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Bondar AN. Mechanisms of long-distance allosteric couplings in proton-binding membrane transporters. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 128:199-239. [PMID: 35034719 DOI: 10.1016/bs.apcsb.2021.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Membrane transporters that use proton binding and proton transfer for function couple local protonation change with changes in protein conformation and water dynamics. Changes of protein conformation might be required to allow transient formation of hydrogen-bond networks that bridge proton donor and acceptor pairs separated by long distances. Inter-helical hydrogen-bond networks adjust rapidly to protonation change, and ensure rapid response of the protein structure and dynamics. Membrane transporters with known three-dimensional structures and proton-binding groups inform on general principles of protonation-coupled protein conformational dynamics. Inter-helical hydrogen bond motifs between proton-binding carboxylate groups and a polar sidechain are observed in unrelated membrane transporters, suggesting common principles of coupling protonation change with protein conformational dynamics.
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Affiliation(s)
- Ana-Nicoleta Bondar
- University of Bucharest, Faculty of Physics, Măgurele, Romania; Forschungszentrum Jülich, Institute of Computational Biomedicine, Jülich, Germany.
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Birkner E, Berglund K, Klein ME, Augustine GJ, Hochgeschwender U. Non-invasive activation of optogenetic actuators. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2014; 8928:89282F. [PMID: 27965518 PMCID: PMC5149403 DOI: 10.1117/12.2044157] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The manipulation of genetically targeted neurons with light (optogenetics) continues to provide unprecedented avenues into studying the function of the mammalian brain. However, potential translation into the clinical arena faces a number of significant hurdles, foremost among them the need for insertion of optical fibers into the brain to deliver light to opsins expressed on neuronal membranes. In order to overcome these hardware-related problems, we have developed an alternative strategy for delivering light to opsins which does not involve fiber implants. Rather, the light is produced by a protein, luciferase, which oxidizes intravenously applied substrate, thereby emitting bioluminescence. In proof-of-principle studies employing a fusion protein of a light-generating luciferase to a light-sensing opsin (luminopsin), we showed that light emitted by Gaussia luciferase is indeed able to activate channelrhodopsin, allowing modulation of neuronal activity when expressed in cultured neurons. Here we assessed applicability of the concept in vivo in mice expressing luminopsins from viral vectors and from genetically engineered transgenes. The experiments demonstrate that intravenously applied substrate reaches neurons in the brain, causing the luciferase to produce bioluminescence which can be imaged in vivo, and that activation of channelrhodopsin by bioluminescence is sufficient to affect behavior. Further developments of such technology based on combining optogenetics with bioluminescence - i.e. combining light-sensing molecules with biologically produced light through luciferases - should bring optogenetics closer to clinical applications.
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Affiliation(s)
| | - Ken Berglund
- Department of Neurobiology, Duke University, Durham, NC, USA
| | | | - George J. Augustine
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
- Institute of Molecular and Cell Biology, Singapore
- Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Ute Hochgeschwender
- Neurotransgenic Laboratory, Duke University, Durham, NC, USA
- Department of Neurobiology, Duke University, Durham, NC, USA
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Berglund K, Birkner E, Augustine GJ, Hochgeschwender U. Light-emitting channelrhodopsins for combined optogenetic and chemical-genetic control of neurons. PLoS One 2013; 8:e59759. [PMID: 23544095 PMCID: PMC3609769 DOI: 10.1371/journal.pone.0059759] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/18/2013] [Indexed: 01/10/2023] Open
Abstract
Manipulation of neuronal activity through genetically targeted actuator molecules is a powerful approach for studying information flow in the brain. In these approaches the genetically targeted component, a receptor or a channel, is activated either by a small molecule (chemical genetics) or by light from a physical source (optogenetics). We developed a hybrid technology that allows control of the same neurons by both optogenetic and chemical genetic means. The approach is based on engineered chimeric fusions of a light-generating protein (luciferase) to a light-activated ion channel (channelrhodopsin). Ionic currents then can be activated by bioluminescence upon activation of luciferase by its substrate, coelenterazine (CTZ), as well as by external light. In cell lines, expression of the fusion of Gaussia luciferase to Channelrhodopsin-2 yielded photocurrents in response to CTZ. Larger photocurrents were produced by fusing the luciferase to Volvox Channelrhodopsin-1. This version allowed chemical modulation of neuronal activity when expressed in cultured neurons: CTZ treatment shifted neuronal responses to injected currents and sensitized neurons to fire action potentials in response to subthreshold synaptic inputs. These luminescent channelrhodopsins--or luminopsins--preserve the advantages of light-activated ion channels, while extending their capabilities. Our proof-of-principle results suggest that this novel class of tools can be improved and extended in numerous ways.
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Affiliation(s)
- Ken Berglund
- Department of Neurobiology, Duke University, Durham, North Carolina, United States of America
| | - Elisabeth Birkner
- Department of Neurobiology, Duke University, Durham, North Carolina, United States of America
- NeuroTransgenic Laboratory, Duke University, Durham, North Carolina, United States of America
| | - George J. Augustine
- Program in Neuroscience and Behavioral Disorders, Duke-NUS Graduate Medical School, Singapore, Singapore
- Center for Functional Connectomics, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Ute Hochgeschwender
- Department of Neurobiology, Duke University, Durham, North Carolina, United States of America
- NeuroTransgenic Laboratory, Duke University, Durham, North Carolina, United States of America
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Lanyi JK. Mechanism of ion transport across membranes. Bacteriorhodopsin as a prototype for proton pumps. J Biol Chem 1997; 272:31209-12. [PMID: 9395442 DOI: 10.1074/jbc.272.50.31209] [Citation(s) in RCA: 166] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- J K Lanyi
- Department of Physiology and Biophysics, University of California, Irvine, California 92697, USA
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Rath P, Spudich E, Neal DD, Spudich JL, Rothschild KJ. Asp76 is the Schiff base counterion and proton acceptor in the proton-translocating form of sensory rhodopsin I. Biochemistry 1996; 35:6690-6. [PMID: 8639619 DOI: 10.1021/bi9600355] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Both sensory rhodopsin I, a phototaxis receptor, and bacteriorhodopsin, a light-driven proton pump, have homologous residues which have been identified as critical for bacteriorhodopsin functioning. This includes Asp76, which in the case of bacteriorhodopsin (Asp85) functions as both the Schiff base counterion and the proton acceptor. Sensory rhodopsin I exists in a pH dependent equilibrium between two different forms in the absence of its transducer protein HtrI. At pH below 7, it exists primarily in a blue form (lambda max = 587 nm) which functions as a phototaxis signal transducer when complexed to HtrI, while at higher pH, it converts to a purple proton-transporting form similar to bacteriorhodopsin (lambda max = 550 nm). We report ATR-FTIR difference spectra obtained from both low- and high-pH forms of purified sensory rhodopsin I reconstituted into lipid vesicles. The low-pH species has an ethylenic C = C stretch mode at 1520 cm-1 which shifts to 1526 cm-1 in the high-pH form. No frequency shift was found for the mutant D76N, in agreement with visible absorption measurements. Weak negative/positive bands at 1763/1751 cm-1 previously assigned to a perturbation of the C = O stretch mode of Asp76 during S373 formation in the low-pH form are replaced by a single intense positive band near 1749 cm-1 in the high-pH form. These results along with the effects of H/D exchange show that Asp76 is protonated in the signal-transducing form of sensory rhodopsin I and is ionized and functions as the counterion and Schiff base proton acceptor in the proton-transporting high-pH form of sensory rhodopsin I similar to bacteriorhodopsin.
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Affiliation(s)
- P Rath
- Department of Physics, Boston University, Boston, Massachusetts 02215, USA
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Rath P, Olson KD, Spudich JL, Rothschild KJ. The Schiff base counterion of bacteriorhodopsin is protonated in sensory rhodopsin I: spectroscopic and functional characterization of the mutated proteins D76N and D76A. Biochemistry 1994; 33:5600-6. [PMID: 8180184 DOI: 10.1021/bi00184a032] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Both sensory rhodopsin I (SR-I), a phototaxis receptor, and bacteriorhodopsin (BR), a light-driven proton pump, share residues which have been identified as critical for BR functioning. This includes Asp76, which in the case of bacteriorhodopsin (Asp85) functions both as the Schiff base counterion and proton acceptor. We found that substituting an Asn for Asp76 (D76N) in SR-I has no effect on its visible absorption unlike the analogous mutation (D85N) in BR which shifts the absorption to longer wavelengths. The mutated proteins D76N and D76A are also fully functional as phototaxis receptors in contrast to BR, where the analogous substitutions block proton transport. D76N was also found to exhibit a spectrally normal SR587-->S373 transition. However, FTIR difference spectroscopy reveals that two bands in the SR587-->S373 difference spectrum at 1766/1749 cm-1 (negative/positive), assigned to the C=O stretch mode of a carboxylic acid, disappear in D76N, although no changes are observed in the carboxylate region. In addition, the kinetics and yield of this photoreaction are altered. On this basis, it is concluded that, unlike Asp85 in bacteriorhodopsin, Asp76 is protonated in SR-I and undergoes an increase in its hydrogen bonding during the SR587-->S373 transition. This model accounts for the difference in color of SR-I and BR and the finding that Asn can substitute for Asp76 without greatly altering the SR-I phenotype. Interestingly, parallels exist between this residue and Asp83 in the visual receptor rhodopsin which has recently been found to exist in a protonated form and to undergo an almost identical change in hydrogen bonding during rhodopsin activation.
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Affiliation(s)
- P Rath
- Department of Physics, Boston University, Massachusetts 02215
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Chapter 15 Halobacterial genes and genomes. ACTA ACUST UNITED AC 1993. [DOI: 10.1016/s0167-7306(08)60264-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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9
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Oesterhelt D, Tittor J, Bamberg E. A unifying concept for ion translocation by retinal proteins. J Bioenerg Biomembr 1992; 24:181-91. [PMID: 1526960 DOI: 10.1007/bf00762676] [Citation(s) in RCA: 176] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
First, halorhodopsin is capable of pumping protons after illumination with green and blue light in the same direction as chloride. Second, mutated bacteriorhodopsin where the proton acceptor Asp85 and the proton donor Asp96 are replaced by Asn showed proton pump activity after illumination with blue light in the same direction as wildtype after green light illumination. These results can be explained by and are discussed in light of our new hypothesis: structural changes in either molecule lead to a change in ion affinity and accessibility for determining the vectoriality of the transport through the two proteins.
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Affiliation(s)
- D Oesterhelt
- Max-Planck-Institu für Biochemie, Martinsried, Germany
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10
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Eisenberg H, Mevarech M, Zaccai G. Biochemical, structural, and molecular genetic aspects of halophilism. ADVANCES IN PROTEIN CHEMISTRY 1992; 43:1-62. [PMID: 1442321 DOI: 10.1016/s0065-3233(08)60553-7] [Citation(s) in RCA: 90] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- H Eisenberg
- Structural Biology Department, Weizmann Institute of Science, Rehovot, Israel
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Salin ML, Duke MV, Ma DP, Boyle JA. Halobacterium halobium Mn-SOD gene: archaebacterial and eubacterial features. FREE RADICAL RESEARCH COMMUNICATIONS 1991; 12-13 Pt 1:443-9. [PMID: 2071048 DOI: 10.3109/10715769109145815] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A 1.8 kb PstI fragment from Halobacterium halobium DNA was found to hybridize to synthetic oligonucleotide probes constructed by using the sequence of the N-terminus of a Mn-containing superoxide dismutase purified from H. halobium. The entire insert containing a 600-bp coding sequence for Mn-SOD and its 5' and 3' flanking regions was sequenced. The derived amino acid sequence of the structural gene showed a similarity to other manganic and iron-containing superoxide dismutases in normally conserved regions. Primer extension analysis of the H. halobium Mn-SOD mRNA showed that gene transcription begins 14 bases upstream of the translational start. A Shine-Dalgarno sequence and archaebacterial consensus promoter sequences were observed. Several other promoter and terminator nucleotide sequences homologous to prokaryotic and eukaryotic organisms were found.
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Affiliation(s)
- M L Salin
- Department of Biochemistry and Molecular Biology, Mississippi State University, MS 39762
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12
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Brown JW, Daniels CJ, Reeve JN. Gene structure, organization, and expression in archaebacteria. Crit Rev Microbiol 1989; 16:287-338. [PMID: 2467783 DOI: 10.3109/10408418909105479] [Citation(s) in RCA: 216] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Major advances have recently been made in understanding the molecular biology of the archaebacteria. In this review, we compare the structure of protein and stable RNA-encoding genes cloned and sequenced from each of the major classes of archaebacteria: the methanogens, extreme halophiles, and acid thermophiles. Protein-encoding genes, including some encoding proteins directly involved in methanogenesis and photoautotrophy, are analyzed on the basis of gene organization and structure, transcriptional control signals, codon usage, and evolutionary conservation. Stable RNA-encoding genes are compared for gene organization and structure, transcriptional signals, and processing events involved in RNA maturation, including intron removal. Comparisons of archaebacterial structures and regulatory systems are made with their eubacterial and eukaryotic homologs.
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Affiliation(s)
- J W Brown
- Department of Biology, Indiana University, Bloomington
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Salin ML, Duke MV, Oesterhelt D, Ma DP. Cloning and determination of the nucleotide sequence of the Mn-containing superoxide dismutase gene from Halobacterium halobium. Gene X 1988; 70:153-9. [PMID: 3240866 DOI: 10.1016/0378-1119(88)90113-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A group of synthetic 17-mer oligodeoxynucleotides (oligos) was constructed to correspond to a sequence of amino acids situated near the N terminus of the manganese-containing superoxide dismutase (Mn-SOD) purified from the halophilic bacterium, Halobacterium halobium. A cosmid library of a Sau3AI partial digest of halobium DNA, cloned into the BamHI site of pHC79, was probed with the radiolabeled oligos. Cosmid DNA was purified from the clone that showed hybridization at the highest stringency. A 1.8-kb PstI fragment of this DNA which hybridized the probes was subcloned into bacteriophage M13 and transfected into Escherichia coli JM101. The entire insert containing a 600-bp sequence coding for Mn-SOD and its 5'- and 3'-flanking regions was sequenced. The derived amino acid sequence of the structural gene showed a similarity to other manganese and iron-containing SODs in normally conserved regions.
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Affiliation(s)
- M L Salin
- Department of Biochemistry, Mississippi State University, MS 39762
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Wölfer U, Dencher NA, Büldt G, Wrede P. Bacteriorhodopsin precursor is processed in two steps. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 174:51-7. [PMID: 3371364 DOI: 10.1111/j.1432-1033.1988.tb14061.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Besides the Coomassie-blue-stained band corresponding to mature bacterioopsin two additional bands of slightly higher apparent molecular masses were observed in purple membrane preparations from Halobacterium halobium by SDS-PAGE. The staining intensity within the triple band pattern varied with the age of the cell culture. For cells in the stationary growth phase the lower band, corresponding to mature bacterioopsin, is the predominant one. Immunodetection and site-specific proteolysis with papain identified the upper band as originating from the previously described precursor of bacterioopsin with its 13-amino-acid-long N-terminal presequence. Our results suggest that the intermediate band is due to a modified precursor of bacterioopsin with a truncated presequence of about eight amino acids. A two-step mechanism for the processing of pre-bacterioopsin to the mature protein in this archaebacterium is proposed.
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Affiliation(s)
- U Wölfer
- Fachbereich Physik, Freie Universität Berlin
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Ovchinnikov YuA, Abdulaev NG, Zolotarev AS, Shmukler BE, Zargarov AA, Kutuzov MA, Telezhinskaya IN, Levina NB. Photosynthetic reaction centre of Chloroflexus aurantiacus. I. Primary structure of L-subunit. FEBS Lett 1988; 231:237-42. [PMID: 2834225 DOI: 10.1016/0014-5793(88)80739-7] [Citation(s) in RCA: 91] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The L-subunit primary structure of the reaction centre from Chloroflexus aurantiacus composed of 310 amino acid residues has been determined by parallel analysis of the protein and corresponding DNA. Significant homology between this protein and L-subunits from reaction centres of purple bacteria is observed. This implies close similarity in the tertiary structure of these proteins.
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Affiliation(s)
- Ovchinnikov YuA
- Shemyakin Institute of Bioorganic Chemistry, USSR Academy of Sciences, Moscow
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