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Saliminasab M, Yamazaki Y, Palmateer A, Harris A, Schubert L, Langner P, Heberle J, Bondar AN, Brown LS. A Proteorhodopsin-Related Photosensor Expands the Repertoire of Structural Motifs Employed by Sensory Rhodopsins. J Phys Chem B 2023; 127:7872-7886. [PMID: 37694950 PMCID: PMC10519204 DOI: 10.1021/acs.jpcb.3c04032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 08/09/2023] [Indexed: 09/12/2023]
Abstract
Microbial rhodopsins are light-activated retinal-binding membrane proteins that perform a variety of ion transport and photosensory functions. They display several cases of convergent evolution where the same function is present in unrelated or very distant protein groups. Here we report another possible case of such convergent evolution, describing the biophysical properties of a new group of sensory rhodopsins. The first representative of this group was identified in 2004 but none of the members had been expressed and characterized. The well-studied haloarchaeal sensory rhodopsins interacting with methyl-accepting Htr transducers are close relatives of the halobacterial proton pump bacteriorhodopsin. In contrast, the sensory rhodopsins we describe here are relatives of proteobacterial proton pumps, proteorhodopsins, but appear to interact with Htr-like transducers likewise, even though they do not conserve the residues important for the interaction of haloarchaeal sensory rhodopsins with their transducers. The new sensory rhodopsins display many unusual amino acid residues, including those around the retinal chromophore; most strikingly, a tyrosine in place of a carboxyl counterion of the retinal Schiff base on helix C. To characterize their unique sequence motifs, we augment the spectroscopy and biochemistry data by structural modeling of the wild-type and three mutants. Taken together, the experimental data, bioinformatics sequence analyses, and structural modeling suggest that the tyrosine/aspartate complex counterion contributes to a complex water-mediated hydrogen-bonding network that couples the protonated retinal Schiff base to an extracellular carboxylic dyad.
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Affiliation(s)
- Maryam Saliminasab
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Yoichi Yamazaki
- Division
of Materials Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Alyssa Palmateer
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Andrew Harris
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Luiz Schubert
- Experimental
Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Pit Langner
- Experimental
Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Joachim Heberle
- Experimental
Molecular Biophysics Group, Department of Physics, Freie Universität Berlin, D-14195 Berlin, Germany
| | - Ana-Nicoleta Bondar
- University
of Bucharest, Faculty of Physics, Atomiştilor 405, Măgurele 077125, Romania
- Forschungszentrum
Jülich, Institute for Neuroscience and Medicine and Institute
for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52428 Jülich, Germany
| | - Leonid S. Brown
- Department
of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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Orekhov P, Bothe A, Steinhoff HJ, Shaitan KV, Raunser S, Fotiadis D, Schlesinger R, Klare JP, Engelhard M. Sensory Rhodopsin I and Sensory Rhodopsin II Form Trimers of Dimers in Complex with their Cognate Transducers. Photochem Photobiol 2018; 93:796-804. [PMID: 28500714 DOI: 10.1111/php.12763] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/02/2017] [Indexed: 12/28/2022]
Abstract
Archaeal photoreceptors consist of sensory rhodopsins in complex with their cognate transducers. After light excitation, a two-component signaling chain is activated, which is homologous to the chemotactic signaling cascades in enterobacteria. The latter system has been studied in detail. From structural and functional studies, a picture emerges which includes stable signaling complexes, which assemble to receptor arrays displaying hexagonal structural elements. At this higher order structural level, signal amplification and sensory adaptation occur. Here, we describe electron microscopy data, which show that also the archaeal phototaxis receptors sensory rhodopsin I and II in complex with their cognate transducers can form hexagonal lattices even in the presence of a detergent. This result could be confirmed by molecular dynamics calculations, which revealed similar structural elements. Calculations of the global modes of motion displayed one mode, which resembles the "U"-"V" transition of the NpSRII:NpHtrII complex, which was previously argued to represent a functionally relevant global conformational change accompanying the activation process [Ishchenko et al. (2013) J. Photochem. Photobiol. B 123, 55-58]. A model of cooperativity at the transmembrane level is discussed.
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Affiliation(s)
- Philipp Orekhov
- Department of Physics, University of Osnabrück, Osnabrück, Germany.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Arne Bothe
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | | | - Stefan Raunser
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Ramona Schlesinger
- Department of Physics, Institute of Experimental Physics, Genetic Biophysics, Freie Universität Berlin, Berlin, Germany
| | - Johann P Klare
- Department of Physics, University of Osnabrück, Osnabrück, Germany
| | - Martin Engelhard
- Department Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
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Pfitzner E, Seki H, Schlesinger R, Ataka K, Heberle J. Disc Antenna Enhanced Infrared Spectroscopy: From Self-Assembled Monolayers to Membrane Proteins. ACS Sens 2018; 3:984-991. [PMID: 29741356 DOI: 10.1021/acssensors.8b00139] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Plasmonic surfaces have emerged as a powerful platform for biomolecular sensing applications and can be designed to optimize the plasmonic resonance for probing molecular vibrations at utmost sensitivity. Here, we present a facile procedure to generate metallic microdisc antenna arrays that are employed in surface-enhanced infrared absorption (SEIRA) spectroscopy of biomolecules. Transmission electron microscopy (TEM) grids are used as shadow mask deployed during physical vapor deposition of gold. The resulting disc-shaped antennas exhibit enhancement factors of the vibrational bands of 4 × 104 giving rise to a detection limit <1 femtomol (10-15 mol) of molecules. Surface-bound monolayers of 4-mercaptobenzoic acid show polyelectrolyte behavior when titrated with cations in the aqueous medium. Conformational rigidity of the self-assembled monolayer is validated by density functional theory calculations. The membrane protein sensory rhodopsin II is tethered to the disc antenna arrays and is fully functional as inferred from the light-induced SEIRA difference spectra. As an advance to previous studies, the accessible frequency range is improved and extended into the fingerprint region.
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Affiliation(s)
- Emanuel Pfitzner
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimalle 14, 14195 Berlin, Germany
| | - Hirofumi Seki
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimalle 14, 14195 Berlin, Germany
- Toray Research Center Inc., 3-3-7 Sonoyama, Otsu, Shiga 520-8567, Japan
| | - Ramona Schlesinger
- Genetic Biophysics, Department of Physics, Freie Universität Berlin, Arnimalle 14, 14195 Berlin, Germany
| | - Kenichi Ataka
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimalle 14, 14195 Berlin, Germany
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimalle 14, 14195 Berlin, Germany
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