1
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Brown LS. Light-driven proton transfers and proton transport by microbial rhodopsins - A biophysical perspective. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183867. [PMID: 35051382 DOI: 10.1016/j.bbamem.2022.183867] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/30/2021] [Accepted: 01/10/2022] [Indexed: 12/31/2022]
Abstract
In the last twenty years, our understanding of the rules and mechanisms for the outward light-driven proton transport (and underlying proton transfers) by microbial rhodopsins has been changing dramatically. It transitioned from a very detailed atomic-level understanding of proton transport by bacteriorhodopsin, the prototypical proton pump, to a confounding variety of sequence motifs, mechanisms, directions, and modes of transport in its newly found homologs. In this review, we will summarize and discuss experimental data obtained on new microbial rhodopsin variants, highlighting their contribution to the refinement and generalization of the ideas crystallized in the previous century. In particular, we will focus on the proton transport (and transfers) vectoriality and their structural determinants, which, in many cases, remain unidentified.
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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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2
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Inoue K. Diversity, Mechanism, and Optogenetic Application of Light-Driven Ion Pump Rhodopsins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:89-126. [PMID: 33398809 DOI: 10.1007/978-981-15-8763-4_6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ion-transporting microbial rhodopsins are widely used as major molecular tools in optogenetics. They are categorized into light-gated ion channels and light-driven ion pumps. While the former passively transport various types of cations and anions in a light-dependent manner, light-driven ion pumps actively transport specific ions, such as H+, Na+, Cl-, against electrophysiological potential by using light energy. Since the ion transport by these pumps induces hyperpolarization of membrane potential and inhibit neural firing, light-driven ion-pumping rhodopsins are mostly applied as inhibitory optogenetics tools. Recent progress in genome and metagenome sequencing identified more than several thousands of ion-pumping rhodopsins from a wide variety of microbes, and functional characterization studies has been revealing many new types of light-driven ion pumps one after another. Since light-gated channels were reviewed in other chapters in this book, here the rapid progress in functional characterization, molecular mechanism study, and optogenetic application of ion-pumping rhodopsins were reviewed.
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Affiliation(s)
- Keiichi Inoue
- The Institute for Solid State Physics, The University of Tokyo, Chiba, Japan.
- PRESTO, Japan Science and Technology Agency, Saitama, Japan.
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3
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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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4
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Harris A, Ljumovic M, Bondar AN, Shibata Y, Ito S, Inoue K, Kandori H, Brown LS. A new group of eubacterial light-driven retinal-binding proton pumps with an unusual cytoplasmic proton donor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1518-29. [PMID: 26260121 DOI: 10.1016/j.bbabio.2015.08.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 08/05/2015] [Accepted: 08/05/2015] [Indexed: 10/23/2022]
Abstract
One of the main functions of microbial rhodopsins is outward-directed light-driven proton transport across the plasma membrane, which can provide sources of energy alternative to respiration and chlorophyll photosynthesis. Proton-pumping rhodopsins are found in Archaea (Halobacteria), multiple groups of Bacteria, numerous fungi, and some microscopic algae. An overwhelming majority of these proton pumps share the common transport mechanism, in which a proton from the retinal Schiff base is first transferred to the primary proton acceptor (normally an Asp) on the extracellular side of retinal. Next, reprotonation of the Schiff base from the cytoplasmic side is mediated by a carboxylic proton donor (Asp or Glu), which is located on helix C and is usually hydrogen-bonded to Thr or Ser on helix B. The only notable exception from this trend was recently found in Exiguobacterium, where the carboxylic proton donor is replaced by Lys. Here we describe a new group of efficient proteobacterial retinal-binding light-driven proton pumps which lack the carboxylic proton donor on helix C (most often replaced by Gly) but possess a unique His residue on helix B. We characterize the group spectroscopically and propose that this histidine forms a proton-donating complex compensating for the loss of the carboxylic proton donor.
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Affiliation(s)
- Andrew Harris
- Department of Physics, University of Guelph, ON, Canada
| | | | | | - Yohei Shibata
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan
| | - Shota Ito
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan
| | - Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan; PRESTO, Japan Science and Technology Agency, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Nagoya, Japan.
| | - Leonid S Brown
- Department of Physics, University of Guelph, ON, Canada.
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5
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Ernst OP, Lodowski DT, Elstner M, Hegemann P, Brown L, Kandori H. Microbial and animal rhodopsins: structures, functions, and molecular mechanisms. Chem Rev 2014; 114:126-63. [PMID: 24364740 PMCID: PMC3979449 DOI: 10.1021/cr4003769] [Citation(s) in RCA: 785] [Impact Index Per Article: 78.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Oliver P. Ernst
- Departments
of Biochemistry and Molecular Genetics, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Toronto, Ontario M5S 1A8, Canada
| | - David T. Lodowski
- Center
for Proteomics and Bioinformatics, Case
Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Marcus Elstner
- Institute
for Physical Chemistry, Karlsruhe Institute
of Technology, Kaiserstrasse
12, 76131 Karlsruhe, Germany
| | - Peter Hegemann
- Institute
of Biology, Experimental Biophysics, Humboldt-Universität
zu Berlin, Invalidenstrasse
42, 10115 Berlin, Germany
| | - Leonid
S. Brown
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Hideki Kandori
- Department
of Frontier Materials, Nagoya Institute
of Technology, Showa-ku, Nagoya 466-8555, Japan
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6
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Saier MH. Microcompartments and protein machines in prokaryotes. J Mol Microbiol Biotechnol 2013; 23:243-69. [PMID: 23920489 DOI: 10.1159/000351625] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The prokaryotic cell was once thought of as a 'bag of enzymes' with little or no intracellular compartmentalization. In this view, most reactions essential for life occurred as a consequence of random molecular collisions involving substrates, cofactors and cytoplasmic enzymes. Our current conception of a prokaryote is far from this view. We now consider a bacterium or an archaeon as a highly structured, nonrandom collection of functional membrane-embedded and proteinaceous molecular machines, each of which serves a specialized function. In this article we shall present an overview of such microcompartments including (1) the bacterial cytoskeleton and the apparati allowing DNA segregation during cell division; (2) energy transduction apparati involving light-driven proton pumping and ion gradient-driven ATP synthesis; (3) prokaryotic motility and taxis machines that mediate cell movements in response to gradients of chemicals and physical forces; (4) machines of protein folding, secretion and degradation; (5) metabolosomes carrying out specific chemical reactions; (6) 24-hour clocks allowing bacteria to coordinate their metabolic activities with the daily solar cycle, and (7) proteinaceous membrane compartmentalized structures such as sulfur granules and gas vacuoles. Membrane-bound prokaryotic organelles were considered in a recent Journal of Molecular Microbiology and Biotechnology written symposium concerned with membranous compartmentalization in bacteria [J Mol Microbiol Biotechnol 2013;23:1-192]. By contrast, in this symposium, we focus on proteinaceous microcompartments. These two symposia, taken together, provide the interested reader with an objective view of the remarkable complexity of what was once thought of as a simple noncompartmentalized cell.
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Affiliation(s)
- Milton H Saier
- Division of Biological Sciences, Department of Molecular Biology, University of California at San Diego, La Jolla, Calif. 92093-0116, USA.
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7
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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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8
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Borshchevskiy VI, Round ES, Popov AN, Büldt G, Gordeliy VI. X-ray-radiation-induced changes in bacteriorhodopsin structure. J Mol Biol 2011; 409:813-25. [PMID: 21530535 DOI: 10.1016/j.jmb.2011.04.038] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 04/12/2011] [Accepted: 04/13/2011] [Indexed: 11/29/2022]
Abstract
Bacteriorhodopsin (bR) provides light-driven vectorial proton transport across a cell membrane. Creation of electrochemical potential at the membrane is a universal step in energy transformation in a cell. Published atomic crystallographic models of early intermediate states of bR show a significant difference between them, and conclusions about pumping mechanisms have been contradictory. Here, we present a quantitative high-resolution crystallographic study of conformational changes in bR induced by X-ray absorption. It is shown that X-ray doses that are usually accumulated during data collection for intermediate-state studies are sufficient to significantly alter the structure of the protein. X-ray-induced changes occur primarily in the active site of bR. Structural modeling showed that X-ray absorption triggers retinal isomerization accompanied by the disappearance of electron densities corresponding to the water molecule W402 bound to the Schiff base. It is demonstrated that these and other X-ray-induced changes may mimic functional conformational changes of bR leading to misinterpretation of the earlier obtained X-ray crystallographic structures of photointermediates.
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Affiliation(s)
- Valentin I Borshchevskiy
- Laboratoire des Protéines Membranaires, Institut de Biologie Structurale J.-P. Ebel, UMR5075 CEA-CNRS-UJF, Grenoble 38027, France
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9
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Morgan JE, Vakkasoglu AS, Lanyi JK, Gennis RB, Maeda A. Coordinating the structural rearrangements associated with unidirectional proton transfer in the bacteriorhodopsin photocycle induced by deprotonation of the proton-release group: a time-resolved difference FTIR spectroscopic study. Biochemistry 2010; 49:3273-81. [PMID: 20232848 DOI: 10.1021/bi901757y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the photocycle of bacteriorhodopsin at pH 7, proton release from the proton releasing group (PRG) to the extracellular medium occurs during formation of the M intermediate. This proton release is inhibited at acidic pH, below the pK(a) of the PRG, approximately 6 in M, and instead occurs later in the cycle as the initial state is restored from the O intermediate. Here, structural changes related to deprotonation of the PRG have been investigated by time-resolved FTIR spectroscopy at 25 degrees C. The vibrational features at 2100-1790, 1730-1685, 1661, and 1130-1045 cm(-1) have greater negative intensity in the pure M-minus-BR spectrum and even in the M-minus-BR spectrum, that is present earlier together with the L-minus-BR spectrum, at pH 7, than in the corresponding M-minus-BR spectra at pH 5 or 4. The D212N mutation abolishes the decreases in the intensities of the broad feature between 1730 and 1685 cm(-1) and the band at 1661 cm(-1). The 1730-1685 cm(-1) feature may arise from transition dipole coupling of the backbone carbonyl groups of Glu204, Phe208, Asp212, and Lys216 interacting with Tyr57 and C(15)-H of the chromophore. The 1661 cm(-1) band, which is insensitive to D(2)O substitution, may arise by interaction of the backbone carbonyl of Asp212 with C(15)-H. The 2100-1790 cm(-1) feature with a trough at 1885 cm(-1) could be due to a water cluster. Depletion of these bands upon deprotonation of the PRG is attributable to disruption of a coordinated structure, held in place by interactions of Asp212. Deprotonation of the PRG is also accompanied by disruption of the interaction of the water molecule near Arg82. The liberated Asp212 may stabilize the protonated state of Asp85 and thus confer unidirectionality to the transport.
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Affiliation(s)
- Joel E Morgan
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Room 2137, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, USA
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10
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Rhinow D, Hampp N. Curvature of purple membranes comprising permanently wedge-shaped bacteriorhodopsin molecules is regulated by lipid content. J Phys Chem B 2010; 114:549-56. [PMID: 19908872 DOI: 10.1021/jp908408d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Purple membrane (PM) from Halobacterium salinarum has been studied by many groups and is commonly described as a flat 2-D crystalline membrane microdomain which contains a hexagonal crystalline lattice of bacteriorhodopsin (BR) trimers in a stoichiometric ratio of 10:1 between lipids and BR. BR is the key protein in the halobacterial photosynthetic system and acts as a light-driven proton pump. Upon absorption of a photon, BR undergoes a cyclic series of intramolecular changes, among them a transient "wedge-like" geometrical change of the protein due to a tilt in helix F, one of the seven alpha-helical domains of BR. Due to the strong coupling between the BRs in the crystalline lattice, this may affect membrane topography. In nature, only low light levels occur and the total number of BRs in the "wedge-shaped" state is negligible. For mutated PMs like PM-D85T and PM-D85N (PM-D85X, X = neutral residue), the change of the membrane topography can be triggered in a pH-dependent manner. PMs containing BR-D85X look like "cups" at certain pH values. How does nature deal with a mutated PM like PM-D96G/F171C/F219L (PM-Tri) which comprises permanently "wedge-shaped" BRs and how does this influence membrane assembly? Astonishingly, we observed that PM-Tri is flat. Obviously, the morphology of Halobacterium salinarum is highly conserved and requires flat PMs to be assembled. We found that the lipid content of PM-Tri is specifically altered to assemble a hexagonal crystalline PM-Tri lattice of flat topography.
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Affiliation(s)
- Daniel Rhinow
- Department of Chemistry, University of Marburg, Hans-Meerwein-Strasse, D-35032 Marburg, Germany
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11
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Matsuoka D, Nakasako M. Prediction of Hydration Structures around Hydrophilic Surfaces of Proteins by Using the Empirical Hydration Distribution Functions from a Database Analysis. J Phys Chem B 2010; 114:4652-63. [DOI: 10.1021/jp9100224] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daisuke Matsuoka
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan, and RIKEN Harima Institute, 1-1-1 Kouto, Mikaduki, Sayo, Hyogo, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan, and RIKEN Harima Institute, 1-1-1 Kouto, Mikaduki, Sayo, Hyogo, Japan
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12
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Antoranz Contera S, Voïtchovsky K, Ryan JF. Controlled ionic condensation at the surface of a native extremophile membrane. NANOSCALE 2010; 2:222-229. [PMID: 20644798 DOI: 10.1039/b9nr00248k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
At the nanoscale level biological membranes present a complex interface with the solvent. The functional dynamics and relative flexibility of membrane components together with the presence of specific ionic effects can combine to create exciting new phenomena that challenge traditional theories such as the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory or models interpreting the role of ions in terms of their ability to structure water (structure making/breaking). Here we investigate ionic effects at the surface of a highly charged extremophile membrane composed of a proton pump (bacteriorhodopsin) and archaeal lipids naturally assembled into a 2D crystal. Using amplitude-modulation atomic force microscopy (AM-AFM) in solution, we obtained sub-molecular resolution images of ion-induced surface restructuring of the membrane. We demonstrate the presence of a stiff cationic layer condensed at its extracellular surface. This layer cannot be explained by traditional continuum theories. Dynamic force spectroscopy experiments suggest that it is produced by electrostatic correlation mediated by a Manning-type condensation of ions. In contrast, the cytoplasmic surface is dominated by short-range repulsive hydration forces. These findings are relevant to archaeal bioenergetics and halophilic adaptation. Importantly, they present experimental evidence of a natural system that locally controls its interactions with the surrounding medium and challenges our current understanding of biological interfaces.
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Affiliation(s)
- Sonia Antoranz Contera
- University of Oxford, Bionanotechnology IRC, Clarendon Laboratory, Physics Department, Parks Road, OX1 3PU, Oxford, UK.
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13
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Hirai T, Subramaniam S, Lanyi JK. Structural snapshots of conformational changes in a seven-helix membrane protein: lessons from bacteriorhodopsin. Curr Opin Struct Biol 2009; 19:433-9. [PMID: 19643594 DOI: 10.1016/j.sbi.2009.07.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Revised: 07/09/2009] [Accepted: 07/10/2009] [Indexed: 11/28/2022]
Abstract
Recent advances in crystallizing integral membrane proteins have led to atomic models for the structures of several seven-helix membrane proteins, including those in the G-protein-coupled receptor family. Further steps toward exploring structure-function relationships will undoubtedly involve determination of the structural changes that occur during the various stages of receptor activation and deactivation. We expect that these efforts will bear many parallels to the studies of conformational changes in bacteriorhodopsin, which still remains the best-studied seven-helix membrane protein. Here, we provide a brief review of some of the lessons learned, the challenges faced, and the controversies over the last decade with determining conformational changes in bacteriorhodopsin. Our hope is that this analysis will be instructive for similar structural studies, especially of other seven-helix membrane proteins, in the coming decade.
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Affiliation(s)
- Teruhisa Hirai
- Three-dimensional Microscopy Research Team, RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.
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14
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Abstract
Recent advances in the crystallography of bacteriorhodopsin, the light-driven proton pump, have yielded structural models for all intermediates of the photochemical cycle. For seven of the species, X-ray diffraction data were collected from trapped photostationary states in crystals, and for the two remaining ones the structures of selected mutants are available. The changes of the retinal chromophore, protein and bound water describe, at an atomic level, how accommodation of the twisted photoisomerized retinal to its binding site causes de-protonation of the retinal Schiff base and initiates cascades of gradual conformational rearrangements of the protein. One cascade propagates in the extracellular direction and results in proton release, and the other in the cytoplasmic direction and results in side-chain and main-chain rearrangements, formation of a chain of hydrogen-bonded water, and proton uptake from the bulk. Such local-global conformational coupling, with gradual spreading of a local perturbation over the rest of the protein, might be the uniting principle of transporters and receptors.
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Affiliation(s)
- Janos K Lanyi
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA.
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15
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Hirai T, Subramaniam S. Protein conformational changes in the bacteriorhodopsin photocycle: comparison of findings from electron and X-ray crystallographic analyses. PLoS One 2009; 4:e5769. [PMID: 19488399 PMCID: PMC2685002 DOI: 10.1371/journal.pone.0005769] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 04/06/2009] [Indexed: 11/18/2022] Open
Abstract
Light-driven conformational changes in the membrane protein bacteriorhodopsin have been studied extensively using X-ray and electron crystallography, resulting in the deposition of >30 sets of coordinates describing structural changes at various stages of proton transport. Using projection difference Fourier maps, we show that coordinates reported by different groups for the same photocycle intermediates vary considerably in the extent and nature of conformational changes. The different structures reported for the same intermediate cannot be reconciled in terms of differing extents of change on a single conformational trajectory. New measurements of image phases obtained by cryo-electron microscopy of the D96G/F171C/F219L triple mutant provide independent validation for the description of the large protein conformational change derived at 3.2 A resolution by electron crystallography of 2D crystals, but do not support atomic models for light-driven conformational changes derived using X-ray crystallography of 3D crystals. Our findings suggest that independent determination of phase information from 2D crystals can be an important tool for testing the accuracy of atomic models for membrane protein conformational changes.
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Affiliation(s)
- Teruhisa Hirai
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (TH); (SS)
| | - Sriram Subramaniam
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (TH); (SS)
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16
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Polívka T, Balashov SP, Chábera P, Imasheva ES, Yartsev A, Sundström V, Lanyi JK. Femtosecond carotenoid to retinal energy transfer in xanthorhodopsin. Biophys J 2009; 96:2268-77. [PMID: 19289053 DOI: 10.1016/j.bpj.2009.01.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 12/17/2008] [Accepted: 01/08/2009] [Indexed: 10/21/2022] Open
Abstract
Xanthorhodopsin of the extremely halophilic bacterium Salinibacter ruber represents a novel antenna system. It consists of a carbonyl carotenoid, salinixanthin, bound to a retinal protein that serves as a light-driven transmembrane proton pump similar to bacteriorhodopsin of archaea. Here we apply the femtosecond transient absorption technique to reveal the excited-state dynamics of salinixanthin both in solution and in xanthorhodopsin. The results not only disclose extremely fast energy transfer rates and pathways, they also reveal effects of the binding site on the excited-state properties of the carotenoid. We compared the excited-state dynamics of salinixanthin in xanthorhodopsin and in NaBH(4)-treated xanthorhodopsin. The NaBH(4) treatment prevents energy transfer without perturbing the carotenoid binding site, and allows observation of changes in salinixanthin excited-state dynamics related to specific binding. The S(1) lifetimes of salinixanthin in untreated and NaBH(4)-treated xanthorhodopsin were identical (3 ps), confirming the absence of the S(1)-mediated energy transfer. The kinetics of salinixanthin S(2) decay probed in the near-infrared region demonstrated a change of the S(2) lifetime from 66 fs in untreated xanthorhodopsin to 110 fs in the NaBH(4)-treated protein. This corresponds to a salinixanthin-retinal energy transfer time of 165 fs and an efficiency of 40%. In addition, binding of salinixanthin to xanthorhodopsin increases the population of the S(*) state that decays in 6 ps predominantly to the ground state, but a small fraction (<10%) of the S(*) state generates a triplet state.
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Affiliation(s)
- Tomás Polívka
- Institute of Physical Biology, University of South Bohemia, Nové Hrady, Czech Republic.
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17
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Kubo M, Kikukawa T, Miyauchi S, Seki A, Kamiya M, Aizawa T, Kawano K, Kamo N, Demura M. Role of Arg123 in Light-driven Anion Pump Mechanisms ofpharaonisHalorhodopsin. Photochem Photobiol 2009; 85:547-55. [DOI: 10.1111/j.1751-1097.2009.00538.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Abstract
Sensory rhodopsin I (SRI) in Halobacterium salinarum acts as a receptor for single-quantum attractant and two-quantum repellent phototaxis, transmitting light stimuli via its bound transducer HtrI. Signal-inverting mutations in the SRI-HtrI complex reverse the single-quantum response from attractant to repellent. Fast intramolecular charge movements reported here reveal that the unphotolyzed SRI-HtrI complex exists in two conformational states, which differ by their connection of the retinylidene Schiff base in the SRI photoactive site to inner or outer half-channels. In single-quantum photochemical reactions, the conformer with the Schiff base connected to the cytoplasmic (CP) half-channel generates an attractant signal, whereas the conformer with the Schiff base connected to the extracellular (EC) half-channel generates a repellent signal. In the wild-type complex the conformer equilibrium is poised strongly in favor of that with CP-accessible Schiff base. Signal-inverting mutations shift the equilibrium in favor of the EC-accessible Schiff base form, and suppressor mutations shift the equilibrium back toward the CP-accessible Schiff base form, restoring the wild-type phenotype. Our data show that the sign of the behavioral response directly correlates with the state of the connectivity switch, not with the direction of proton movements or changes in acceptor pK(a). These findings identify a shared fundamental process in the mechanisms of transport and signaling by the rhodopsin family. Furthermore, the effects of mutations in the HtrI subunit of the complex on SRI Schiff base connectivity indicate that the two proteins are tightly coupled to form a single unit that undergoes a concerted conformational transition.
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19
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Kawamura I, Ohmine M, Tanabe J, Tuzi S, Saitô H, Naito A. Dynamic aspects of extracellular loop region as a proton release pathway of bacteriorhodopsin studied by relaxation time measurements by solid state NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3090-7. [DOI: 10.1016/j.bbamem.2007.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2007] [Revised: 11/02/2007] [Accepted: 11/05/2007] [Indexed: 11/30/2022]
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20
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Kawamura I, Degawa Y, Yamaguchi S, Nishimura K, Tuzi S, Saitô H, Naito A. Pressure-induced isomerization of retinal on bacteriorhodopsin as disclosed by fast magic angle spinning NMR. Photochem Photobiol 2007; 83:346-50. [PMID: 17076543 DOI: 10.1562/2006-06-20-rc-941] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Bacteriorhodopsin (bR) is a retinal protein in purple membrane of Halobacterium salinarum, which functions as a light-driven proton pump. We have detected pressure-induced isomerization of retinal in bR by analyzing 15N cross polarization-magic angle spinning (CP-MAS) NMR spectra of [zeta-15N]Lys-labeled bR. In the 15N-NMR spectra, both all-trans and 13-cis retinal configurations have been observed in the Lys N(zeta) in protonated Schiff base at 148.0 and 155.0 ppm, respectively, at the MAS frequency of 4 kHz in the dark. When the MAS frequency was increased up to 12 kHz corresponding to the sample pressure of 63 bar, the 15N-NMR signals of [zeta-15N]Lys in Schiff base of retinal were broadened. On the other hand, other [zeta-15N]Lys did not show broadening. Subsequently, the increased signal intensity of [zeta-15N]Lys in Schiff base of 13-cis retinal at 155.0 ppm was observed when the MAS frequency was decreased from 12 to 4 kHz. These results showed that the equilibrium constant of [all-trans-bR]/[13-cis-bR] in retinal decreased by the pressure of 63 bar. It was also revealed that the structural changes induced by the pressure occurred in the vicinity of retinal. Therefore, microscopically, hydrogen-bond network around retinal would be disrupted or distorted by a constantly applied pressure. It is, therefore, clearly demonstrated that increased pressure induced by fast MAS frequencies generated isomerization of retinal from all-trans to 13-cis state in the membrane protein bR.
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Affiliation(s)
- Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, Hodogaya-ku, Yokohama, Japan
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21
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Klare JP, Chizhov I, Engelhard M. Microbial rhodopsins: scaffolds for ion pumps, channels, and sensors. Results Probl Cell Differ 2007; 45:73-122. [PMID: 17898961 DOI: 10.1007/400_2007_041] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Microbial rhodopsins have been intensively researched for the last three decades. Since the discovery of bacteriorhodopsin, the scope of microbial rhodopsins has been considerably extended, not only in view of the large number of family members, but also their functional properties as pumps, sensors, and channels. In this review, we give a short overview of old and newly discovered microbial rhodopsins, the mechanism of signal transfer and ion transfer, and we discuss structural and mechanistic aspects of phototaxis.
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Affiliation(s)
- Johann P Klare
- Fachbereich Physik, University Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany
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22
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Hendler RW. An apparent general solution for the kinetic models of the bacteriorhodopsin photocycles. J Phys Chem B 2007; 109:16515-28. [PMID: 16853100 DOI: 10.1021/jp052733h] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
For the past decade, the field of Bacteriorhodopsin (BR) research has been influenced by a kinetic view of the photocycle as a reversible, homogeneous, model (RHM) with a linear sequence of intermediates. More recently, we proposed a much different model which consists of essentially unidirectional, parallel (i.e., heterogeneous) cycles (UPM) (Hendler, R. W.; Shrager, R. I.; Bose, S. J. Phys. Chem. B 2001, 105, 3319-3328). It is important to try to resolve which of the two models is more likely to be correct, because models influence and provide a basis for further experimentation. Therefore, in this communication, we reexamine the basis for the RHM with a focus on the most recent and complete description of this model (van Stokkum, I., H., M.; Lozier, R. J. Phys. Chem. B 2002, 106, 3477-3485) vis a vis the UPM in an in-depth study. We show that (i) the tested RHM does not really work for the data of van Stokkum and Lozier nor ours; (ii) no previously published RHM model has been shown to work for data under any conditions; (iii) there are many published observations that are difficult if not impossible to explain by RHM, but are readily explained by parallel cycles. It is also shown that either a UPM or a parallel cycle model with limited reversibility correctly describes photocycle data collected at pH 5, 7, and 9 and at 10, 20, and 30 degrees and is consistent with all known experimental observations.
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Affiliation(s)
- Richard W Hendler
- Laboratory of Cell Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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23
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Zimányi L, Saltiel J, Brown LS, Lanyi JK. A priori resolution of the intermediate spectra in the bacteriorhodopsin photocycle: the time evolution of the L spectrum revealed. J Phys Chem A 2007; 110:2318-21. [PMID: 16480288 PMCID: PMC2561303 DOI: 10.1021/jp056874v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Resolution of the spectra of the intermediates in the photocycle of wild-type bacteriorhodopsin (BR) was achieved by singular value decomposition with exponential-fit-assisted self-modeling (SVD-EFASM) treatment of multichannel difference spectra measured at 5 degrees C during the course of the photocycle. New is the finding that two spectrally distinct L intermediates, L(1) and L(2), form sequentially. Our conclusion is that the photocycle is more complex than most published schemes. The dissection of the spectrally different L forms eliminates stoichiometric discrepancies usually appearing as systematically varying total intermediate concentrations before the onset of BR recovery. In addition, our analysis reveals that the red tails in the spectra of K and L(1) are more substantial than those of L(2) and BR. We suggest that these subtle differences in the shapes of the spectra reflect torsional and/or environmental differences in the retinyl chromophore.
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Affiliation(s)
- László Zimányi
- Institute of Biophysics, Biological Research Center of the Hungarian Academy of Sciences, P.O.Box 521, Szeged, Hungary, H-6701
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| | - Jack Saltiel
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306-4390 USA
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| | - Leonid S. Brown
- Department of Physics, University of Guelph, Guelph, ON, Canada
| | - Janos K. Lanyi
- Department of Physiology and Biophysics, University of California, Irvine, CA, USA
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24
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Lanyi JK. Studies of the Bacteriorhodopsin Photocycle without the Use of Light: Clues to Proton Transfer Coupled Reactions. J Mol Microbiol Biotechnol 2007; 12:210-7. [PMID: 17587869 DOI: 10.1159/000099642] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In the photochemical cycle of bacteriorhodopsin, the light-driven proton pump of halobacteria, only the first step, the isomerization of the all-trans retinal to 13-cis, is dependent on illumination. Because the steps that accomplish the translocation of a proton during the ensuing reaction sequence of intermediate states are thermal reactions, they have direct analogies with such steps in other ion pumps. In a surprisingly large number of cases, the reactions of the photocycle could be studied without using light. This review recounts experiments of this kind, and what they contribute to understanding the transport mechanism of this pump, and perhaps indirectly other ion pumps as well.
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Affiliation(s)
- Janos K Lanyi
- Department of Physiology and Biophysics, University of California, Irvine, California 92697-4560, USA.
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25
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Kawamura I, Kihara N, Ohmine M, Nishimura K, Tuzi S, Saitô H, Naito A. Solid-State NMR Studies of Two Backbone Conformations at Tyr185 as a Function of Retinal Configurations in the Dark, Light, and Pressure Adapted Bacteriorhodopsins. J Am Chem Soc 2007; 129:1016-7. [PMID: 17263367 DOI: 10.1021/ja0664887] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Izuru Kawamura
- Graduate School of Engineering, Yokohama National University, 79-5 Tokiwadai Hodogaya-ku, Yokohama 240-8501, Japan
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26
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Coureux PD, Genick UK. Triggering and Monitoring Light‐Sensing Reactions in Protein Crystals. Methods Enzymol 2007; 422:305-37. [PMID: 17628146 DOI: 10.1016/s0076-6879(06)22015-9] [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: 05/16/2023]
Abstract
Many bacterial photoreceptors signal via histidine kinases. The light-activated nature of these proteins provides unique experimental opportunities to study their molecular mechanisms of signal transduction. One of these opportunities is the combined application of X-ray crystallography and optical spectroscopy in protein crystals. By combining these two methods it is possible to correlate protein structure to protein function in a way that is exceedingly difficult or impossible to achieve in most other experimental systems. This chapter is divided into two parts. The first part provides a brief overview of light-regulated histidine kinases and the most important techniques for studying the structure of photocycle intermediates by crystallography. The second part of the chapter is dedicated to practical advice on how to select, mount, activate, and monitor the structural and spectroscopic responses of photoreceptor crystals. This chapter is intended for readers who want to start using these experimental tools themselves or who wish to understand enough about the techniques to critically evaluate the work of others.
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27
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Lanyi JK, Schobert B. Structural changes in the L photointermediate of bacteriorhodopsin. J Mol Biol 2006; 365:1379-92. [PMID: 17141271 PMCID: PMC1851893 DOI: 10.1016/j.jmb.2006.11.016] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Revised: 10/27/2006] [Accepted: 11/03/2006] [Indexed: 11/25/2022]
Abstract
The L to M reaction of the bacteriorhodopsin photocycle includes the crucial proton transfer from the retinal Schiff base to Asp85. In spite of the importance of the L state in deciding central issues of the transport mechanism in this pump, the serious disagreements among the three published crystallographic structures of L have remained unresolved. Here, we report on the X-ray diffraction structure of the L state, to 1.53-1.73 A resolutions, from replicate data sets collected from six independent crystals. Unlike earlier studies, the partial occupancy refinement uses diffraction intensities from the same crystals before and after the illumination to produce the trapped L state. The high reproducibility of inter-atomic distances, and bond angles and torsions of the retinal, lends credibility to the structural model. The photoisomerized 13-cis retinal in L is twisted at the C(13)=C(14) and C(15)=NZ double-bonds, and the Schiff base does not lose its connection to Wat402 and, therefore, to the proton acceptor Asp85. The protonation of Asp85 by the Schiff base in the L-->M reaction is likely to occur, therefore, via Wat402. It is evident from the structure of the L state that various conformational changes involving hydrogen-bonding residues and bound water molecules begin to propagate from the retinal to the protein at this stage already, and in both extracellular and cytoplasmic directions. Their rationales in the transport can be deduced from the way their amplitudes increase in the intermediates that follow L in the reaction cycle, and from the proton transfer reactions with which they are associated.
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Affiliation(s)
- Janos K Lanyi
- Department of Physiology & Biophysics, University of California, Irvine, CA 92697, USA.
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28
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Lanyi JK, Schobert B. Propagating structural perturbation inside bacteriorhodopsin: crystal structures of the M state and the D96A and T46V mutants. Biochemistry 2006; 45:12003-10. [PMID: 17002299 PMCID: PMC2782524 DOI: 10.1021/bi061310i] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The X-ray diffraction structure of the non-illuminated D96A bacteriorhodopsin mutant reveals structural changes as far away as 15 A from residue 96, at the retinal, Trp-182, Ala-215, and waters 501, 402, and 401. The Asp-to-Ala side-chain replacement breaks its hydrogen bond with Thr-46, and the resulting separation of the cytoplasmic ends of helices B and C is communicated to the retinal region through a chain of covalent and hydrogen bonds. The unexpected long-range consequences of the D96A mutation include breaking the hydrogen bond between O of Ala-215 and water 501 and the formation of a new hydrogen bond between water molecules 401 and 402 in the extracellular region. Because in the T46V mutant a new water molecule appears at Asp-96 and its hydrogen-bond to Ile-45 replaces Thr-46 as its link to helix B, the separation of helices B and C is smaller than that in D96A, and there are no atomic displacements elsewhere in the protein. Propagation of conformational changes along the chain between the retinal and Thr-46 had been observed earlier in the crystal structures of the D96N and E204Q mutants but in the trapped M state. Consistent with the perturbation of the retinal region in D96A, little change of the Thr-46 region occurs between the non-illuminated and M states of this mutant. It appears that a local perturbation can propagate along a track in both directions between the retinal and the Asp-96/Thr-46 pair, either from photoisomerization of the retinal in the wild-type protein in one case or from the D96A mutation in the other.
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Affiliation(s)
- Janos K Lanyi
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA.
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29
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Lanyi JK. Proton transfers in the bacteriorhodopsin photocycle. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:1012-8. [PMID: 16376293 DOI: 10.1016/j.bbabio.2005.11.003] [Citation(s) in RCA: 158] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Revised: 11/08/2005] [Accepted: 11/10/2005] [Indexed: 11/23/2022]
Abstract
The steps in the mechanism of proton transport in bacteriorhodopsin include examples for most kinds of proton transfer reactions that might occur in a transmembrane pump: proton transfer via a bridging water molecule, coupled protonation/deprotonation of two buried groups separated by a considerable distance, long-range proton migration over a hydrogen-bonded aqueous chain, and capture as well as release of protons at the membrane-water interface. The conceptual and technical advantages of this system have allowed close examination of many of these model reactions, some at an atomic level.
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Affiliation(s)
- Janos K Lanyi
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA.
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30
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Gunner MR, Mao J, Song Y, Kim J. Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:942-68. [PMID: 16905113 PMCID: PMC2760439 DOI: 10.1016/j.bbabio.2006.06.005] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2006] [Revised: 06/07/2006] [Accepted: 06/13/2006] [Indexed: 11/15/2022]
Abstract
A protein structure should provide the information needed to understand its observed properties. Significant progress has been made in developing accurate calculations of acid/base and oxidation/reduction reactions in proteins. Current methods and their strengths and weaknesses are discussed. The distribution and calculated ionization states in a survey of proteins is described, showing that a significant minority of acidic and basic residues are buried in the protein and that most of these remain ionized. The electrochemistry of heme and quinones are considered. Proton transfers in bacteriorhodopsin and coupled electron and proton transfers in photosynthetic reaction centers, 5-coordinate heme binding proteins and cytochrome c oxidase are highlighted as systems where calculations have provided insight into the reaction mechanism.
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Affiliation(s)
- M R Gunner
- Physics Department City College of New York, New York, NY 10031, USA.
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31
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Efremov R, Gordeliy VI, Heberle J, Büldt G. Time-resolved microspectroscopy on a single crystal of bacteriorhodopsin reveals lattice-induced differences in the photocycle kinetics. Biophys J 2006; 91:1441-51. [PMID: 16731567 PMCID: PMC1518640 DOI: 10.1529/biophysj.106.083345] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The determination of the intermediate state structures of the bacteriorhodopsin photocycle has lead to an unprecedented level of understanding of the catalytic process exerted by a membrane protein. However, the crystallographic structures of the intermediate states are only relevant if the working cycle is not impaired by the crystal lattice. Therefore, we applied visible and Fourier transform infrared spectroscopy (FTIR) microspectroscopy with microsecond time resolution to compare the photoreaction of a single bacteriorhodopsin crystal to that of bacteriorhodopsin residing in the native purple membrane. The analysis of the FTIR difference spectra of the resolved intermediate states reveals great similarity in structural changes taking place in the crystal and in PM. However, the kinetics of the photocycle are significantly altered in the three-dimensional crystal as compared to PM. Strikingly, the L state decay is accelerated in the crystal, whereas the M decay is delayed. The physical origin of this deviation and the implications for trapping of intermediate states are discussed. As a methodological advance, time-resolved step-scan FTIR spectroscopy on a single protein crystal is demonstrated for the first time which may be used in the future to gauge the functionality of other crystallized proteins with the molecular resolution of vibrational spectroscopy.
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Affiliation(s)
- R Efremov
- Forschungszentrum Jülich, IBI-2: Structural Biology, 52425 Jülich, Germany
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32
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Kandt C, Gerwert K, Schlitter J. Water dynamics simulation as a tool for probing proton transfer pathways in a heptahelical membrane protein. Proteins 2006; 58:528-37. [PMID: 15609339 DOI: 10.1002/prot.20343] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The proton transfer pathway in a heptahelical membrane protein, the light-driven proton pump bacteriorhodopsin (BR), is probed by a combined approach of structural analysis of recent X-ray models and molecular dynamics (MD) simulations that provide the diffusion pathways of internal and external water molecules. Analyzing the hydrogen-bond contact frequencies of the water molecules with protein groups, the complete proton pathway through the protein is probed. Beside the well-known proton binding sites in the protein interior-the protonated Schiff base, Asp85 and Asp96, and the H(5)O(2) (+) complex stabilized by Glu204 and Glu194-the proton release and uptake pathways to the protein surfaces are described in great detail. Further residues were identified, by mutation of which the proposed pathways can be verified. In addition the diffusion pathway of water 502 from Lys216 to Asp96 is shown to cover the positions of the intruding waters 503 and 504 in the N-intermediate. The transiently established water chain in the N-state provides a proton pathway from Asp96 to the Schiff base in the M- to N-transition in a Grotthus-like mechanism, as concluded earlier from time-resolved Fourier transform infrared experiments [le Coutre et al., Proc Nat Acad Sci USA 1995;92:4962-4966].
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Affiliation(s)
- Christian Kandt
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, Bochum, Germany
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33
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Ming M, Lu M, Balashov SP, Ebrey TG, Li Q, Ding J. pH dependence of light-driven proton pumping by an archaerhodopsin from Tibet: comparison with bacteriorhodopsin. Biophys J 2006; 90:3322-32. [PMID: 16473896 PMCID: PMC1432102 DOI: 10.1529/biophysj.105.076547] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2005] [Accepted: 01/19/2006] [Indexed: 11/18/2022] Open
Abstract
The pH-dependence of photocycle of archaerhodopsin 4 (AR4) was examined, and the underlying proton pumping mechanism investigated. AR4 is a retinal-containing membrane protein isolated from a strain of halobacteria from a Tibetan salt lake. It acts as a light-driven proton pump like bacteriorhodopsin (BR). However, AR4 exhibits an "abnormal" feature--the time sequence of proton release and uptake is reversed at neutral pH. We show here that the temporal sequence of AR4 reversed to "normal"--proton release preceding proton uptake--when the pH is increased above 8.6. We estimated the pK(a) of the proton release complex (PRC) in the M-intermediate to be approximately 8.4, much higher than 5.7 of wide-type BR. The pH-dependence of the rate constant of M-formation shows that the pK(a) of PRC in the initial state of AR4 is approximately 10.4, whereas it is 9.7 in BR. Thus in AR4, the chromophore photoisomerization and subsequent proton transport from the Schiff base to Asp-85 is coupled to a decrease in the pK(a) of PRC from 10.4 to 8.4, which is 2 pK units less than in BR (4 units). This weakened coupling accounts for the lack of early proton release at neutral pH and the reversed time sequence of proton release and uptake in AR4. Nevertheless the PRC in AR4 effectively facilitates deprotonation of primary proton acceptor and recovery of initial state at neutral pH. We found also that all pK(a)s of the key amino acid residues in AR4 were elevated compared to those of BR.
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Affiliation(s)
- Ming Ming
- Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, China
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34
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Brown LS, Jung KH. Bacteriorhodopsin-like proteins of eubacteria and fungi: the extent of conservation of the haloarchaeal proton-pumping mechanism. Photochem Photobiol Sci 2006; 5:538-46. [PMID: 16761082 DOI: 10.1039/b514537f] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A stereotypical image of a retinal-binding proton pump derived from extensive studies of halobacterial ion-transporting and sensory rhodopsins is a fast-cycling protein which possesses two strategically placed carboxylic acids serving as proton donor and acceptor for the retinal Schiff base. We review recent biophysical and bioinformatic data on the novel eubacterial and eucaryotic rhodopsins to analyze the extent of conservation of the haloarchaeal mechanism of transmembrane proton transport. We show that only the most essential elements of the haloarchaeal proton-pumping machinery are conserved universally, and that a mere presence of these elements in primary structures does not guarantee the proton-pumping ability.
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Affiliation(s)
- Leonid S Brown
- Department of Physics, University of Guelph, Guelph, Ontario N1G 2W1, Canada.
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Misquitta LV, Misquitta Y, Cherezov V, Slattery O, Mohan JM, Hart D, Zhalnina M, Cramer WA, Caffrey M. Membrane protein crystallization in lipidic mesophases with tailored bilayers. Structure 2005; 12:2113-24. [PMID: 15576026 DOI: 10.1016/j.str.2004.09.020] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2004] [Revised: 09/24/2004] [Accepted: 09/24/2004] [Indexed: 11/18/2022]
Abstract
Monoacylglycerols have been used as bilayered hosts for growing crystals of membrane proteins. To date, the lipids used have had chains 16 and 18 carbon atoms long. We hypothesized that a shorter-chained lipid producing a thinner bilayer would facilitate the so-called in meso crystallization process. A 14 carbon monoacylglycerol was chosen as the lipid with which to test the proposal. To be compatible with the in meso method, a cis olefinic bond was placed in its acyl chain at a location arrived at by rational design. The target lipid was synthesized and was shown to form the requisite mesophase at room temperature. In support of the hypothesis, it produced crystals of bacteriorhodopsin and the outer membrane transporter, BtuB. The latter is the first beta barrel protein to be crystallized by the in meso method. Protein stability in the short-chain lipid and how this relates to crystallogenesis are discussed.
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Affiliation(s)
- Lisa V Misquitta
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
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Mason AJ, Turner GJ, Glaubitz C. Conformational heterogeneity of transmembrane residues after the Schiff base reprotonation of bacteriorhodopsin. FEBS J 2005; 272:2152-64. [PMID: 15853800 DOI: 10.1111/j.1742-4658.2005.04633.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
bR, N-like and O-like intermediate states of [15N]methionine-labelled wild type and D85N/T170C bacteriorhodopsin were accumulated in native membranes by controlling the pH of the preparations. 15N cross polarization and magic angle sample spinning (CPMAS) NMR spectroscopy allowed resolution of seven out of nine resonances in the bR-state. It was possible to assign some of the observed resonances by using 13C/15N rotational echo double resonance (REDOR) NMR and Mn2+ quenching as well as D2O exchange, which helps to identify conformational changes after the bacteriorhodopsin Schiff base reprotonation. The significant differences in chemical shifts and linewidths detected for some of the resonances in N- and O-like samples indicate changes in conformation, structural heterogeneity or altered molecular dynamics in parts of the protein.
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Affiliation(s)
- A James Mason
- Centre for Biomolecular Magnetic Resonance and Institut für Biophysikalische Chemie, J.W. Goethe Universität, Frankfurt, Germany
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Kamikubo H, Kataoka M. Can the low-resolution structures of photointermediates of bacteriorhodopsin explain their crystal structures? Biophys J 2004; 88:1925-31. [PMID: 15596495 PMCID: PMC1305245 DOI: 10.1529/biophysj.104.045831] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To understand the molecular mechanism of light-driven proton pumps, the structures of the photointermediates of bacteriorhodopsin have been intensively investigated. Low-resolution diffraction techniques have demonstrated substantial conformational changes at the helix level in the M and N intermediates, between which there are noticeable differences. The intermediate structures at atomic resolution have also been solved by x-ray crystallography. Although the crystal structures have demonstrated local structural changes, such as hydrogen bond network rearrangements including water molecules, the large conformational changes at the helix level are not necessarily observed. Furthermore, the two reported crystal structures of an intermediate accumulated using a common method were distinct. To reconcile these apparent discrepancies, low-resolution projection maps were calculated from the crystal structures and compared to the low-resolution intermediate structures obtained using native membranes. The crystal structures can be categorized into three groups, which qualitatively correspond to the low-resolution structures of the M1-type, M2-type, and N-type determined in the native membrane. Based on these results, we conclude that at least three types of intermediate structures play a role during the photocycle.
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Affiliation(s)
- Hironari Kamikubo
- Graduate School of Materials Science, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
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Lanyi JK. What is the real crystallographic structure of the L photointermediate of bacteriorhodopsin? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1658:14-22. [PMID: 15282169 DOI: 10.1016/j.bbabio.2004.03.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2004] [Revised: 03/16/2004] [Accepted: 03/16/2004] [Indexed: 11/21/2022]
Abstract
In the last few years, three laboratories have reported three entirely different crystallographic models for the L photointermediate of bacteriorhodopsin. All are from X-ray diffraction of illuminated crystals that contain L in photostationary states created at similar cryogenic temperatures. This article compares the models and their implications, the crystallographic statistics and the methods used to derive them, as well as their agreement with non-crystallographic information.
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Affiliation(s)
- Janos K Lanyi
- Department of Physiology and Biophysics, College of Medicine, University of California, 349-D Medical Science, Irvine, CA 92697-4560, USA.
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Oka T, Inoue K, Kataoka M, Yagi N. Structural transition of bacteriorhodopsin is preceded by deprotonation of Schiff base: microsecond time-resolved x-ray diffraction study of purple membrane. Biophys J 2004; 88:436-42. [PMID: 15516520 PMCID: PMC1305020 DOI: 10.1529/biophysj.104.051748] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The structural changes in the photoreaction cycle of bacteriorhodopsin, a light-driven proton pump, was investigated at a resolution of 7 angstroms by a time-resolved x-ray diffraction experiment utilizing synchrotron x rays from an undulator of SPring-8. The x-ray diffraction measurement system, used in coupling with a pulsed YAG laser, enabled us to record a diffraction pattern from purple membrane film at a time-resolution of 6 micros over the time domain of 5 micros to 500 ms. In the time domain, the functionally most important M-intermediate appears. A series of time-resolved x-ray diffraction data after photo-excitation showed clear intensity changes caused by the conformational changes of helix G in the M-intermediate. The population of the reaction intermediate was prominently observed at approximately 5 ms after a photo-stimulus. In contrast, absorption measurement indicated the deprotonation of the Schiff base predominantly occurred at approximately 300 micros after a photo-stimulus. These results showed that the conformational changes characterizing structurally the M-intermediate predominantly occur at a later stage of the deprotonation of the Schiff base. Thus, the M-intermediate can be divided into two metastable stages with different physical characteristics.
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Affiliation(s)
- Toshihiko Oka
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa, Japan.
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Furutani Y, Bezerra AG, Waschuk S, Sumii M, Brown LS, Kandori H. FTIR Spectroscopy of the K Photointermediate ofNeurosporaRhodopsin: Structural Changes of the Retinal, Protein, and Water Molecules after Photoisomerization†. Biochemistry 2004; 43:9636-46. [PMID: 15274618 DOI: 10.1021/bi049158c] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Neurospora rhodopsin (NR, also known as NOP-1) is the first rhodopsin of the haloarchaeal type found in eucaryotes. NR demonstrates a very high degree of conservation of the amino acids that constitute the proton-conducting pathway in bacteriorhodopsin (BR), a light-driven proton pump of archaea. Nevertheless, NR does not appear to pump protons, suggesting the absence of the reprotonation switch that is necessary for the active transport. The photocycle of NR is much slower than that of BR, similar to the case of pharaonis phoborhodopsin (ppR), an archaeal photosensory protein. The functional and photochemical differences between NR and BR should be explained in the structural context. In this paper, we studied the structural changes of NR following retinal photoisomerization by means of low-temperature Fourier transform infrared (FTIR) spectroscopy and compared the obtained spectra with those for BR. For the spectroscopic analysis, we established the light-adaptation procedure for NR reconstituted into 1,2-dimyristoyl-sn-glycero- 3-phosphocholine/1,2-dimyristoyl-sn-glycero-3-phosphate (DMPC/DMPA) liposomes, which takes approximately 2 orders of magnitudes longer than in BR. The structure of the retinal chromophore and the hydrogen-bonding strength of the Schiff base in NR are similar to those in BR. Unique spectral features are observed for the S-H stretching vibrations of cysteine and amide-I vibrations for NR before and after retinal isomerization. In NR, there are no spectral changes assignable to the amide bands of alpha helices. The most prominent difference between NR and BR was seen for the water O-D stretching vibrations (measured in D(2)O). Unlike for haloarchaeal rhodopsins such as BR and ppR, no O-D stretches of water under strong hydrogen-bonded conditions (<2400 cm(-1)) were observed in the NR(K) minus NR difference spectra. This suggests a unique hydrogen-bonded network of the Schiff base region, which may be responsible for the lack of the reprotonation switch in NR.
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Affiliation(s)
- Yuji Furutani
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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