotrimer stabilization. This finding was supported by QM calculations. In a functional respect, differences in the reaction property in the ground and photoexcited states were revealed. The analysis of photointermediates revealed a decrease in the accumulation of O, which is important for Cl(-) release, and the acceleration of the decay rate in L1 and L2, which are involved in Cl(-) transfer inside the molecule, in the trimer-dissociated mutants. Interestingly, the affinity of them to Cl(-) in the photoexcited state increased rather than the trimer, whereas that in the ground state was almost the same without relation to the oligomeric state. It was also observed that the efficient recovery of the photocycle to the ground state was inhibited in the mutants. In addition, a branched pathway that was not included in Cl(-) transportation was predicted. These results suggest that the trimer assembly may contribute to the regulation of the dynamics in the excited state of NpHR.
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Lobasso S, Lopalco P, Vitale R, Saponetti MS, Capitanio G, Mangini V, Milano F, Trotta M, Corcelli A. The light-activated proton pump Bop I of the archaeon Haloquadratum walsbyi. Photochem Photobiol 2012; 88:690-700. [PMID: 22248212 DOI: 10.1111/j.1751-1097.2012.01089.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have isolated and characterized the light-driven proton pump Bop I from the ultrathin square archaeon Haloquadratum walsbyi, the most abundant component of the dense microbial community inhabiting hypersaline environments. The disruption of cells by hypo-osmotic shock yielded Bop I retinal protein highly enriched membranes, which contain one main 27 kDa protein band together with a high content of the carotenoid bacterioruberin. Light-induced pH changes were observed in suspensions of Bop I retinal protein-enriched membranes under sustained illumination. Solubilization of H. walsbyi cells with Triton X-100, followed by phenyl-Sepharose chromatography, resulted in isolation of two purified Bop I retinal protein bands; mass spectrometry analysis revealed that the Bop I was present as only protein in both the bands. The study of light/dark adaptations, M-decay kinetics, responses to titration with alkali in the dark and endogenous lipid compositions of the two Bop I retinal protein bands showed functional differences that could be attributed to different protein aggregation states. Proton-pumping activity of Bop I during the photocycle was observed in liposomes constituted of archaeal lipids. Similarities and differences of Bop I with other archaeal proton-pumping retinal proteins will be discussed.
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Affiliation(s)
- Simona Lobasso
- Department of Basic Medical Sciences, University of Bari Aldo Moro, Bari, Italy
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45
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Chow BY, Han X, Boyden ES. Genetically encoded molecular tools for light-driven silencing of targeted neurons. PROGRESS IN BRAIN RESEARCH 2012; 196:49-61. [PMID: 22341320 PMCID: PMC3553588 DOI: 10.1016/b978-0-444-59426-6.00003-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The ability to silence, in a temporally precise fashion, the electrical activity of specific neurons embedded within intact brain tissue, is important for understanding the role that those neurons play in behaviors, brain disorders, and neural computations. "Optogenetic" silencers, genetically encoded molecules that, when expressed in targeted cells within neural networks, enable their electrical activity to be quieted in response to pulses of light, are enabling these kinds of causal circuit analyses studies. Two major classes of optogenetic silencer are in broad use in species ranging from worm to monkey: light-driven inward chloride pumps, or halorhodopsins, and light-driven outward proton pumps, such as archaerhodopsins and fungal light-driven proton pumps. Both classes of molecule, when expressed in neurons via viral or other transgenic means, enable the targeted neurons to be hyperpolarized by light. We here review the current status of these sets of molecules, and discuss how they are being discovered and engineered. We also discuss their expression properties, ionic properties, spectral characteristics, and kinetics. Such tools may not only find many uses in the quieting of electrical activity for basic science studies but may also, in the future, find clinical uses for their ability to safely and transiently shut down cellular electrical activity in a precise fashion.
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Affiliation(s)
- Brian Y Chow
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
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46
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Plazzo AP, De Franceschi N, Da Broi F, Zonta F, Sanasi MF, Filippini F, Mongillo M. Bioinformatic and mutational analysis of channelrhodopsin-2 protein cation-conducting pathway. J Biol Chem 2011; 287:4818-25. [PMID: 22139833 DOI: 10.1074/jbc.m111.326207] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Channelrhodopsin-2 (ChR2) is a light-gated cation channel widely used as a biotechnological tool to control membrane depolarization in various cell types and tissues. Although several ChR2 variants with modified properties have been generated, the structural determinants of the protein function are largely unresolved. We used bioinformatic modeling of the ChR2 structure to identify the putative cationic pathway within the channel, which is formed by a system of inner cavities that are uniquely present in this microbial rhodopsin. Site-directed mutagenesis combined with patch clamp analysis in HeLa cells was used to determine key residues involved in ChR2 conductance and selectivity. Among them, Gln-56 is important for ion conductance, whereas Ser-63, Thr-250, and Asn-258 are previously unrecognized residues involved in ion selectivity and photocurrent kinetics. This study widens the current structural information on ChR2 and can assist in the design of new improved variants for specific biological applications.
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Affiliation(s)
- Anna Pia Plazzo
- Department of Biomedical Sciences, University of Padova, viale Colombo 3, 35100 Padova, Italy
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47
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Kanada S, Takeguchi Y, Murakami M, Ihara K, Kouyama T. Crystal structures of an O-like blue form and an anion-free yellow form of pharaonis halorhodopsin. J Mol Biol 2011; 413:162-76. [PMID: 21871461 DOI: 10.1016/j.jmb.2011.08.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 08/06/2011] [Accepted: 08/09/2011] [Indexed: 10/17/2022]
Abstract
Halorhodopsin from Natronomonas pharaonis (pHR) was previously crystallized into a monoclinic space group C2, and the structure of the chloride-bound purple form was determined. Here, we report the crystal structures of two chloride-free forms of pHR, that is, an O-like blue form and an M-like yellow form. When the C2 crystal was soaked in a chloride-free alkaline solution, the protein packing was largely altered and the yellow form containing all-trans retinal was generated. Upon neutralization, this yellow form was converted into the blue form. From structural comparison of the different forms of pHR, it was shown that the removal of a chloride ion from the primary binding site (site I), which is located between the retinal Schiff base and Thr126, is accompanied by such a deformation of helix C that the side chain of Thr126 moves toward helix G, leading to a significant shrinkage of site I. A large structural change is also induced in the chloride uptake pathway, where a flip motion of the side chain of Glu234 is accompanied by large movements of the surrounding aromatic residues. Irrespective of different charge distributions at the active site, there was no large difference in the structures of the yellow form and the blue form. It is shown that the yellow-to-purple transition is initiated by the entrance of one water and one HCl to the active site, where the proton and the chloride ion in HCl are transferred to the Schiff base and site I, respectively.
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Affiliation(s)
- Soun Kanada
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
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48
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Chow BY, Chuong AS, Klapoetke NC, Boyden ES. Synthetic physiology strategies for adapting tools from nature for genetically targeted control of fast biological processes. Methods Enzymol 2011; 497:425-43. [PMID: 21601097 DOI: 10.1016/b978-0-12-385075-1.00018-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The life and operation of cells involve many physiological processes that take place over fast timescales of milliseconds to minutes. Genetically encoded technologies for driving or suppressing specific fast physiological processes in intact cells, perhaps embedded within intact tissues in living organisms, are critical for the ability to understand how these physiological processes contribute to emergent cellular and organismal functions and behaviors. Such "synthetic physiology" tools are often incredibly complex molecular machines, in part because they must operate at high speeds, without causing side effects. We here explore how synthetic physiology molecules can be identified and deployed in cells, and how the physiology of these molecules in cellular contexts can be assessed and optimized. For concreteness, we discuss these methods in the context of the "optogenetic" light-gated ion channels and pumps that we have developed over the past few years as synthetic physiology tools and widely disseminated for use in neuroscience for probing the role of specific brain cell types in neural computations, behaviors, and pathologies. We anticipate that some of the insights revealed here may be of general value for the field of synthetic physiology, as they raise issues that will be of importance for the development and use of high-performance, high-speed, side-effect free physiological control tools in heterologous expression systems.
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Affiliation(s)
- Brian Y Chow
- Synthetic Neurobiology Group, The Media Laboratory and McGovern Institute, Departments of Biological Engineering and Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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49
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Imasheva ES, Balashov SP, Wang JM, Lanyi JK. Removal and reconstitution of the carotenoid antenna of xanthorhodopsin. J Membr Biol 2010; 239:95-104. [PMID: 21104180 PMCID: PMC3030941 DOI: 10.1007/s00232-010-9322-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2010] [Accepted: 11/05/2010] [Indexed: 11/24/2022]
Abstract
Salinixanthin, a C40-carotenoid acyl glycoside, serves as a light-harvesting antenna in the retinal-based proton pump xanthorhodopsin of Salinibacter ruber. In the crystallographic structure of this protein, the conjugated chain of salinixanthin is located at the protein–lipid boundary and interacts with residues of helices E and F. Its ring, with a 4-keto group, is rotated relative to the plane of the π-system of the carotenoid polyene chain and immobilized in a binding site near the β-ionone retinal ring. We show here that the carotenoid can be removed by oxidation with ammonium persulfate, with little effect on the other chromophore, retinal. The characteristic CD bands attributed to bound salinixanthin are now absent. The kinetics of the photocycle is only slightly perturbed, showing a 1.5-fold decrease in the overall turnover rate. The carotenoid-free protein can be reconstituted with salinixanthin extracted from the cell membrane of S. ruber. Reconstitution is accompanied by restoration of the characteristic vibronic structure of the absorption spectrum of the antenna carotenoid, its chirality, and the excited-state energy transfer to the retinal. Minor modification of salinixanthin, by reducing the carbonyl C=O double bond in the ring to a C-OH, suppresses its binding to the protein and eliminates the antenna function. This indicates that the presence of the 4-keto group is critical for carotenoid binding and efficient energy transfer.
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Affiliation(s)
- Eleonora S Imasheva
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697-4560, USA
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50
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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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