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Mackintosh MJ, Hoischen D, Martin HD, Schapiro I, Gärtner W. Merocyanines form bacteriorhodopsins with strongly bathochromic absorption maxima. Photochem Photobiol Sci 2024; 23:31-53. [PMID: 38070056 DOI: 10.1007/s43630-023-00496-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/13/2023] [Indexed: 02/02/2024]
Abstract
There is a need to shift the absorbance of biomolecules to the optical transparency window of tissue for applications in optogenetics and photo-pharmacology. There are a few strategies to achieve the so-called red shift of the absorption maxima. Herein, a series of 11 merocyanine dyes were synthesized and employed as chromophores in place of retinal in bacteriorhodopsin (bR) to achieve a bathochromic shift of the absorption maxima relative to bR's [Formula: see text] of 568 nm. Assembly with the apoprotein bacterioopsin (bO) led to stable, covalently bound chromoproteins with strongly bathochromic absorbance bands, except for three compounds. Maximal red shifts were observed for molecules 9, 2, and 8 in bR where the [Formula: see text] was 766, 755, and 736 nm, respectively. While these three merocyanines have different end groups, they share a similar structural feature, namely, a methyl group which is located at the retinal equivalent position 13 of the polyene chain. The absorption and fluorescence data are also presented for the retinal derivatives in their aldehyde, Schiff base (SB), and protonated SB (PSB) forms in solution. According to their hemicyanine character, the PSBs and their analogue bRs exhibited fluorescence quantum yields (Φf) several orders of magnitude greater than native bR (Φf 0.02 to 0.18 versus 1.5 × 10-5 in bR) while also exhibiting much smaller Stokes shifts than bR (400 to 1000 cm-1 versus 4030 cm-1 in bR). The experimental results are complemented by quantum chemical calculations where excellent agreement between the experimental [Formula: see text] and the calculated [Formula: see text] was achieved with the second-order algebraic-diagrammatic construction [ADC(2)] method. In addition, quantum mechanics/molecular mechanics (QM/MM) calculations were employed to shed light on the origin of the bathochromic shift of merocyanine 2 in bR compared with native bR.
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Affiliation(s)
- Megan J Mackintosh
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Dorothee Hoischen
- Institute for Organic Chemistry and Macromolecular Chemistry, University of Düsseldorf, 40225, Düsseldorf, Germany
- ISK Biosciences Europe N.V., 1831, Diegem, Belgium
| | - Hans-Dieter Martin
- Institute for Organic Chemistry and Macromolecular Chemistry, University of Düsseldorf, 40225, Düsseldorf, Germany
| | - Igor Schapiro
- Fritz Haber Center for Molecular Dynamics, Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem, Israel.
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Hasegawa H, Sakamoto K, Shomura K, Sano Y, Kasai K, Tanaka S, Okada-Shudo Y, Otomo A. Biomaterial-Based Biomimetic Visual Sensors: Inkjet Patterning of Bacteriorhodopsin. ACS APPLIED MATERIALS & INTERFACES 2023; 15:45137-45145. [PMID: 37702224 DOI: 10.1021/acsami.3c07540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Biomimetic visual sensors utilizing bacteriorhodopsin (bR) were fabricated by using an inkjet method. The inkjet printer facilitated the jetting of the bR suspension, allowing for the deposition of bR films. The resulting inkjet-printed bR film exhibited time-differential photocurrent response characteristics similar to those of a dip-coated bR film. By adjusting the number of printed bR film layers, the intensity of the photocurrent could be easily controlled. Moreover, the inkjet printing technique enabled unconstrained patterning, facilitating the design of various visual information processing functions, such as visual filters. In this study, we successfully fabricated two visual filters, namely, a two-dimensional Difference of Gaussian (DOG) filter and a Gabor filter. The printed DOG filter demonstrated edge detection capabilities corresponding to contour recognition in visual receptive fields. On the other hand, the printed Gabor filter proved effective in detecting objects of specific sizes as well as their motion and orientation. The integration of bR and the inkjet method holds significant potential for the widespread implementation of highly functional biomaterial-based visual sensors. These sensors have the capability to provide real-time visual information while operating in an energy-efficient manner.
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Affiliation(s)
- Hiroyuki Hasegawa
- Faculty of Education, Shimane University, Matsue, Shimane 690-8504, Japan
- Graduate School of Natural Science and Technology, Shimane University, Matsue, Shimane 690-8504, Japan
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Kairi Sakamoto
- Graduate School of Natural Science and Technology, Shimane University, Matsue, Shimane 690-8504, Japan
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Kazuya Shomura
- Faculty of Education, Shimane University, Matsue, Shimane 690-8504, Japan
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Yuka Sano
- Faculty of Education, Shimane University, Matsue, Shimane 690-8504, Japan
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Katsuyuki Kasai
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Shukichi Tanaka
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
| | - Yoshiko Okada-Shudo
- Graduate School of Informatics and Engineering, The University of Electro-Communications, Chofu, Tokyo 182-8585, Japan
| | - Akira Otomo
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe 651-2492, Japan
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Bryl K. Fluorescence Resonance Energy Transfer (FRET) as a Spectroscopic Ruler for the Investigation of Protein Induced Lipid Membrane Curvature: Bacteriorhodopsin and Bacteriorhodopsin Analogs in Model Lipid Membranes. APPLIED SPECTROSCOPY 2023; 77:187-199. [PMID: 36229916 DOI: 10.1177/00037028221135645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Bacteriorhodopsin (bR) is a light-driven proton pump existing in the purple membranes (PM) of Halobacterium salinarum. The effects associated with changes in proton distribution (proton gradient, membrane electric potential) play a key role in ATPase stimulation. However, how the bioenergetic modulus (bR-PM-ATPase) functions remains unclear. One can find indications that hydrophobic matching and the curvature of the lipid membrane may form a functional link between bR and ATPase. To verify whether an interaction between bR and lipids can lead to curvature of the lipid membrane, a spectroscopic ruler, that is, a fluorescence resonance energy transfer (FRET) tool, was used. The distances from fluorescent lipid probes [octadecyl rhodamine B chloride (RhB), 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI), 16-(9-anthroyloxy) palmitic acid (16AP), and hydrophobic probe 1,6-diphenyl-1,3,5-hexatriene (DPH), to the retinal chromophore of bR incorporated into phospholipid vesicles, were measured. The incorporation of retinal analogues with changed shape and/or altered electronic properties into the binding site of a bR or bR mutant were used to strengthen the feedback between the protein surrounding and chromophore. The experiments were performed with wild-type and D96N-mutated bR carrying retinal or 14-(12-,10-, 13,14-bi-) fluororetinal. As far as it is known, this is the first time that results obtained by the FRET method show that bR can induce a change in lipid structure interpreted as hydrophobically induced curving of the lipid membrane. Evidence was provided that the chromophore contributed to this effect. The extent of contribution was dependent on the chromophore structure in close vicinity to the place of its link with opsin. The implications of these findings for bR-PM-ATPase module functioning are also discussed.
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Affiliation(s)
- Krzysztof Bryl
- Department of Physics and Biophysics, 49674University of Warmia and Mazury, Olsztyn, Poland
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4
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de Grip WJ, Ganapathy S. Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering. Front Chem 2022; 10:879609. [PMID: 35815212 PMCID: PMC9257189 DOI: 10.3389/fchem.2022.879609] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023] Open
Abstract
The first member and eponym of the rhodopsin family was identified in the 1930s as the visual pigment of the rod photoreceptor cell in the animal retina. It was found to be a membrane protein, owing its photosensitivity to the presence of a covalently bound chromophoric group. This group, derived from vitamin A, was appropriately dubbed retinal. In the 1970s a microbial counterpart of this species was discovered in an archaeon, being a membrane protein also harbouring retinal as a chromophore, and named bacteriorhodopsin. Since their discovery a photogenic panorama unfolded, where up to date new members and subspecies with a variety of light-driven functionality have been added to this family. The animal branch, meanwhile categorized as type-2 rhodopsins, turned out to form a large subclass in the superfamily of G protein-coupled receptors and are essential to multiple elements of light-dependent animal sensory physiology. The microbial branch, the type-1 rhodopsins, largely function as light-driven ion pumps or channels, but also contain sensory-active and enzyme-sustaining subspecies. In this review we will follow the development of this exciting membrane protein panorama in a representative number of highlights and will present a prospect of their extraordinary future potential.
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Affiliation(s)
- Willem J. de Grip
- Leiden Institute of Chemistry, Department of Biophysical Organic Chemistry, Leiden University, Leiden, Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Srividya Ganapathy
- Department of Imaging Physics, Delft University of Technology, Netherlands
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5
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Islam MS, Gaston JP, Baker MAB. Fluorescence Approaches for Characterizing Ion Channels in Synthetic Bilayers. MEMBRANES 2021; 11:857. [PMID: 34832086 PMCID: PMC8619978 DOI: 10.3390/membranes11110857] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 12/12/2022]
Abstract
Ion channels are membrane proteins that play important roles in a wide range of fundamental cellular processes. Studying membrane proteins at a molecular level becomes challenging in complex cellular environments. Instead, many studies focus on the isolation and reconstitution of the membrane proteins into model lipid membranes. Such simpler, in vitro, systems offer the advantage of control over the membrane and protein composition and the lipid environment. Rhodopsin and rhodopsin-like ion channels are widely studied due to their light-interacting properties and are a natural candidate for investigation with fluorescence methods. Here we review techniques for synthesizing liposomes and for reconstituting membrane proteins into lipid bilayers. We then summarize fluorescence assays which can be used to verify the functionality of reconstituted membrane proteins in synthetic liposomes.
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Affiliation(s)
- Md. Sirajul Islam
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
| | - James P. Gaston
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
| | - Matthew A. B. Baker
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, NSW 2052, Australia; (M.S.I.); (J.P.G.)
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
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Maag D, Mast T, Elstner M, Cui Q, Kubař T. O to bR transition in bacteriorhodopsin occurs through a proton hole mechanism. Proc Natl Acad Sci U S A 2021; 118:e2024803118. [PMID: 34561302 PMCID: PMC8488608 DOI: 10.1073/pnas.2024803118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2021] [Indexed: 12/27/2022] Open
Abstract
Extensive classical and quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations are used to establish the structural features of the O state in bacteriorhodopsin (bR) and its conversion back to the bR ground state. The computed free energy surface is consistent with available experimental data for the kinetics and thermodynamics of the O to bR transition. The simulation results highlight the importance of the proton release group (PRG, consisting of Glu194/204) and the conserved arginine 82 in modulating the hydration level of the protein cavity. In particular, in the O state, deprotonation of the PRG and downward rotation of Arg82 lead to elevated hydration level and a continuous water network that connects the PRG to the protonated Asp85. Proton exchange through this water network is shown by ∼0.1-μs semiempirical QM/MM free energy simulations to occur through the generation and propagation of a proton hole, which is relayed by Asp212 and stabilized by Arg82. This mechanism provides an explanation for the observation that the D85S mutant of bacteriorhodopsin pumps chloride ions. The electrostatics-hydration coupling mechanism and the involvement of all titration states of water are likely applicable to many biomolecules involved in bioenergetic transduction.
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Affiliation(s)
- Denis Maag
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Thilo Mast
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
- Institute for Biological Interfaces, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department of Chemistry, Boston University, Boston, MA 02215
- Department of Physics, Boston University, Boston, MA 02215
- Department of Biomedical Engineering, Boston University, Boston, MA 02215
| | - Tomáš Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany;
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Merino N, Kawai M, Boyd ES, Colman DR, McGlynn SE, Nealson KH, Kurokawa K, Hongoh Y. Single-Cell Genomics of Novel Actinobacteria With the Wood-Ljungdahl Pathway Discovered in a Serpentinizing System. Front Microbiol 2020; 11:1031. [PMID: 32655506 PMCID: PMC7325909 DOI: 10.3389/fmicb.2020.01031] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/27/2020] [Indexed: 01/04/2023] Open
Abstract
Serpentinite-hosted systems represent modern-day analogs of early Earth environments. In these systems, water-rock interactions generate highly alkaline and reducing fluids that can contain hydrogen, methane, and low-molecular-weight hydrocarbons-potent reductants capable of fueling microbial metabolism. In this study, we investigated the microbiota of Hakuba Happo hot springs (∼50°C; pH∼10.5-11), located in Nagano (Japan), which are impacted by the serpentinization process. Analysis of the 16S rRNA gene amplicon sequences revealed that the bacterial community comprises Nitrospirae (47%), "Parcubacteria" (19%), Deinococcus-Thermus (16%), and Actinobacteria (9%), among others. Notably, only 57 amplicon sequence variants (ASV) were detected, and fifteen of these accounted for 90% of the amplicons. Among the abundant ASVs, an early-branching, uncultivated actinobacterial clade identified as RBG-16-55-12 in the SILVA database was detected. Ten single-cell genomes (average pairwise nucleotide identity: 0.98-1.00; estimated completeness: 33-93%; estimated genome size: ∼2.3 Mb) that affiliated with this clade were obtained. Taxonomic classification using single copy genes indicates that the genomes belong to the actinobacterial class-level clade UBA1414 in the Genome Taxonomy Database. Based on metabolic pathway predictions, these actinobacteria are anaerobes, capable of glycolysis, dissimilatory nitrate reduction and CO2 fixation via the Wood-Ljungdahl (WL) pathway. Several other genomes within UBA1414 and two related class-level clades also encode the WL pathway, which has not yet been reported for the Actinobacteria phylum. For the Hakuba actinobacterium, the energy metabolism related to the WL pathway is likely supported by a combination of the Rnf complex, group 3b and 3d [NiFe]-hydrogenases, [FeFe]-hydrogenases, and V-type (H+/Na+ pump) ATPase. The genomes also harbor a form IV ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) complex, also known as a RubisCO-like protein, and contain signatures of interactions with viruses, including clustered regularly interspaced short palindromic repeat (CRISPR) regions and several phage integrases. This is the first report and detailed genome analysis of a bacterium within the Actinobacteria phylum capable of utilizing the WL pathway. The Hakuba actinobacterium is a member of the clade UBA1414/RBG-16-55-12, formerly within the group "OPB41." We propose to name this bacterium 'Candidatus Hakubanella thermoalkaliphilus.'
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Affiliation(s)
- Nancy Merino
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States.,Biosciences and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, CA, United States
| | - Mikihiko Kawai
- School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan.,Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Eric S Boyd
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Daniel R Colman
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT, United States
| | - Shawn E McGlynn
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Biofunctional Catalyst Research Team, RIKEN Center for Sustainable Resource Science, Saitama, Japan.,Blue Marble Space Institute of Science, Seattle, WA, United States
| | - Kenneth H Nealson
- Department of Earth Sciences, University of Southern California, Los Angeles, CA, United States
| | - Ken Kurokawa
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,Department of Informatics, National Institute of Genetics, Shizuoka, Japan
| | - Yuichi Hongoh
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan.,School of Life Sciences and Technology, Tokyo Institute of Technology, Tokyo, Japan
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8
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Oleinikov VA, Solovyeva DO, Zaitsev SY. Nanohybrid Structures Based on Plasmonic or Fluorescent Nanoparticles and Retinal-Containing Proteins. BIOCHEMISTRY (MOSCOW) 2020; 85:S196-S212. [PMID: 32087060 DOI: 10.1134/s0006297920140102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Rhodopsins are light-sensitive membrane proteins enabling transmembrane charge separation (proton pump) on absorption of a light quantum. Bacteriorhodopsin (BR) is a transmembrane protein from halophilic bacteria that belongs to the rhodopsin family. Potential applications of BR are considered so promising that the number of studies devoted to the use of BR itself, its mutant variants, as well as hybrid materials containing BR in various areas grows steadily. Formation of hybrid structures combining BR with nanoparticles is an essential step in promotion of BR-based devices. However, rapid progress, continuous emergence of new data, as well as challenges of analyzing the entire data require regular reviews of the achievements in this area. This review is devoted to the issues of formation of materials based on hybrids of BR with fluorescent semiconductor nanocrystals (quantum dots) and with noble metal (silver, gold) plasmonic nanoparticles. Recent data on formation of thin (mono-) and thick (multi-) layers from materials containing BR and BR/nanoparticle hybrids are presented.
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Affiliation(s)
- V A Oleinikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia. .,Institute of Engineering Physics for Biomedicine, National Research Nuclear University MEPhI, Moscow, 115409, Russia
| | - D O Solovyeva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,Institute of Engineering Physics for Biomedicine, National Research Nuclear University MEPhI, Moscow, 115409, Russia
| | - S Yu Zaitsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, 117997, Russia.,L. K. Ernst Federal Science Center for Animal Husbandry, Dubrovitsy, Moscow Region, 142132, Russia
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9
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Krivenkov V, Samokhvalov P, Nabiev I. Remarkably enhanced photoelectrical efficiency of bacteriorhodopsin in quantum dot – Purple membrane complexes under two-photon excitation. Biosens Bioelectron 2019; 137:117-122. [DOI: 10.1016/j.bios.2019.05.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/14/2019] [Accepted: 05/03/2019] [Indexed: 01/16/2023]
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10
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Stability of the two-dimensional lattice of bacteriorhodopsin reconstituted in partially fluorinated phosphatidylcholine bilayers. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:631-642. [DOI: 10.1016/j.bbamem.2018.12.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/27/2018] [Accepted: 12/20/2018] [Indexed: 11/21/2022]
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Pohlschroder M, Pfeiffer F, Schulze S, Abdul Halim MF. Archaeal cell surface biogenesis. FEMS Microbiol Rev 2018; 42:694-717. [PMID: 29912330 PMCID: PMC6098224 DOI: 10.1093/femsre/fuy027] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/12/2018] [Indexed: 12/13/2022] Open
Abstract
Cell surfaces are critical for diverse functions across all domains of life, from cell-cell communication and nutrient uptake to cell stability and surface attachment. While certain aspects of the mechanisms supporting the biosynthesis of the archaeal cell surface are unique, likely due to important differences in cell surface compositions between domains, others are shared with bacteria or eukaryotes or both. Based on recent studies completed on a phylogenetically diverse array of archaea, from a wide variety of habitats, here we discuss advances in the characterization of mechanisms underpinning archaeal cell surface biogenesis. These include those facilitating co- and post-translational protein targeting to the cell surface, transport into and across the archaeal lipid membrane, and protein anchoring strategies. We also discuss, in some detail, the assembly of specific cell surface structures, such as the archaeal S-layer and the type IV pili. We will highlight the importance of post-translational protein modifications, such as lipid attachment and glycosylation, in the biosynthesis as well as the regulation of the functions of these cell surface structures and present the differences and similarities in the biogenesis of type IV pili across prokaryotic domains.
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Affiliation(s)
| | - Friedhelm Pfeiffer
- Computational Biology Group, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Stefan Schulze
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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12
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Elghobashi-Meinhardt N, Phatak P, Bondar AN, Elstner M, Smith JC. Catalysis of Ground State cis[Formula: see text] trans Isomerization of Bacteriorhodopsin's Retinal Chromophore by a Hydrogen-Bond Network. J Membr Biol 2018. [PMID: 29516110 DOI: 10.1007/s00232-018-0027-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
For the photocycle of the membrane protein bacteriorhodopsin to proceed efficiently, the thermal 13-cis to all-trans back-isomerization of the retinal chromophore must return the protein to its resting state on a time-scale of milliseconds. Here, we report on quantum mechanical/molecular mechanical energy calculations examining the structural and energetic determinants of the retinal cis-trans isomerization in the protein environment. The results suggest that a hydrogen-bonded network consisting of the retinal Schiff base, active site amino acid residues, and water molecules can stabilize the twisted retinal, thus reducing the intrinsic energy cost of the cis-trans thermal isomerization barrier.
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Affiliation(s)
- Nadia Elghobashi-Meinhardt
- Department of Physical and Theoretical Chemistry, Theoretical Molecular Biophysics, Institute for Chemistry und Biochemistry, Freie Universität Berlin, Fabeckstr. 36a, Berlin, 14169, Germany.
| | - Prasad Phatak
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, 38106, Braunschweig, Germany.,BASF SE, Carl-Bosch Strasse 38, 67056, Ludwigshafen am Rhein, Germany
| | - Ana-Nicoleta Bondar
- Department of Physics, Theoretical Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Marcus Elstner
- Department of Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institut of Technology, Kaiserstrasse 12, 76131, Karlsruhe, Germany
| | - Jeremy C Smith
- Oak Ridge National Laboratory, Center for Molecular Biophysics, P.O. Box 2008 MS6309, Oak Ridge, TN, 37831-6309, USA.,Department of Biochemistry and Molecular and Cellular Biology, University of Tennessee, Knoxville, USA
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13
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Few-cycle pulse generation from noncollinear optical parametric amplifier with static dispersion compensation. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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14
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Wang M, Yu Y, Shao J, Heng BC, Ye H. Engineering synthetic optogenetic networks for biomedical applications. QUANTITATIVE BIOLOGY 2017. [DOI: 10.1007/s40484-017-0105-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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15
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Photocyclic behavior of rhodopsin induced by an atypical isomerization mechanism. Proc Natl Acad Sci U S A 2017; 114:E2608-E2615. [PMID: 28289214 DOI: 10.1073/pnas.1617446114] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Vertebrate rhodopsin (Rh) contains 11-cis-retinal as a chromophore to convert light energy into visual signals. On absorption of light, 11-cis-retinal is isomerized to all-trans-retinal, constituting a one-way reaction that activates transducin (Gt) followed by chromophore release. Here we report that bovine Rh, regenerated instead with a six-carbon-ring retinal chromophore featuring a C11=C12 double bond locked in its cis conformation (Rh6mr), employs an atypical isomerization mechanism by converting 11-cis to an 11,13-dicis configuration for prolonged Gt activation. Time-dependent UV-vis spectroscopy, HPLC, and molecular mechanics analyses revealed an atypical thermal reisomerization of the 11,13-dicis to the 11-cis configuration on a slow timescale, which enables Rh6mr to function in a photocyclic manner similar to that of microbial Rhs. With this photocyclic behavior, Rh6mr repeatedly recruits and activates Gt in response to light stimuli, making it an excellent candidate for optogenetic tools based on retinal analog-bound vertebrate Rhs. Overall, these comprehensive structure-function studies unveil a unique photocyclic mechanism of Rh activation by an 11-cis-to-11,13-dicis isomerization.
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16
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Häder DP, Iseki M. Photomovement in Euglena. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 979:207-235. [DOI: 10.1007/978-3-319-54910-1_11] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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17
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Li D, Wang Y, Du H, Xu S, Li Z, Yang Y, Wang C. Nanoscale Electric Characteristics and Oriented Assembly of Halobacterium salinarum Membrane Revealed by Electric Force Microscopy. NANOMATERIALS 2016; 6:nano6110197. [PMID: 28335325 PMCID: PMC5245739 DOI: 10.3390/nano6110197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/28/2016] [Accepted: 10/08/2016] [Indexed: 11/25/2022]
Abstract
Purple membranes (PM) of the bacteria Halobacterium salinarum are a unique natural membrane where bacteriorhodopsin (BR) can convert photon energy and pump protons. Elucidating the electronic properties of biomembranes is critical for revealing biological mechanisms and developing new devices. We report here the electric properties of PMs studied by using multi-functional electric force microscopy (EFM) at the nanoscale. The topography, surface potential, and dielectric capacity of PMs were imaged and quantitatively measured in parallel. Two orientations of PMs were identified by EFM because of its high resolution in differentiating electrical characteristics. The extracellular (EC) sides were more negative than the cytoplasmic (CP) side by 8 mV. The direction of potential difference may facilitate movement of protons across the membrane and thus play important roles in proton pumping. Unlike the side-dependent surface potentials observed in PM, the EFM capacitive response was independent of the side and was measured to be at a dC/dz value of ~5.25 nF/m. Furthermore, by modification of PM with de novo peptides based on peptide-protein interaction, directional oriented PM assembly on silicon substrate was obtained for technical devices. This work develops a new method for studying membrane nanoelectronics and exploring the bioelectric application at the nanoscale.
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Affiliation(s)
- Denghua Li
- Agricultural Information Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Information Service Technology of Ministry of Agriculture, Beijing 100081, China.
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.
| | - Yibing Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.
| | - Huiwen Du
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.
| | - Shiwei Xu
- Agricultural Information Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Information Service Technology of Ministry of Agriculture, Beijing 100081, China.
| | - Zhemin Li
- Agricultural Information Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Agricultural Information Service Technology of Ministry of Agriculture, Beijing 100081, China.
| | - Yanlian Yang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.
| | - Chen Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China.
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18
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Abstract
Severe loss of photoreceptor cells in inherited or acquired retinal degenerative diseases can result in partial loss of sight or complete blindness. The optogenetic strategy for restoration of vision utilizes optogenetic tools to convert surviving inner retinal neurons into photosensitive cells; thus, light sensitivity is imparted to the retina after the death of photoreceptor cells. Proof-of-concept studies, especially those using microbial rhodopsins, have demonstrated restoration of light responses in surviving retinal neurons and visually guided behaviors in animal models. Significant progress has also been made in improving microbial rhodopsin-based optogenetic tools, developing virus-mediated gene delivery, and targeting specific retinal neurons and subcellular compartments of retinal ganglion cells. In this article, we review the current status of the field and outline further directions and challenges to the advancement of this strategy toward clinical application and improvement in the outcomes of restored vision.
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Affiliation(s)
- Zhuo-Hua Pan
- Department of Ophthalmology, Kresge Eye Institute, Wayne State University School of Medicine, Detroit, Michigan 48201; , , .,Department of Anatomy and Cell Biology, Wayne State University School of Medicine, Detroit, Michigan 48201;
| | - Qi Lu
- Department of Anatomy and Cell Biology, Wayne State University School of Medicine, Detroit, Michigan 48201;
| | - Anding Bi
- Department of Ophthalmology, Kresge Eye Institute, Wayne State University School of Medicine, Detroit, Michigan 48201; , ,
| | | | - Gary W Abrams
- Department of Ophthalmology, Kresge Eye Institute, Wayne State University School of Medicine, Detroit, Michigan 48201; , ,
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Lu H, Yuan W, Zhou J, Chong PLG. Glucose Synthesis in a Protein-Based Artificial Photosynthesis System. Appl Biochem Biotechnol 2015; 177:105-17. [PMID: 26170084 DOI: 10.1007/s12010-015-1731-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/22/2015] [Indexed: 11/28/2022]
Abstract
The objective of this study was to understand glucose synthesis of a protein-based artificial photosynthesis system affected by operating conditions, including the concentrations of reactants, reaction temperature, and illumination. Results from non-vesicle-based glyceraldehyde-3-phosphate (GAP) and glucose synthesis showed that the initial concentrations of ribulose-1,5-bisphosphate (RuBP) and adenosine triphosphate (ATP), lighting source, and temperature significantly affected glucose synthesis. Higher initial concentrations of RuBP and ATP significantly enhanced GAP synthesis, which was linearly correlated to glucose synthesis, confirming the proper functions of all catalyzing enzymes in the system. White fluorescent light inhibited artificial photosynthesis and reduced glucose synthesis by 79.2 % compared to in the dark. The reaction temperature of 40 °C was optimum, whereas lower or higher temperature reduced glucose synthesis. Glucose synthesis in the vesicle-based artificial photosynthesis system reconstituted with bacteriorhodopsin, F 0 F 1 ATP synthase, and polydimethylsiloxane-methyloxazoline-polydimethylsiloxane triblock copolymer was successfully demonstrated. This system efficiently utilized light-induced ATP to drive glucose synthesis, and 5.2 μg ml(-1) glucose was synthesized in 0.78-ml reaction buffer in 7 h. Light-dependent reactions were found to be the bottleneck of the studied artificial photosynthesis system.
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Affiliation(s)
- Hao Lu
- Department of Biological and Agricultural Engineering, North Carolina State University, Raleigh, NC, 27695, USA
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Affiliation(s)
- Sansa Dutta
- Department
of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Lev Weiner
- Department
of Chemical Research Support, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mordechai Sheves
- Department
of Organic Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
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21
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Novel expression and characterization of a light driven proton pump archaerhodopsin 4 in a Halobacterium salinarum strain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:390-398. [DOI: 10.1016/j.bbabio.2014.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 12/22/2014] [Accepted: 12/25/2014] [Indexed: 11/19/2022]
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22
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Krivenkov V, Samokhvalov P, Solovyeva D, Bilan R, Chistyakov A, Nabiev I. Two-photon-induced Förster resonance energy transfer in a hybrid material engineered from quantum dots and bacteriorhodopsin. OPTICS LETTERS 2015; 40:1440-1443. [PMID: 25831354 DOI: 10.1364/ol.40.001440] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Energy transfer from nanostructures to biological supramolecular photosystems is an important fundamental issue related to the possible influence of nanoobjects on biological functions. We demonstrate here two-photon-induced Förster resonance energy transfer (FRET) from fluorescent CdSe/ZnS quantum dots (QDs) to the photosensitive protein bacteriorhodopsin (bR) in a QD-bR hybrid material. The two-photon absorption cross section of QDs has been found to be about two orders of magnitude larger than that of bR. Therefore, highly selective two-photon excitation of QDs in QD-bR complexes is possible. Moreover, the efficiency of FRET from QDs to bR is sufficient to initiate bR photoconversion through two-photon excitation of QDs in the infrared spectral region. The data demonstrate that the effective spectral range in which the bR biological function is excited can be extended beyond the band where the protein itself utilizes light energy, which could open new ways to use this promising biotechnological material.
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23
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Haloarchaea and the formation of gas vesicles. Life (Basel) 2015; 5:385-402. [PMID: 25648404 PMCID: PMC4390858 DOI: 10.3390/life5010385] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 01/19/2015] [Accepted: 01/26/2015] [Indexed: 11/17/2022] Open
Abstract
Halophilic Archaea (Haloarchaea) thrive in salterns containing sodium chloride concentrations up to saturation. Many Haloarchaea possess genes encoding gas vesicles, but only a few species, such as Halobacterium salinarum and Haloferax mediterranei, produce these gas-filled, proteinaceous nanocompartments. Gas vesicles increase the buoyancy of cells and enable them to migrate vertically in the water body to regions with optimal conditions. Their synthesis depends on environmental factors, such as light, oxygen supply, temperature and salt concentration. Fourteen gas vesicle protein (gvp) genes are involved in their formation, and regulation of gvp gene expression occurs at the level of transcription, including the two regulatory proteins, GvpD and GvpE, but also at the level of translation. The gas vesicle wall is solely formed of proteins with the two major components, GvpA and GvpC, and seven additional accessory proteins are also involved. Except for GvpI and GvpH, all of these are required to form the gas permeable wall. The applications of gas vesicles include their use as an antigen presenter for viral or pathogen proteins, but also as a stable ultrasonic reporter for biomedical purposes.
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Abstract
Optogenetics is an innovative technique for optical control of cells. This field has exploded over the past decade or so and has given rise to great advances in neuroscience. A variety of applications both from the basic and applied research have emerged, turning the early ideas into a powerful paradigm for cell biology, neuroscience and medical research. This review aims at highlighting the basic concepts that are essential for a comprehensive understanding of optogenetics and some important biological/biomedical applications. Further, emphasis is placed on advancement in optogenetics-associated light-based methods for controlling gene expression, spatially-controlled optogenetic stimulation and detection of cellular activities.
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Affiliation(s)
- Samarendra K. Mohanty
- Biophysics and Physiology Group, Department of Physics, The University of Texas at Arlington, USA. Tel. 817-272-1177, Fax: +1-817-272-3637
| | - Vasudevan Lakshminarayananan
- School of Optometry and Vision Science, Departments of Physics and Electrical and Computer Engineering, University of Waterloo, Waterloo, ON Canada. Department of Physics, Unviersity of Michigan, Ann Arbor, USA
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Krivenkov V, Linkov P, Solovyeva D, Bilan R, Chistyakov A, Nabiev I. Energy Transfer Processes Under One-and Two-photon Excitation of Nano-biohybrid Structures based on Semiconductor Quantum Dots and Purple Membranes. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.phpro.2015.09.135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Halorhodopsin pumps Cl- and bacteriorhodopsin pumps protons by a common mechanism that uses conserved electrostatic interactions. Proc Natl Acad Sci U S A 2014; 111:16377-82. [PMID: 25362051 DOI: 10.1073/pnas.1411119111] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Key mutations differentiate the functions of homologous proteins. One example compares the inward ion pump halorhodopsin (HR) and the outward proton pump bacteriorhodopsin (BR). Of the nine essential buried ionizable residues in BR, six are conserved in HR. However, HR changes three BR acids, D85 in a central cluster of ionizable residues, D96, nearer the intracellular, and E204, nearer the extracellular side of the membrane to the small, neutral amino acids T111, V122, and T230, respectively. In BR, acidic amino acids are stationary anions whose proton affinity is modulated by conformational changes, establishing a sequence of directed binding and release of protons. Multiconformation continuum electrostatics calculations of chloride affinity and residue protonation show that, in reaction intermediates where an acid is ionized in BR, a Cl(-) is bound to HR in a position near the deleted acid. In the HR ground state, Cl(-) binds tightly to the central cluster T111 site and weakly to the extracellular T230 site, recovering the charges on ionized BR-D85 and neutral E204 in BR. Imposing key conformational changes from the BR M intermediate into the HR structure results in the loss of Cl(-) from the central T111 site and the tight binding of Cl(-) to the extracellular T230 site, mirroring the changes that protonate BR-D85 and ionize E204 in BR. The use of a mobile chloride in place of D85 and E204 makes HR more susceptible to the environmental pH and salt concentrations than BR. These studies shed light on how ion transfer mechanisms are controlled through the interplay of protein and ion electrostatics.
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Inoue K, Koua FHM, Kato Y, Abe-Yoshizumi R, Kandori H. Spectroscopic study of a light-driven chloride ion pump from marine bacteria. J Phys Chem B 2014; 118:11190-9. [PMID: 25166488 DOI: 10.1021/jp507219q] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Thousands of light-driven proton-pumping rhodopsins have been found in marine microbes, and a light-driven sodium-ion pumping rhodopsin was recently discovered, which utilizes sunlight for the energy source of the cell. Similarly, a light-driven chloride-ion pump has been found from marine bacteria, and three eubacterial light-driven pumps possess the DTE (proton pump), NDQ (sodium-ion pump), and NTQ (chloride-ion pump) motifs corresponding to the D85, T89, and D96 positions in bacteriorhodopsin (BR). The corresponding motif of the known haloarchaeal chloride-ion pump, halorhodopsin (HR), is TSA, which is entirely different from the NTQ motif of a eubacterial chloride-ion pump. It is thus intriguing to compare the molecular mechanism of these two chloride-ion pumps. Here we report the spectroscopic study of Fulvimarina rhodopsin (FR), a eubacterial light-driven chloride-ion pump from marine bacterium. FR binds a chloride-ion near the retinal chromophore and chloride-ion binding causes a spectral blue-shift. FR predominantly possesses an all-trans retinal, which is responsible for the light-driven chloride-ion pump. Upon light absorption, the red-shifted K intermediate is formed, followed by the appearance of the L and O intermediates. When the M intermediate does not form, this indicates that the Schiff base remains in the protonated state during the photocycle. These molecular mechanisms are common in HR, and a common mechanism for chloride-ion pumping by evolutionarily distant proteins suggests the importance of the electric quadrupole in the Schiff base region and their changes through hydrogen-bonding alterations. One noticeable difference between FR and HR is the uptake of chloride-ion from the extracellular surface. While the uptake occurs upon decay of the O intermediate in HR, chloride-ion uptake accompanies the rise of the O intermediate in FR. This suggests the presence of a second chloride-ion binding site near the extracellular surface of FR, which is unique to the NTQ rhodopsin.
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Affiliation(s)
- Keiichi Inoue
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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28
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Carvalho LS, Vandenberghe LH. Promising and delivering gene therapies for vision loss. Vision Res 2014; 111:124-33. [PMID: 25094052 DOI: 10.1016/j.visres.2014.07.013] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/25/2014] [Accepted: 07/28/2014] [Indexed: 12/14/2022]
Abstract
The maturity in our understanding of the genetics and the pathogenesis of disease in degenerative retinal disorders has intersected in past years with a novel treatment paradigm in which a genetic intervention may lead to sustained therapeutic benefit, and in some cases even restoration of vision. Here, we review this prospect of retinal gene therapy, discuss the enabling technologies that have led to first-in-human demonstrations of efficacy and safety, and the road that led to this exciting point in time.
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Affiliation(s)
- Livia S Carvalho
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Harvard University, 20 Staniford Street, Boston, MA 02114, USA
| | - Luk H Vandenberghe
- Schepens Eye Research Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Harvard University, 20 Staniford Street, Boston, MA 02114, USA.
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29
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Zhang Z, Jin Z, Zhao Y, Zhang Z, Li R, Xiao J, Wu J. Systematic study on G-protein couple receptor prototypes: did they really evolve from prokaryotic genes? IET Syst Biol 2014; 8:154-61. [PMID: 25075528 PMCID: PMC8687355 DOI: 10.1049/iet-syb.2013.0037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
G‐protein couple receptor (GPCR) is one of the most striking examples of signalling proteins and it is only observed in eukaryotes. Based on various GPCR identification methods and classification systems, several evolutionary presumptions of different GPCR families have been reported. However, the prototype of GPCR still limits our knowledge. By investigating its structure and domain variance, the authors propose that GPCR might be evolved from prokaryotic world. The results given by the authors indicate that metabotropic glutamate receptor family would be the ancestor of GPCR. Phylogenetic analysis hints that one of metabotropic glutamate receptor GABA is possibly formed and evolved from the ancient chemical union of bacteriorhodopsin and periplasmic binding protein. The results obtained by the authors also unprecedentedly demonstrate that specific domains and identical structures are shown in each type of GPCR, which provides unique opportunities for future strategies on GPCR orphans’ prediction and classification.
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Affiliation(s)
- Zaichao Zhang
- College of Life Science, Graduate University of Chinese Academy of Sciences, No.9A Yuquan Rd, Shijingshan District, Beijing 100049, People's Republic of China
| | - Zhong Jin
- Supercomputing Center, Computer Network Information Center, Chinese Academy of Sciences, No.4, South Four Street Zhongguancun, Haidian District, Beijing 100190, People's Republic of China
| | - Yongbing Zhao
- College of Life Science, Graduate University of Chinese Academy of Sciences, No.9A Yuquan Rd, Shijingshan District, Beijing 100049, People's Republic of China
| | - Zhewen Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No.1-7, Beichen W Rd, Chaoyang District, Beijing, People's Republic of China, 100101
| | - Rujiao Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No.1-7, Beichen W Rd, Chaoyang District, Beijing, People's Republic of China, 100101
| | - Jingfa Xiao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No.1-7, Beichen W Rd, Chaoyang District, Beijing, People's Republic of China, 100101
| | - Jiayan Wu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, No.1-7, Beichen W Rd, Chaoyang District, Beijing, People's Republic of China, 100101.
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30
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31
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Functional characterization of flavobacteria rhodopsins reveals a unique class of light-driven chloride pump in bacteria. Proc Natl Acad Sci U S A 2014; 111:6732-7. [PMID: 24706784 DOI: 10.1073/pnas.1403051111] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Light-activated, ion-pumping rhodopsins are broadly distributed among many different bacteria and archaea inhabiting the photic zone of aquatic environments. Bacterial proton- or sodium-translocating rhodopsins can convert light energy into a chemiosmotic force that can be converted into cellular biochemical energy, and thus represent a widespread alternative form of photoheterotrophy. Here we report that the genome of the marine flavobacterium Nonlabens marinus S1-08(T) encodes three different types of rhodopsins: Nonlabens marinus rhodopsin 1 (NM-R1), Nonlabens marinus rhodopsin 2 (NM-R2), and Nonlabens marinus rhodopsin 3 (NM-R3). Our functional analysis demonstrated that NM-R1 and NM-R2 are light-driven outward-translocating H(+) and Na(+) pumps, respectively. Functional analyses further revealed that the light-activated NM-R3 rhodopsin pumps Cl(-) ions into the cell, representing the first chloride-pumping rhodopsin uncovered in a marine bacterium. Phylogenetic analysis revealed that NM-R3 belongs to a distinct phylogenetic lineage quite distant from archaeal inward Cl(-)-pumping rhodopsins like halorhodopsin, suggesting that different types of chloride-pumping rhodopsins have evolved independently within marine bacterial lineages. Taken together, our data suggest that similar to haloarchaea, a considerable variety of rhodopsin types with different ion specificities have evolved in marine bacteria, with individual marine strains containing as many as three functionally different rhodopsins.
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32
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Zaitsev SY, Solovyeva DO, Nabiev IR. Nanobiohybrid structures based on the organized films of photosensitive membrane proteins. RUSSIAN CHEMICAL REVIEWS 2014. [DOI: 10.1070/rc2014v083n01abeh004372] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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Stäubert C, Le Duc D, Schöneberg T. Examining the Dynamic Evolution of G Protein-Coupled Receptors. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2014. [DOI: 10.1007/978-1-62703-779-2_2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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34
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Álvarez R, Vaz B, Gronemeyer H, de Lera ÁR. Functions, therapeutic applications, and synthesis of retinoids and carotenoids. Chem Rev 2013; 114:1-125. [PMID: 24266866 DOI: 10.1021/cr400126u] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Rosana Álvarez
- Departamento de Química Orgánica, Centro de Investigación Biomédica (CINBIO), and Instituto de Investigación Biomédica de Vigo (IBIV), Universidade de Vigo , 36310 Vigo, Spain
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35
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Du H, Li D, Wang Y, Wang C, Zhang D, Yang YL, Wang C. Determination of the Surface Charge Density and Temperature Dependence of Purple Membrane by Electric Force Microscopy. J Phys Chem B 2013; 117:9895-9. [DOI: 10.1021/jp403075w] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Huiwen Du
- National Center for Nanoscience and Technology, Beijing 100190, People’s
Republic of China
- Department of Chemistry, Tsinghua University, Beijing 100084,
China
| | - Denghua Li
- National Center for Nanoscience and Technology, Beijing 100190, People’s
Republic of China
| | - Yibing Wang
- National Center for Nanoscience and Technology, Beijing 100190, People’s
Republic of China
| | - Chenxuan Wang
- National Center for Nanoscience and Technology, Beijing 100190, People’s
Republic of China
- Department of Chemistry, Tsinghua University, Beijing 100084,
China
| | - Dongdong Zhang
- National Center for Nanoscience and Technology, Beijing 100190, People’s
Republic of China
| | - Yan-lian Yang
- National Center for Nanoscience and Technology, Beijing 100190, People’s
Republic of China
| | - Chen Wang
- National Center for Nanoscience and Technology, Beijing 100190, People’s
Republic of China
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36
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Pal R, Sekharan S, Batista VS. Spectral Tuning in Halorhodopsin: The Chloride Pump Photoreceptor. J Am Chem Soc 2013; 135:9624-7. [DOI: 10.1021/ja404600z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Rhitankar Pal
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut
06520-8107, United States
| | - Sivakumar Sekharan
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut
06520-8107, United States
| | - Victor S. Batista
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, Connecticut
06520-8107, United States
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37
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Ishchenko A, Round E, Borshchevskiy V, Grudinin S, Gushchin I, Klare J, Balandin T, Remeeva A, Engelhard M, Büldt G, Gordeliy V. Ground state structure of D75N mutant of sensory rhodopsin II in complex with its cognate transducer. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2013; 123:55-8. [DOI: 10.1016/j.jphotobiol.2013.03.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2012] [Revised: 02/27/2013] [Accepted: 03/19/2013] [Indexed: 11/15/2022]
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38
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G N, Tan A, Farhatnia Y, Rajadas J, Hamblin MR, Khaw PT, Seifalian AM. Channelrhodopsins: visual regeneration and neural activation by a light switch. N Biotechnol 2013; 30:461-74. [PMID: 23664865 DOI: 10.1016/j.nbt.2013.04.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/28/2013] [Accepted: 04/16/2013] [Indexed: 01/09/2023]
Abstract
The advent of optogenetics provides a new direction for the field of neuroscience and biotechnology, serving both as a refined investigative tool and as potential cure for many medical conditions via genetic manipulation. Although still in its infancy, recent advances in optogenetics has made it possible to remotely manipulate in vivo cellular functions using light. Coined Nature Methods' 'Method of the Year' in 2010, the optogenetic toolbox has the potential to control cell, tissue and even animal behaviour. This optogenetic toolbox consists of light-sensitive proteins that are able to modulate membrane potential in response to light. Channelrhodopsins (ChR) are light-gated microbial ion channels, which were first described in green algae. ChR2 (a subset of ChR) is a seven transmembrane α helix protein, which evokes membrane depolarization and mediates an action potential upon photostimulation with blue (470 nm) light. By contrast to other seven-transmembrane proteins that require second messengers to open ion channels, ChR2 form ion channels themselves, allowing ultrafast depolarization (within 50 milliseconds of illumination). It has been shown that integration of ChR2 into various tissues of mice can activate neural circuits, control heart muscle contractions, and even restore breathing after spinal cord injury. More compellingly, a plethora of evidence has indicated that artificial expression of ChR2 in retinal ganglion cells can reinstate visual perception in mice with retinal degeneration.
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Affiliation(s)
- Natasha G
- Centre for Nanotechnology & Regenerative Medicine, UCL Division of Surgery & Interventional Science, University College London, London, UK
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39
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Neumann-Verhoefen MK, Neumann K, Bamann C, Radu I, Heberle J, Bamberg E, Wachtveitl J. Ultrafast Infrared Spectroscopy on Channelrhodopsin-2 Reveals Efficient Energy Transfer from the Retinal Chromophore to the Protein. J Am Chem Soc 2013; 135:6968-76. [DOI: 10.1021/ja400554y] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Mirka-Kristin Neumann-Verhoefen
- Institute of Physical and Theoretical
Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Karsten Neumann
- Institute of Physical and Theoretical
Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
| | - Christian Bamann
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt
am Main, Germany
| | - Ionela Radu
- Department
of Physics, Molecular
Biospectroscopy, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Joachim Heberle
- Department of Physics, Experimental
Molecular Biophysics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Ernst Bamberg
- Max Planck Institute of Biophysics, Max-von-Laue Strasse 3, 60438 Frankfurt
am Main, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical
Chemistry, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue Strasse 7, 60438 Frankfurt am Main, Germany
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40
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Kritsky MS, Telegina TA, Vechtomova YL, Buglak AA. Why flavins are not competitors of chlorophyll in the evolution of biological converters of solar energy. Int J Mol Sci 2012; 14:575-93. [PMID: 23271372 PMCID: PMC3565283 DOI: 10.3390/ijms14010575] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Revised: 12/10/2012] [Accepted: 12/13/2012] [Indexed: 12/17/2022] Open
Abstract
Excited flavin molecules can photocatalyze reactions, leading to the accumulation of free energy in the products, and the data accumulated through biochemical experiments and by modeling prebiological processes suggest that flavins were available in the earliest stages of evolution. Furthermore, model experiments have shown that abiogenic flavin conjugated with a polyamino acid matrix, a pigment that photocatalyzes the phosphorylation of ADP to form ATP, could have been present in the prebiotic environment. Indeed, excited flavin molecules play key roles in many photoenzymes and regulatory photoreceptors, and the substantial structural differences between photoreceptor families indicate that evolution has repeatedly used flavins as chromophores for photoreceptor proteins. Some of these photoreceptors are equipped with a light-harvesting antenna, which transfers excitation energy to chemically reactive flavins in the reaction center. The sum of the available data suggests that evolution could have led to the formation of a flavin-based biological converter to convert light energy into energy in the form of ATP.
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Affiliation(s)
- Mikhail S. Kritsky
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, House 33, Building 2, Leninsky Prospekt, Moscow 119071, Russia; E-Mails: (T.A.T.); (Y.L.V.); (A.A.B.)
| | - Taisiya A. Telegina
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, House 33, Building 2, Leninsky Prospekt, Moscow 119071, Russia; E-Mails: (T.A.T.); (Y.L.V.); (A.A.B.)
| | - Yulia L. Vechtomova
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, House 33, Building 2, Leninsky Prospekt, Moscow 119071, Russia; E-Mails: (T.A.T.); (Y.L.V.); (A.A.B.)
| | - Andrey A. Buglak
- A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, House 33, Building 2, Leninsky Prospekt, Moscow 119071, Russia; E-Mails: (T.A.T.); (Y.L.V.); (A.A.B.)
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Gehring WJ. The evolution of vision. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2012; 3:1-40. [DOI: 10.1002/wdev.96] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Herz J, Verhoefen MK, Weber I, Bamann C, Glaubitz C, Wachtveitl J. Critical role of Asp227 in the photocycle of proteorhodopsin. Biochemistry 2012; 51:5589-600. [PMID: 22738119 DOI: 10.1021/bi3003764] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photocycle of the proton acceptor complex mutant D227N of the bacterial retinal protein proteorhodopsin is investigated employing steady state pH-titration experiments in the UV-visible range as well as femtosecond-pump-probe spectroscopy and flash photolysis in the visible spectral range. The evaluation of the pH-dependent spectra showed that the neutralization of the charge at position 227 has a remarkable influence on the ground state properties of the protein. Both the pK(a) values of the primary proton acceptor and of the Schiff base are considerably decreased. Femtosecond-time-resolved measurements demonstrate that the general S(1) deactivation pathway; that is, the K-state formation is preserved in the D227N mutant. However, the pH-dependence of the reaction rate is lost by the substitution of Asp227 with an asparagine. Also no significant kinetic differences are observed upon deuteration. This is explained by the lack of a strongly hydrogen-bonded water in the vicinity of Asp97, Asp227, and the Schiff base or a change in the hydrogen bonding of it (Ikeda et al. (2007) Biochemistry 46, 5365-5373). The flash photolysis measurements prove a considerably elongated photocycle with pronounced pH-dependence. Interestingly, at pH 9 the M-state is visible until the end of the reaction cycle, leading to the conclusion that the mutation does not only lower the pK(a) of the Schiff base in the unphotolyzed ground state but also prevents an efficient reprotonation reaction.
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Affiliation(s)
- Julia Herz
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe-University, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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Shimano T, Fyk–Kolodziej B, Asako M, Tomoda K, Bledsoe S, Pan Z, Molitor S, Holt A. Histological and Physiological Investigation of Channelrhodopsin–2 and Halorhodopsin in the Dorsal Cochlear Nucleus. J Otol 2011. [DOI: 10.1016/s1672-2930(11)50002-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Petzold B, Park SJ, Ponce P, Roozeboom C, Powell C, Goodman M, Pruitt B. Caenorhabditis elegans body mechanics are regulated by body wall muscle tone. Biophys J 2011; 100:1977-85. [PMID: 21504734 PMCID: PMC3077690 DOI: 10.1016/j.bpj.2011.02.035] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Revised: 02/07/2011] [Accepted: 02/22/2011] [Indexed: 11/27/2022] Open
Abstract
Body mechanics in the nematode Caenorhabditis elegans are central to both mechanosensation and locomotion. Previous work revealed that the mechanics of the outer shell, rather than internal hydrostatic pressure, dominates stiffness. This shell is comprised of the cuticle and the body wall muscles, either of which could contribute to the body mechanics. Here, we tested the hypothesis that the muscles are an important contributor by modulating muscle tone using optogenetic and pharmacological tools, and measuring animal stiffness using piezoresistive microcantilevers. As a proxy for muscle tone, we measured changes in animal length under the same treatments. We found that treatments that induce muscle contraction generally resulted in body shortening and stiffening. Conversely, methods to relax the muscles more modestly increased length and decreased stiffness. The results support the idea that body wall muscle activation contributes significantly to and can modulate C. elegans body mechanics. Modulation of body stiffness would enable nematodes to tune locomotion or swimming gaits and may have implications in touch sensation.
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Affiliation(s)
- Bryan C. Petzold
- Department of Mechanical Engineering, Stanford University Schools of Engineering and Medicine, Stanford, California
| | - Sung-Jin Park
- Department of Mechanical Engineering, Stanford University Schools of Engineering and Medicine, Stanford, California
| | - Pierre Ponce
- Department of Electrical Engineering, Stanford University Schools of Engineering and Medicine, Stanford, California
| | - Clifton Roozeboom
- Department of Mechanical Engineering, Stanford University Schools of Engineering and Medicine, Stanford, California
| | - Chloé Powell
- Department of Molecular and Cellular Physiology, Stanford University Schools of Engineering and Medicine, Stanford, California
| | - Miriam B. Goodman
- Department of Molecular and Cellular Physiology, Stanford University Schools of Engineering and Medicine, Stanford, California
| | - Beth L. Pruitt
- Department of Mechanical Engineering, Stanford University Schools of Engineering and Medicine, Stanford, California
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Strotmann R, Schröck K, Böselt I, Stäubert C, Russ A, Schöneberg T. Evolution of GPCR: change and continuity. Mol Cell Endocrinol 2011; 331:170-8. [PMID: 20708652 DOI: 10.1016/j.mce.2010.07.012] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Revised: 06/28/2010] [Accepted: 07/13/2010] [Indexed: 12/26/2022]
Abstract
Once introduced into the very early eukaryotic blueprint, seven-transmembrane receptors soon became the central and versatile components of the evolutionary highly successful G protein-coupled transmembrane signaling mechanism. In contrast to all other components of this signal transduction pathway, G protein-coupled receptors (GPCR) evolved in various structural families, eventually comprising hundreds of members in vertebrate genomes. Their functional diversity is in contrast to the conserved transmembrane core and the invariant set of intracellular signaling mechanisms, and it may be the interplay of these properties that is the key to the evolutionary success of GPCR. The GPCR repertoires retrieved from extant vertebrate genomes are the recent endpoints of this long evolutionary process. But the shaping of the fine structure and the repertoire of GPCR is still ongoing, and signatures of recent selection acting on GPCR genes can be made visible by modern population genetic methods. The very dynamic evolution of GPCR can be analyzed from different perspectives: at the levels of sequence comparisons between species from different families, orders and classes, and at the level of populations within a species. Here, we summarize the main conclusions from studies at these different levels with a specific focus on the more recent evolutionary dynamics of GPCR.
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Affiliation(s)
- Rainer Strotmann
- Institute of Biochemistry, Medical Faculty, University of Leipzig, Germany.
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Verhoefen MK, Bamann C, Blöcher R, Förster U, Bamberg E, Wachtveitl J. The photocycle of channelrhodopsin-2: ultrafast reaction dynamics and subsequent reaction steps. Chemphyschem 2011; 11:3113-22. [PMID: 20730849 DOI: 10.1002/cphc.201000181] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The photocycle of channelrhodopsin-2 is investigated in a comprehensive study by ultrafast absorption and fluorescence spectroscopy as well as flash photolysis in the visible spectral range. The ultrafast techniques reveal an excited-state decay mechanism analogous to that of the archaeal bacteriorhodopsin and sensory rhodopsin II from Natronomonas pharaonis. After a fast vibrational relaxation of the excited-state population with 150 fs its decay with mainly 400 fs is observed. Hereby, both the initial all-trans retinal ground state and the 13-cis-retinal K photoproduct are populated. The reaction proceeds with a 2.7 ps component assigned to cooling processes. Small spectral shifts are observed on a 200 ps timescale. They are attributed to conformational rearrangements in the retinal binding pocket. The subsequent dynamics progresses with the formation of an M-like intermediate (7 and 120 μs), which decays into red-shifted states within 3 ms. Ground-state recovery including channel closing and reisomerization of the retinal chromophore occurs in a triexponential manner (6 ms, 33 ms, 3.4 s). To learn more about the energy barriers between the different photocycle intermediates, temperature-dependent flash photolysis measurements are performed between 10 and 30°C. The first five time constants decrease with increasing temperature. The calculated thermodynamic parameters indicate that the closing mechanism is controlled by large negative entropy changes. The last time constant is temperature independent, which demonstrates that the photocycle is most likely completed by a series of individual steps recovering the initial structure.
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Affiliation(s)
- Mirka-Kristin Verhoefen
- Institute of Physical and Theoretical Chemistry, Johann Wolfgang Goethe University Frankfurt, Max von Laue-Straße 7, 60438 Frankfurt am Main, Germany
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Muraoka T, Shima T, Hamada T, Morita M, Takagi M, Kinbara K. Mimicking multipass transmembrane proteins: synthesis, assembly and folding of alternating amphiphilic multiblock molecules in liposomal membranes. Chem Commun (Camb) 2011; 47:194-6. [DOI: 10.1039/c0cc02420a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Hydroxylamine as a thermal destabiliser of bacteriorhodopsin. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2010; 39:1605-11. [DOI: 10.1007/s00249-010-0618-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 06/26/2010] [Accepted: 06/29/2010] [Indexed: 11/26/2022]
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50
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Rakovich A, Sukhanova A, Bouchonville N, Lukashev E, Oleinikov V, Artemyev M, Lesnyak V, Gaponik N, Molinari M, Troyon M, Rakovich YP, Donegan JF, Nabiev I. Resonance energy transfer improves the biological function of bacteriorhodopsin within a hybrid material built from purple membranes and semiconductor quantum dots. NANO LETTERS 2010; 10:2640-2648. [PMID: 20521831 DOI: 10.1021/nl1013772] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Purple membrane (PM) from bacteria Halobacterium salinarum contains a photochromic protein bacteriorhodopsin (bR) arranged in a 2D hexagonal nanocrystalline lattice (Figure 1 ). Absorption of light by the protein-bound chromophore retinal results in pumping the protons through the PM creating an electrochemical gradient which is then used by the ATPases to energize the cellular processes. Energy conversion, photochromism, and photoelectrism are the inherent effects which are employed in many bR technical applications. bR, along with the other photosensitive proteins, is not able to deal with the excess energy of photons in UV and blue spectral region and utilizes less than 0.5% of the energy from the available incident solar light for its biological function. Here, we proceed with optimization of bR functions through the engineering of a "nanoconverter" of solar energy based on semiconductor quantum dots (QDs) tagged with the PM. These nanoconverters are able to harvest light from deep-UV to the visible region and to transfer this additionally collected energy to bR via Förster resonance energy transfer (FRET). We show that specific nanobio-optical and spatial coupling of QDs (donor) and bR retinal (acceptor) provide a means to achieve FRET with efficiency approaching 100%. We have finally demonstrated that the integration of QDs within PM significantly increases the efficiency of light-driven transmembrane proton pumping, which is the main bR biological function. This new QD-PM hybrid material will have numerous optoelectronic, photonic, and photovoltaic applications based on its energy conversion, photochromism, and photoelectrism properties.
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