bacteriorhodopsins

Summary

Summary: Rhodopsins found in the PURPLE MEMBRANE of halophilic archaea such as HALOBACTERIUM HALOBIUM. Bacteriorhodopsins function as an energy transducers, converting light energy into electrochemical energy via PROTON PUMPS.

Top Publications

  1. Sudo Y, Spudich J. Three strategically placed hydrogen-bonding residues convert a proton pump into a sensory receptor. Proc Natl Acad Sci U S A. 2006;103:16129-34 pubmed
    ..The results demonstrate that evolution accomplished an elegant but simple conversion: The essential differences between transport and signaling proteins in the rhodopsin family are far less than previously imagined...
  2. Lanyi J, Schobert B. Propagating structural perturbation inside bacteriorhodopsin: crystal structures of the M state and the D96A and T46V mutants. Biochemistry. 2006;45:12003-10 pubmed publisher
  3. Saeedi P, Moosaabadi J, Sebtahmadi S, Behmanesh M, Mehrabadi J. Site-directed mutagenesis in bacteriorhodopsin mutants and their characterization for bioelectrical and biotechnological equipment. Biotechnol Lett. 2012;34:455-62 pubmed publisher
    ..However, mutants D85Q and D85N were almost inactive; and D85N had a prolonged M state, suggesting that it could be utilized in light memories. ..
  4. Lazarova T, Querol E, Padrós E. Coupling between the retinal thermal isomerization and the Glu194 residue of bacteriorhodopsin. Photochem Photobiol. 2009;85:617-23 pubmed publisher
    ..After 14 days in the dark the 13-cis to all-trans ratio was 1:3 in the mutant, compared to 2:1 in the wild type. These data clearly indicate the involvement of Glu194 in control of the rate of all-trans to 13-cis thermal isomerization...
  5. Dér A, Valkai S, Fábián L, Ormos P, Ramsden J, Wolff E. Integrated optical switching based on the protein bacteriorhodopsin. Photochem Photobiol. 2007;83:393-6 pubmed
    ..1 and 2) demonstrating a real switching effect by bR (efficiency higher than 90%) due to the M-state. Our results also imply that the refractive index change of the K-state (9 x 10(-4)) is high enough for fast switching. ..
  6. Bolhuis H, Palm P, Wende A, Falb M, Rampp M, Rodriguez Valera F, et al. The genome of the square archaeon Haloquadratum walsbyi : life at the limits of water activity. BMC Genomics. 2006;7:169 pubmed
  7. Gohon Y, Dahmane T, Ruigrok R, Schuck P, Charvolin D, Rappaport F, et al. Bacteriorhodopsin/amphipol complexes: structural and functional properties. Biophys J. 2008;94:3523-37 pubmed publisher
    ..In the absence of free APol, BR/APol particles can autoassociate into small or large ordered fibrils...
  8. Cappuccio J, Blanchette C, Sulchek T, Arroyo E, Kralj J, Hinz A, et al. Cell-free co-expression of functional membrane proteins and apolipoprotein, forming soluble nanolipoprotein particles. Mol Cell Proteomics. 2008;7:2246-53 pubmed publisher
  9. Hagedorn R, Gradmann D, Hegemann P. Dynamics of voltage profile in enzymatic ion transporters, demonstrated in electrokinetics of proton pumping rhodopsin. Biophys J. 2008;95:5005-13 pubmed publisher
    ..This analysis quantitatively infers dynamic changes of the voltage profile and of the pK values of the H(+)-binding sites involved...

Scientific Experts

More Information

Publications62

  1. Hirai T, Subramaniam S, Lanyi J. Structural snapshots of conformational changes in a seven-helix membrane protein: lessons from bacteriorhodopsin. Curr Opin Struct Biol. 2009;19:433-9 pubmed publisher
    ..Our hope is that this analysis will be instructive for similar structural studies, especially of other seven-helix membrane proteins, in the coming decade. ..
  2. Patil A, Premaruban T, Berthoumieu O, Watts A, Davis J. Enhanced photocurrent in engineered bacteriorhodopsin monolayer. J Phys Chem B. 2012;116:683-9 pubmed publisher
    ..Given the uniquely photoresponsive, wavelength-selective, and photostable characteristics of this protein, the work has implications for utilization in solar energy capture and photodetector devices. ..
  3. Morgan J, Vakkasoglu A, Lanyi J, Lugtenburg J, Gennis R, Maeda A. Structure changes upon deprotonation of the proton release group in the bacteriorhodopsin photocycle. Biophys J. 2012;103:444-52 pubmed publisher
  4. Wang T, Sessions A, Lunde C, Rouhani S, Glaeser R, Duan Y, et al. Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway. Structure. 2013;21:290-7 pubmed publisher
    ..We suspect that this protonation-switch mechanism could also be utilized in other proton pumps to minimize backflow and reinforce directionality. ..
  5. Mathesz A, Fábián L, Valkai S, Alexandre D, Marques P, Ormos P, et al. High-speed integrated optical logic based on the protein bacteriorhodopsin. Biosens Bioelectron. 2013;46:48-52 pubmed publisher
    ..The results are expected to have important implications for finding novel, alternative solutions in all-optical data processing research. ..
  6. Clemens M, Phatak P, Cui Q, Bondar A, Elstner M. Role of Arg82 in the early steps of the bacteriorhodopsin proton-pumping cycle. J Phys Chem B. 2011;115:7129-35 pubmed publisher
    ..The calculations indicate that protonation of Asp85 leads to a fast reorientation of the Arg82 side chain toward the extracellular proton release group. ..
  7. Katzen F, Fletcher J, Yang J, Kang D, Peterson T, Cappuccio J, et al. Insertion of membrane proteins into discoidal membranes using a cell-free protein expression approach. J Proteome Res. 2008;7:3535-42 pubmed publisher
    ..The approach provides a platform amenable to high-throughput structural and functional characterization of a variety of traditionally intractable drug targets. ..
  8. Yokoyama Y, Sonoyama M, Nakano T, Mitaku S. Structural change of bacteriorhodopsin in the purple membrane above pH 10 decreases heterogeneity of the irreversible photobleaching components. J Biochem. 2007;142:325-33 pubmed
    ..A model for the changes in kinetic behaviour and molecular structure around pH 10 is discussed, focusing on changes in charge distribution upon alkalinization. ..
  9. Sudo Y, Furutani Y, Spudich J, Kandori H. Early photocycle structural changes in a bacteriorhodopsin mutant engineered to transmit photosensory signals. J Biol Chem. 2007;282:15550-8 pubmed
    ..We also succeeded in measurements of L minus initial state spectra of BR-T, which are the first FTIR spectra of L intermediates among sensory rhodopsins...
  10. Perálvarez Marín A, Lorenz Fonfria V, Bourdelande J, Querol E, Kandori H, Padrós E. Inter-helical hydrogen bonds are essential elements for intra-protein signal transduction: the role of Asp115 in bacteriorhodopsin transport function. J Mol Biol. 2007;368:666-76 pubmed
    ..It also supports the idea that intra-helical hydrogen bonding clusters in the buried regions of transmembrane proteins can be potential elements in intra-protein signal transduction...
  11. Kwon S, Kim B, Song J, Kwak M, Lee C, Yoon J, et al. Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins. Genome Biol Evol. 2013;5:187-99 pubmed publisher
  12. Liu W, Hanson M, Stevens R, Cherezov V. LCP-Tm: an assay to measure and understand stability of membrane proteins in a membrane environment. Biophys J. 2010;98:1539-48 pubmed publisher
    ..This assay has the potential to guide protein engineering efforts and identify stabilizing conditions that may improve the chances of obtaining high-resolution structures of intrinsically unstable membrane proteins...
  13. Chen D, Lanyi J. Structural changes in the N and N' states of the bacteriorhodopsin photocycle. Biophys J. 2009;96:2779-88 pubmed publisher
    ..The structural changes reverse their directions and decay in the N' state. ..
  14. Gerwert K, Freier E, Wolf S. The role of protein-bound water molecules in microbial rhodopsins. Biochim Biophys Acta. 2014;1837:606-13 pubmed publisher
    ..This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks...
  15. Dahmane T, Rappaport F, Popot J. Amphipol-assisted folding of bacteriorhodopsin in the presence or absence of lipids: functional consequences. Eur Biophys J. 2013;42:85-101 pubmed publisher
    ..BR interactions with lipids, however, contribute to an effective photocycle...
  16. Sharma A, Walsh D, Bapteste E, Rodriguez Valera F, Ford Doolittle W, Papke R. Evolution of rhodopsin ion pumps in haloarchaea. BMC Evol Biol. 2007;7:79 pubmed
    ..In this initial study, we assess the roles of LGT and gene loss in the evolution of haloarchaeal rhodopsin ion pump genes, using phylogenetics and comparative genomics approaches...
  17. Lanyi J, Schobert B. Structural changes in the L photointermediate of bacteriorhodopsin. J Mol Biol. 2007;365:1379-92 pubmed publisher
    ..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...
  18. Li R, Cui X, Hu W, Lu Z, Li C. Fabrication of oriented poly-L-lysine/bacteriorhodopsin-embedded purple membrane multilayer structure for enhanced photoelectric response. J Colloid Interface Sci. 2010;344:150-7 pubmed publisher
    ..The photocurrent of bR-PM from the film through PLL assembler is higher than those assembled by other polycations, thus rendering a new platform to effectively enhance the bR photoelectric responses...
  19. Kato H, Zhang F, Yizhar O, Ramakrishnan C, Nishizawa T, Hirata K, et al. Crystal structure of the channelrhodopsin light-gated cation channel. Nature. 2012;482:369-74 pubmed publisher
  20. Zhang J, Yamazaki Y, Hikake M, Murakami M, Ihara K, Kouyama T. Crystal structure of the O intermediate of the Leu93?Ala mutant of bacteriorhodopsin. Proteins. 2012;80:2384-96 pubmed publisher
    ..Another significant difference is seen in the pH dependence of the structure of the proton release group, the pK(a) value of which is suggested to be much lower in O(slow) than in M...
  21. Freier E, Wolf S, Gerwert K. Proton transfer via a transient linear water-molecule chain in a membrane protein. Proc Natl Acad Sci U S A. 2011;108:11435-9 pubmed publisher
    ..Our discovery provides insight into proton-transfer mechanisms through hydrophobic core regions of ubiquitous membrane spanning proteins such as G-protein coupled receptors or cytochrome C oxidases. ..
  22. 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 pubmed publisher
    ..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. ..
  23. Sharma A, Sommerfeld K, Bullerjahn G, Matteson A, Wilhelm S, Jezbera J, et al. Actinorhodopsin genes discovered in diverse freshwater habitats and among cultivated freshwater Actinobacteria. ISME J. 2009;3:726-37 pubmed publisher
    ..The co-occurrence of an acI organism with a specific ActR variant in a mixed culture supports our hypothesis. ..
  24. Tarasov V, Besir H, Schwaiger R, Klee K, Furtwängler K, Pfeiffer F, et al. A small protein from the bop-brp intergenic region of Halobacterium salinarum contains a zinc finger motif and regulates bop and crtB1 transcription. Mol Microbiol. 2008;67:772-80 pubmed publisher
    ..In silico analysis of the genomes from H. salinarum and other archaea revealed a large family of similar small zinc finger motif proteins, some of which may also be involved in transcription regulation of their adjacent genes. ..
  25. Geibel S, Lörinczi E, Bamberg E, Friedrich T. Voltage dependence of proton pumping by bacteriorhodopsin mutants with altered lifetime of the M intermediate. PLoS ONE. 2013;8:e73338 pubmed publisher
    ..Thus, M-stabilizing mutations, including the triple mutation, drastically interfere with electrochemical H(+) gradient generation. ..
  26. Gillespie N, Ren L, Ramos L, Daniell H, Dews D, Utzat K, et al. Characterization and photochemistry of 13-desmethyl bacteriorhodopsin. J Phys Chem B. 2005;109:16142-52 pubmed
  27. Brown M, Heyn M, Job C, Kim S, Moltke S, Nakanishi K, et al. Solid-state 2H NMR spectroscopy of retinal proteins in aligned membranes. Biochim Biophys Acta. 2007;1768:2979-3000 pubmed
    ..Torsional strain is relaxed in the meta I state that precedes subsequent receptor activation. Comparison of the two retinal proteins using solid-state 2H NMR is thus illuminating in terms of their different biological functions...
  28. Joh N, Min A, Faham S, Whitelegge J, Yang D, Woods V, et al. Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins. Nature. 2008;453:1266-70 pubmed publisher
    ..Weak hydrogen-bonding should be reflected in considerations of membrane protein folding, dynamics, design, evolution and function. ..
  29. Wang T, Facciotti M, Duan Y. Schiff base switch II precedes the retinal thermal isomerization in the photocycle of bacteriorhodopsin. PLoS ONE. 2013;8:e69882 pubmed publisher
    ..Our simulations indicate that the thermal isomerization of retinal from 13-cis back to all-trans likely occurs independently from and after the SB C15?=?NZ rotation in the N-to-O transition. ..
  30. Bondar A, Suhai S, Fischer S, Smith J, Elstner M. Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: a theoretical analysis of structural elements. J Struct Biol. 2007;157:454-69 pubmed
  31. del Rosario R, Oppawsky C, Tittor J, Oesterhelt D. Modeling the membrane potential generation of bacteriorhodopsin. Math Biosci. 2010;225:68-80 pubmed publisher
    ..We also show that a decay term is necessary for modeling the rate of change of the membrane potential. ..
  32. Fábián L, Heiner Z, Mero M, Kiss M, Wolff E, Ormos P, et al. Protein-based ultrafast photonic switching. Opt Express. 2011;19:18861-70 pubmed publisher
    ..The results may serve as a basis for the future realization of protein-based integrated optical devices that can eventually lead to a conceptual revolution in the development of telecommunications technologies. ..
  33. Belrhali H, Nollert P, Royant A, Menzel C, Rosenbusch J, Landau E, et al. Protein, lipid and water organization in bacteriorhodopsin crystals: a molecular view of the purple membrane at 1.9 A resolution. Structure. 1999;7:909-17 pubmed
    ..Proton translocation from the Schiff base to the extracellular medium is mediated by a hydrogen-bond network that involves charged residues and water molecules...
  34. Grigorieff N, Ceska T, Downing K, Baldwin J, Henderson R. Electron-crystallographic refinement of the structure of bacteriorhodopsin. J Mol Biol. 1996;259:393-421 pubmed publisher
    ..The ordered and disordered regions of the structure are described by the temperature factor distribution...
  35. Kandori H, Furutani Y, Shimono K, Shichida Y, Kamo N. Internal water molecules of pharaonis phoborhodopsin studied by low-temperature infrared spectroscopy. Biochemistry. 2001;40:15693-8 pubmed
    ..These observations are consistent with the crystallographic structures of ppR and BR. The water structure and structural changes upon photoisomerization of ppR are discussed here on the basis of their infrared spectra. ..
  36. Kolbe M, Besir H, Essen L, Oesterhelt D. Structure of the light-driven chloride pump halorhodopsin at 1.8 A resolution. Science. 2000;288:1390-6 pubmed
    ..Ion dragging across the protonated Schiff base explains why chloride and proton translocation modes are mechanistically equivalent in archaeal rhodopsins...
  37. Kataoka M, Kamikubo H. Structures of photointermediates and their implications for the proton pump mechanism. Biochim Biophys Acta. 2000;1460:166-76 pubmed
    ..Based on the clarified global conformational change, we propose a model for the molecular mechanism of the proton pump. The global structural change is suggested to be a key component in establishing vectorial proton transport. ..
  38. Oka T, Yagi N, Fujisawa T, Kamikubo H, Tokunaga F, Kataoka M. Time-resolved x-ray diffraction reveals multiple conformations in the M-N transition of the bacteriorhodopsin photocycle. Proc Natl Acad Sci U S A. 2000;97:14278-82 pubmed
    ..The observed structural change at the F helix will increase access of the Schiff base and D96 to the cytoplasmic surface and facilitate the proton transfer steps that begin with the decay of the M state. ..
  39. Royant A, Nollert P, Edman K, Neutze R, Landau E, Pebay Peyroula E, et al. X-ray structure of sensory rhodopsin II at 2.1-A resolution. Proc Natl Acad Sci U S A. 2001;98:10131-6 pubmed
    ..The high-resolution structure of pSRII provides a structural basis to elucidate the mechanisms of phototransduction and color tuning...
  40. Leong D, Boyer H, Betlach M. Transcription of genes involved in bacterio-opsin gene expression in mutants of a halophilic archaebacterium. J Bacteriol. 1988;170:4910-5 pubmed
    ..These and other results lead us to propose that (i) brp gene expression can affect bat gene expression and (ii) the putative bat gene is involved in activating bop and brp gene expression...
  41. Jussila T, Li M, Tkachenko N, Parkkinen S, Li B, Jiang L, et al. Transient absorption and photovoltage study of' self-assembled bacteriorhodopsin/polycation multilayer films. Biosens Bioelectron. 2002;17:509-15 pubmed
    ..A simultaneous two-exponential decay in millisecond time domain was observed at red wavelengths. The source of the red-shifted absorption is suggested to be the C(610) intermediate of the cis photocycle of bR. ..
  42. Lanyi J, Schobert B. Crystallographic structure of the retinal and the protein after deprotonation of the Schiff base: the switch in the bacteriorhodopsin photocycle. J Mol Biol. 2002;321:727-37 pubmed
  43. Hiraki K, Hamanaka T, Zheng X, Shinada T, Kim J, Yoshihara K, et al. Bacteriorhodopsin analog regenerated with 13-desmethyl-13-iodoretinal. Biophys J. 2002;83:3460-9 pubmed
    ..13-I-bR is an advantageous specimen for kinetic investigations of light-induced structural changes associated with the proton pumping cycle by x-ray diffraction. ..
  44. Hayashi S, Tajkhorshid E, Schulten K. Molecular dynamics simulation of bacteriorhodopsin's photoisomerization using ab initio forces for the excited chromophore. Biophys J. 2003;85:1440-9 pubmed
    ..Supported by comparison with dynamic spectral modulations observed in femtosecond spectroscopy, the results identify the principal molecular motion during photoisomerization. ..
  45. Lanyi J, Schobert B. Local-global conformational coupling in a heptahelical membrane protein: transport mechanism from crystal structures of the nine states in the bacteriorhodopsin photocycle. Biochemistry. 2004;43:3-8 pubmed
    ..Such local-global conformational coupling between the ligand-binding site and the distant regions of the protein may be the shared mechanism of ion pumps and G-protein related receptors. ..
  46. Klare J, Bordignon E, Engelhard M, Steinhoff H. Sensory rhodopsin II and bacteriorhodopsin: light activated helix F movement. Photochem Photobiol Sci. 2004;3:543-7 pubmed
    ..In the second part, the helix F movement observed for both sensory rhodopsin and bacteriorhodopsin is evaluated and discussed in order to establish a common mechanism after photoreceptor activation. ..
  47. Takeda K, Matsui Y, Kamiya N, Adachi S, Okumura H, Kouyama T. Crystal structure of the M intermediate of bacteriorhodopsin: allosteric structural changes mediated by sliding movement of a transmembrane helix. J Mol Biol. 2004;341:1023-37 pubmed
    ..But, no appreciable change is induced in the peptide backbone of helices A,D, E and F. These structural changes are discussed from the viewpoint of translocation of water molecules...
  48. Horn C, Steinem C. Photocurrents generated by bacteriorhodopsin adsorbed on nano-black lipid membranes. Biophys J. 2005;89:1046-54 pubmed
    ..By adding the proton ionophore carbonyl cyanide-m-chlorophenylhydrazone the conductivity of the nano-BLMs increases, resulting in a higher stationary current, which proves that proton conductance occurs across the nano-BLMs...
  49. Shimono K, Furutani Y, Kandori H, Kamo N. A pharaonis phoborhodopsin mutant with the same retinal binding site residues as in bacteriorhodopsin. Biochemistry. 2002;41:6504-9 pubmed
    ..We conclude that the principal factor of the smaller than expected opsin shift in BR/ppR is the strong association of the Schiff base with the surrounding counterion complex. ..
  50. Edman K, Royant A, Larsson G, Jacobson F, Taylor T, van der Spoel D, et al. Deformation of helix C in the low temperature L-intermediate of bacteriorhodopsin. J Biol Chem. 2004;279:2147-58 pubmed publisher
    ..Implications regarding the structural mechanism for proton pumping by bacteriorhodopsin are discussed...
  51. Luecke H, Schobert B, Richter H, Cartailler J, Lanyi J. Structure of bacteriorhodopsin at 1.55 A resolution. J Mol Biol. 1999;291:899-911 pubmed publisher
    ..A bilayer of 18 tightly bound lipid chains forms an annulus around the protein in the crystal. Contacts between the trimers in the membrane plane are mediated almost exclusively by lipids...
  52. Lanyi J. What is the real crystallographic structure of the L photointermediate of bacteriorhodopsin?. Biochim Biophys Acta. 2004;1658:14-22 pubmed
    ..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. ..
  53. Koch M, Oesterhelt D. MpcT is the transducer for membrane potential changes in Halobacterium salinarum. Mol Microbiol. 2005;55:1681-94 pubmed
    ..Htr14 was therefore renamed to Membrane potential change Transducer, or MpcT. It is the first transducer for which the causative stimulus could be narrowed to a change in DeltaPsi, as opposed to a change in pH or cellular redox state. ..