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Kim EH, Park S, Kim YK, Moon M, Park J, Lee KJ, Lee S, Kim YP. Self-luminescent photodynamic therapy using breast cancer targeted proteins. SCIENCE ADVANCES 2020; 6:eaba3009. [PMID: 32917700 PMCID: PMC7486108 DOI: 10.1126/sciadv.aba3009] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 07/23/2020] [Indexed: 05/10/2023]
Abstract
Despite the potential of photodynamic therapy (PDT), its comprehensive use in cancer treatment has not been achieved because of the nondegradable risks of photosensitizing drugs and limits of light penetration and instrumentation. Here, we present bioluminescence (BL)-induced proteinaceous PDT (BLiP-PDT), through the combination of luciferase and a reactive oxygen species (ROS)-generating protein (Luc-RGP), which is self-luminescent and degradable. After exposure to coelenterazine-h as a substrate for luciferase without external light irradiation, Luc-RGP fused with a small lead peptide-induced breast cancer cell death through the generation of BL-sensitive ROS in the plasma membrane. Even with extremely low light energy, BLiP-PDT exhibited targeted effects in primary breast cancer cells from patients and in in vivo tumor xenograft mouse models. These findings suggest that BLiP-PDT is immediately useful as a promising theranostic approach against various cancers.
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Affiliation(s)
- Eun Hye Kim
- Department of Life Science, Hanyang University, Seoul 04763, Korea
| | - Sangwoo Park
- Gwangju Center, Korea Basic Science Institute (KBSI), Gwangju 61186, Korea
| | - Yun Kyu Kim
- Department of Convergence Medicine, Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea
| | - Minwoo Moon
- Department of Life Science, Hanyang University, Seoul 04763, Korea
| | - Jeongwon Park
- Gwangju Center, Korea Basic Science Institute (KBSI), Gwangju 61186, Korea
| | - Kyung Jin Lee
- Department of Convergence Medicine, Asan Institute for Life Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea.
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Seongsoo Lee
- Gwangju Center, Korea Basic Science Institute (KBSI), Gwangju 61186, Korea.
| | - Young-Pil Kim
- Department of Life Science, Hanyang University, Seoul 04763, Korea.
- Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
- Research Institute for Convergence of Basic Sciences, Hanyang University, Seoul 04763, Korea
- Institute of Nano Science and Technology, Hanyang University, Seoul 04763, Korea
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pH-sensitive vibrational probe reveals a cytoplasmic protonated cluster in bacteriorhodopsin. Proc Natl Acad Sci U S A 2017; 114:E10909-E10918. [PMID: 29203649 DOI: 10.1073/pnas.1707993114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Infrared spectroscopy has been used in the past to probe the dynamics of internal proton transfer reactions taking place during the functional mechanism of proteins but has remained mostly silent to protonation changes in the aqueous medium. Here, by selectively monitoring vibrational changes of buffer molecules with a temporal resolution of 6 µs, we have traced proton release and uptake events in the light-driven proton-pump bacteriorhodopsin and correlate these to other molecular processes within the protein. We demonstrate that two distinct chemical entities contribute to the temporal evolution and spectral shape of the continuum band, an unusually broad band extending from 2,300 to well below 1,700 cm-1 The first contribution corresponds to deprotonation of the proton release complex (PRC), a complex in the extracellular domain of bacteriorhodopsin where an excess proton is shared by a cluster of internal water molecules and/or ionic E194/E204 carboxylic groups. We assign the second component of the continuum band to the proton uptake complex, a cluster with an excess proton reminiscent to the PRC but located in the cytoplasmic domain and possibly stabilized by D38. Our findings refine the current interpretation of the continuum band and call for a reevaluation of the last proton transfer steps in bacteriorhodopsin.
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Polli D, Rivalta I, Nenov A, Weingart O, Garavelli M, Cerullo G. Tracking the primary photoconversion events in rhodopsins by ultrafast optical spectroscopy. Photochem Photobiol Sci 2015; 14:213-28. [DOI: 10.1039/c4pp00370e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We review the most recent experimental and computational efforts aimed at exposing the very early phases of the ultrafast isomerization in visual Rhodopsins and we discuss future advanced experiments and calculations.
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Affiliation(s)
- D. Polli
- IFN-CNR
- Dipartimento di Fisica
- Politecnico di Milano
- 20133 Milano
- Italy
| | - I. Rivalta
- Université de Lyon
- CNRS
- Institut de Chimie de Lyon
- École Normale Supérieure de Lyon
- F-69364 Lyon Cedex 07
| | - A. Nenov
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- 40126 Bologna
- Italy
| | - O. Weingart
- Institut für Theoretische Chemie und Computerchemie
- Heinrich-Heine-Universität Düsseldorf
- Universitätsstr. 1
- 40225 Düsseldorf
- Germany
| | - M. Garavelli
- Université de Lyon
- CNRS
- Institut de Chimie de Lyon
- École Normale Supérieure de Lyon
- F-69364 Lyon Cedex 07
| | - G. Cerullo
- IFN-CNR
- Dipartimento di Fisica
- Politecnico di Milano
- 20133 Milano
- Italy
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Schimz A, Hildebrand E. Photosensing and Processing of Sensory Signals inHalobacterim halobium. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/j.1438-8677.1988.tb00020.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Abstract
Genetically encoded, single-component optogenetic tools have made a significant impact on neuroscience, enabling specific modulation of selected cells within complex neural tissues. As the optogenetic toolbox contents grow and diversify, the opportunities for neuroscience continue to grow. In this review, we outline the development of currently available single-component optogenetic tools and summarize the application of various optogenetic tools in diverse model organisms.
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Affiliation(s)
- Lief Fenno
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
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Otomo J, Tomioka A, Kinosita K, Miyata H, Takenaka Y, Kouyama T, Ikegami A. Chromophore of Bacteriorhodopsin is Closer to the Cytoplasmic Surface of Purple Membrane: Fluorescence Energy Transfer on Oriented Membrane Sheets. Biophys J 2010; 54:57-64. [PMID: 19431725 DOI: 10.1016/s0006-3495(88)82930-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Transmembrane location of the retinal chromophore, either native or reduced in situ to a fluorescent derivative, of the purple membrane of Halobacterium halobium was investigated with fluorescence energy transfer techniques. Single sheets of purple membrane, either native or reduced with borohydride, were adsorbed on polylysine-coated glass; the orientation, whether the exposed surfaces were cytoplasmic or extracellular, was controlled by adjusting the pH of the membrane suspension before the adsorption. On the exposed surface of the reduced membrane, a layer of cytochrome c, hemoglobin, or ferritin was deposited. The rate of excitation energy transfer from the fluorescent chromophore in the membrane to the colored protein was greater when the protein was on the cytoplasmic surface of the membrane than when it was on the extracellular surface. Analysis in which uniform distribution of the protein on the surface was assumed showed that the reduced chromophore is situated at a depth of <1.5 nm from the cytoplasmic surface. The location of the native retinal chromophore was examined by depositing a small amount of tris(2,2'-bipyridyl)ruthenium(II) complex on the native membrane adsorbed on the glass. Energy transfer from the luminescent complex to the retinal chromosphore was more efficient on the cytoplasmic surface than on the extracellular surface, suggesting that the native chromophore is also on the cytoplasmic side. From these and previous results we conclude that the chromophore, whether native or reduced, of bacteriorhodopsin is located at a depth of 1.0 +/- 0.3 nm from the cytoplasmic surface of purple membrane.
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Kometani T, Kinosita K, Furuno T, Kouyama T, Ikegami A. Transmembrane location of retinal in purple membrane: fluorescence energy transfer in maximally packed donor-acceptor systems. Biophys J 2010; 52:509-17. [PMID: 19431704 DOI: 10.1016/s0006-3495(87)83240-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Transmembrane location of the retinal chromophore in the purple membrane of Halobacterium halobium was investigated in three different systems in which excitation energy transfer between the chromophore and external dye molecules condensed on the membrane surfaces was observed. In system ii, the energy donor was the retinal chromophore converted in situ to a fluorescent derivative. The fluorescent membranes were embedded in solid cobalt-EDTA, which served as energy acceptors. System iii was similar to system ii, except that the acceptors were tris(2,2'-bipyridyl)ruthenium(II) complex in solid form. The positively charged ruthenium complex had a radius of 0.7 nm, whereas the cobalt complex in system ii was smaller (radius approximately 0.4 nm) and negatively charged. System iv was stacked sheets of native purple membrane with interspersed ruthenium complex; energy transfer from the luminescent ruthenuim complex to the native retinal chromophore was observed. The energy transfer rates in these three systems, and in two additional systems already described (Kouyama, T., K. Kinosita, Jr., and A. Ikegami, 1983, J. Mol. Biol., 165:91-107), were all consistent with a location of the retinal chromophore at a depth of 1.0 +/- 0.3 nm from a surface of the purple membrane. All the analyses in the present work involved an assumption that contacts between the external dye molecules and membrane surfaces were maximal; the depth values obtained cannot be underestimates. The chromophore therefore must be outside the middle one-third of the thickness, approximately 4.5 nm, of the purple membrane.
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Tittor J, Oesterhelt D, Maurer R, Desel H, Uhl R. The photochemical cycle of halorhodopsin: absolute spectra of intermediates obtained by flash photolysis and fast difference spectra measurements. Biophys J 2010; 52:999-1006. [PMID: 19431713 DOI: 10.1016/s0006-3495(87)83292-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Results of experiments using flash photolysis and fast difference spectroscopy suggest an extended version of the earlier published scheme of the photochemical cycle of halorhodopsin. Detailed experimental verification of the suggested photocycle is given. Due to the high resolution of the time-resolved difference spectra, absolute spectra of the intermediates in the photocycle were derived, allowing the interpretation of complex kinetic absorbance changes.
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9
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Zhang Y, Su T, Hu KS. Melittin-regenerated purple membrane. BIOCHEMISTRY (MOSCOW) 2009; 74:1375-81. [PMID: 19961420 DOI: 10.1134/s0006297909120128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have investigated the character of melittin-regenerated purple membrane. Adding melittin to blue membrane causes the color transition and partial regeneration of the photocycle and the proton pump. The reconstitution of bacteriorhodopsin by melittin is proved to be charge-dependent. In studying the location of melittin binding on the blue membrane, we suggest that melittin anchors on the membrane through both hydrophobic and electrostatic interactions. The electrostatic interaction is dominant. The binding sites for the electrostatic interaction should be on the surface of the membrane.
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Affiliation(s)
- Yue Zhang
- Institute of Biophysics, Academia Sinica, Beijing, 100101, PR China
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10
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Birnbaum D, Seltzer S. A HIGHLY REACTIVE HETEROATOM ANALOG OF RETINAL AND ITS INTERACTION WITH BACTERIORHODOPSIN. Photochem Photobiol 2008. [DOI: 10.1111/j.1751-1097.1992.tb08520.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Fahey RC, Sundquist AR. Evolution of glutathione metabolism. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 64:1-53. [PMID: 1675828 DOI: 10.1002/9780470123102.ch1] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- R C Fahey
- Department of Chemistry, University of California, San Diego, La Jolla
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12
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Grzesiek S, Dencher NA. Time-course and stoichiometry of light-induced proton release and uptake during the photocycle of bacteriorhodopsin. FEBS Lett 2001. [DOI: 10.1016/0014-5793(86)81045-6] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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15
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Metzler DE, Metzler CM, Sauke DJ. Light and Life. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50026-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Hampp N. Bacteriorhodopsin as a Photochromic Retinal Protein for Optical Memories. Chem Rev 2000; 100:1755-1776. [PMID: 11777419 DOI: 10.1021/cr980072x] [Citation(s) in RCA: 234] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Norbert Hampp
- Institute for Physical Chemistry, University of Marburg, D-35032 Marburg, Germany, and Materials Science Center, D-35032 Marburg, Germany
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17
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Seltzer S. 13-Acetoxy-13-desmethylretinal-14-3H: Synthesis and Interaction with Bacterioopsin. Photochem Photobiol 1999. [DOI: 10.1111/j.1751-1097.1999.tb08270.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Molecular sensors based on the photoelectric effect of bacteriorhodopsin: Origin of differential responsivity. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 1997. [DOI: 10.1016/s0928-4931(97)00011-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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19
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Sugiyama Y, Yamada N, Mukohata Y. The light-driven proton pump, cruxrhodopsin-2 in Haloarcula sp. arg-2 (bR+, hR-), and its coupled ATP formation. BIOCHIMICA ET BIOPHYSICA ACTA 1994; 1188:287-92. [PMID: 7803445 DOI: 10.1016/0005-2728(94)90047-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Haloarcula sp. arg-2, a natural bacterial isolate from Andes heights, has a light-driven proton pump but not a light-driven anion pump. We have cloned and sequenced the gene encoding for the proton pump which has been named cruxrhodopsin-2. The gene consists of 768 bp encoding 255 amino acids with a molecular mass of 27,544 Da. The deduced amino acid sequence of cruxrhodopsin-2 is 77%, 50%, 48% and 48% identical to those of cruxrhodopsin-1, bacteriorhodopsin, archaerhodopsin-1 and archaerhodopsin-2, respectively. The charged amino acids important for the proton pump function were conserved among all these molecules. Cruxrhodopsin-2 accounted for 0.05 nmol/mg protein in arg-2, which was 20-30-fold less than the proportion of bacteriorhodopsin in Halobacterium salinarium R1M1. In contrast to R1M1, under anaerobic conditions, arg-2 showed light-induced proton extrusion concomitant with an increase in ATP level without transient proton uptake. Dicyclohexylcarbodiimide enhanced the rate and extent of proton extrusion and inhibited ATP formation in the light. The apparent stoichiometry of H+/ATP was estimated to be more than three in this natural bR+hR- strain.
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Affiliation(s)
- Y Sugiyama
- Department of Biology, School of Science, Nagoya University, Japan
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20
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Sineshchekov OA, Govorunova EG, Dér A, Keszthelyi L, Nultsch W. Photoinduced electric currents in carotenoid-deficient Chlamydomonas mutants reconstituted with retinal and its analogs. Biophys J 1994; 66:2073-84. [PMID: 8075341 PMCID: PMC1275933 DOI: 10.1016/s0006-3495(94)81002-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Reconstitution of the photoelectric responses involved in photosensory transduction in "blind" cells of Chlamydomonas reinhardtii carotenoid-deficient mutants was studied by means of a recently developed population method. Both the photoreceptor current and the regenerative response can be restored by addition of all-trans-retinal, 9-demethyl-retinal, or dimethyl-octatrienal, while the retinal analogs prevented from 13-cis/trans isomerization, 13-demethyl-retinal and citral, are not effective. Fluence dependence, spectral sensitivity, and effect of hydroxylamine treatment on retinal-induced photoelectric responses are similar to those found earlier in green strains of Chlamydomonas, although an alternative mechanism of antenna directivity in white cells of reconstituted "blind" mutants (likely based on the focusing effect of the transparent cell bodies) leads to the reversed sign of phototaxis in mutant cells under the same conditions. The results obtained indicate that both photoreceptor current and regenerative response are initiated by the same or similar rhodopsins with arhaebacterial-like chromophore(s) and prove directly the earlier suggested identity of the photoreceptor pigment(s) involved in photomotile and photoelectric responses in flagellated algae.
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22
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23
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Hong F. Photovoltaic effects in biomembranes/spl minus/reverse-engineering naturally occurring molecular optoelectronic devices. ACTA ACUST UNITED AC 1994. [DOI: 10.1109/51.265777] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Sonar S, Patel N, Fischer W, Rothschild KJ. Cell-free synthesis, functional refolding, and spectroscopic characterization of bacteriorhodopsin, an integral membrane protein. Biochemistry 1993; 32:13777-81. [PMID: 8268152 DOI: 10.1021/bi00213a004] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Bacteriorhodopsin (bR) is an integral membrane protein which functions as a light-driven proton pump in Halobacterium halobium (also known as Halobacterium salinarium). The cell-free synthesis of bR in quantities sufficient for FTIR and NMR spectroscopy and the ability to selectively isotope label bR using aminoacylated suppressor tRNAs would provide a powerful approach for studying the role of specific amino acid residues. However, no integral membrane protein has yet been expressed in a cell-free system in quantities sufficient for such biophysical studies. We report the cell-free synthesis of bacterioopsin, its purification, its refolding in polar lipids from H. halobium, and its regeneration with all-trans-retinal to yield bacteriorhodopsin in a form functionally similar to bR in purple membrane. Importantly, the yields obtained from in vitro and in vivo expression are comparable. Functionality of the cell-free expressed bR is established using static and time-resolved absorption spectroscopy and FTIR difference spectroscopy.
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Affiliation(s)
- S Sonar
- Physics Department, Boston University, Massachusetts 02215
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25
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Zhang YN, el-Sayed MA, Stern LJ, Marti T, Mogi T, Khorana HG. Effects of mutagenetic substitution of prolines on the rate of deprotonation and reprotonation of the Schiff base during the photocycle of bacteriorhodopsin. Photochem Photobiol 1993; 57:1027-31. [PMID: 8367532 DOI: 10.1111/j.1751-1097.1993.tb02966.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Membrane-buried proline residues are found in many transport proteins. To study their roles in the structure and function of bacteriorhodopsin (bR), effects of the individual substitutions of Pro-50, Pro-91 and Pro-186 on the deprotonation and reprotonation kinetics of the Schiff base (SB) were determined by flash photolysis. The obtained rate constants and the amplitudes of the slow and fast components were compared with those of ebR (wild-type bR, the native protein that is expressed in Escherichia coli). The deprotonation rates of PSB were found to be 10 times faster than that of ebR for P50A, P91A and P91G mutants, and 4 times faster for the P50G mutant. These mutations also increased the initial reprotonation rate of the SB, although the overall change in the reprotonation rate is not as significant as that in the deprotonation rate. Our results indicate that Pro-50 and Pro-91, as well as Pro-186, are important for the proton-pumping function of bR.
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Affiliation(s)
- Y N Zhang
- Department of Chemistry and Biochemistry, University of California, Los Angeles 90024
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Sankararamakrishnan R, Vishveshwara S. Characterization of proline-containing alpha-helix (helix F model of bacteriorhodopsin) by molecular dynamics studies. Proteins 1993; 15:26-41. [PMID: 8451238 DOI: 10.1002/prot.340150105] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Many of the bilayer spanning segments of membrane transport proteins contain proline residues, and most of them are believed to occur in alpha-helical form. A proline residue in the middle of an alpha-helix is known to produce a bend in the helix, and recent studies have focused on characterizing such a bend at atomic level. In the present case, molecular dynamics (MD) studies are carried out on helix F model of bacteriorhodopsin (BR) Ace-(Ala)7-Trp-(Ala)2-Tyr-Pro-(Ala)2-Trp- (Ala)8-NHMe and compared with Ace-(Ala)7-Trp-(Ala)2-Tyr-(Ala)3-Trp-(Ala)8-NHMe in which the proline is replaced by alanine. The bend in the helix is characterized by structural parameters such as kink angle (alpha), wobble angle (theta), virtual torsion angle (rho), and the hydrogen bond distance d (Op-3 ... Np+1). The average values and the flexibility involved in these parameters are evaluated. The correlation among the bend related parameters are estimated. The equilibrium side chain orientations of tryptophan and tyrosine residues are discussed and compared with those found in the recently proposed model of bacteriorhodopsin. Finally, a detailed characterization of the bend in terms of secondary structures such as alpha I, alpha II and goniometric helices are discussed, which can be useful in the interpretation of the experimental results on the secondary structures of membrane proteins involving the proline residue.
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Barsukov IL, Nolde DE, Lomize AL, Arseniev AS. Three-dimensional structure of proteolytic fragment 163-231 of bacterioopsin determined from nuclear magnetic resonance data in solution. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 206:665-72. [PMID: 1606953 DOI: 10.1111/j.1432-1033.1992.tb16972.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
546 NOESY cross-peak volumes were measured in the two-dimensional NOESY spectrum of proteolytic fragment 163-231 of bacterioopsin in organic solution. These data and 42 detected hydrogen bonds were applied for determining the peptide spatial structure. The fold of the polypeptide chain was determined by local structure analysis, a distance geometry approach and systematic search for energetically allowed side-chain rotamers which are consistent with experimental NOESY cross-peak volumes. The effective rotational correlation time of 6 ns for the molecule was evaluated from optimization of the local structure to meet NOE data and from the dependence on mixing time of the NiH/Ci alpha H cross-peak volumes of the residues in alpha-helical conformation. The resulting structure has two well defined alpha-helical regions, 168-191 and 198-227, with root-mean-square deviation 44 pm and 69 pm, respectively, between the backbone atoms in 14 final energy refined conformations. The alpha-helices correspond to transmembrane segments F and G of bacteriorhodopsin. The segment F contains proline 186, which introduces a kink of about 25 degrees with a disruption of the hydrogen bond with the NH group of the following residue. The segments are connected by a flexible loop region 192-197. Torsion angles chi 1 are unequivocally defined for 62% of side chains in the alpha-helices but half of them differ from electron cryo-microscopy (ECM) model of bacteriorhodopsin, apparently because of the low resolution of ECM. Nevertheless, the F and G segments can be packed as in the ECM model and with side-chain conformations consistent with all NMR data in solution.
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Affiliation(s)
- I L Barsukov
- Shemyakin Institute of Bioorganic Chemistry, Academy of Sciences of Russia, Moscow
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29
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Hildebrand E, Schimz A. THE SENSORY PHOTORECEPTORS OF Halobacterium halobium REVISITED: ACTION SPECTRA and INFLUENCE OF BACKGROUND LIGHT. Photochem Photobiol 1991. [DOI: 10.1111/j.1751-1097.1991.tb02126.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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30
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Dér A, Száraz S, Tóth-Boconádi R, Tokaji Z, Keszthelyi L, Stoeckenius W. Alternative translocation of protons and halide ions by bacteriorhodopsin. Proc Natl Acad Sci U S A 1991; 88:4751-5. [PMID: 1647014 PMCID: PMC51744 DOI: 10.1073/pnas.88.11.4751] [Citation(s) in RCA: 74] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Bacteriorhodopsin (bR568) in purple membrane near pH 2 shifts its absorption maximum from 568 to 605 nm forming the blue protein bRacid605, which no longer transports protons and which shows no transient deprotonation of the Schiff base upon illumination. Continued acid titration with HCl or HBr but not H2SO4 restores the purple chromophore to yield bRHCl564 or bRHBr568. These acid purple forms also regain transmembrane charge transport, but no transient Schiff base deprotonation is observed. In contrast to bR568, no rate decrease of the bRacidpurple transport kinetics is detected in 2H2O; however, the transport rate decreases by a factor of approximately 2 in bRHBr568 compared with bRHCl564. The data indicate that in the acid purple form bR transports the halide anions instead of protons. We present a testable model for the transport mechanism, which should also be applicable to halorhodopsin.
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Affiliation(s)
- A Dér
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94143
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31
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The secondary β-deuterium isotope effect in dark adaptation of bacteriorhodopsin containing retinal-20,20,20-d3. Bioorg Chem 1991. [DOI: 10.1016/0045-2068(91)90040-v] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Barsukov IL, Abdulaeva GV, Arseniev AS, Bystrov VF. Sequence-specific 1H-NMR assignment and conformation of proteolytic fragment 163-231 of bacterioopsin. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 192:321-7. [PMID: 2209589 DOI: 10.1111/j.1432-1033.1990.tb19230.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Proteolytic fragment 163-231 of bacterioopsin was isolated from Halobacterium halobium purple membrane treated with NaBH4 and papain under nondenaturing conditions. Two-dimensional 1H-NMR spectra of (163-231)-bacterioopsin solubilized in chloroform/methanol (1:1), 0.1 M LiClO4 indicated the existence of one predominant conformation. Most of the resonances in the 1H-NMR spectra of (163-231)-bacterioopsin were assigned by two-dimensional techniques. Two extended right-handed alpha-helical regions Ala168-Ile191 and Asn202-Arg227 were identified on the basis of NOE connectivities and deuterium exchange rates. The N-terminal part of the peptide is flexible and the region of Gly192-Leu201 adopts a specific conformation. The protons of OH groups of Thr178, Ser183 and Ser214 slowly exchange with solvent, and side-chain conformations of these residues, as evaluated by NOE connectivities of OH protons, are optimal for the formation of hydrogen bonds between OH and backbone carbonyl groups.
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Affiliation(s)
- I L Barsukov
- Shemyakin Institute of Bioorganic Chemistry, USSR Academy of Sciences
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33
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Fisher KA, Yanagimoto KC, Whitfield SL, Thomson RE, Gustafsson MG, Clarke J. Scanning tunneling microscopy of planar biomembranes. Ultramicroscopy 1990; 33:117-26. [PMID: 2219538 DOI: 10.1016/0304-3991(90)90014-d] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We combined planar membrane monolayer techniques with scanning tunneling microscopy (STM) to measure the thickness of metal-coated purple membrane (PM) isolated from Halobacterium halobium. Although the metal coating precluded obtaining high-resolution lateral information, it facilitated obtaining high-resolution vertical information. For example, the apparent mean thickness of planar PM and variations in thickness of enzyme-treated PM could be detected and quantified at sub-nanometer resolution.
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Affiliation(s)
- K A Fisher
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0130
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34
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Schäfer GÃ, Anemüller S, Moll R, Meyer W, Lübben M. Electron transport and energy conservation in the archaebacteriumSulfolobus acidocaldarius. FEMS Microbiol Lett 1990. [DOI: 10.1111/j.1574-6968.1990.tb04106.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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35
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Fisher KA, Whitfield SL, Thomson RE, Yanagimoto KC, Gustafsson MG, Clarke J. Measuring changes in membrane thickness by scanning tunneling microscopy. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1023:325-34. [PMID: 2334726 DOI: 10.1016/0005-2736(90)90123-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We investigated the feasibility of using the scanning tunneling microscope (STM) as a morphometric tool to measure the thickness of biomembranes. Planar monolayers of oriented purple membrane (PM) were prepared, nitrogen-dried or freeze-etched, and coated with metal. PM thickness was quantified by STM and transmission electron microscopy. STM calibration and the effect of contamination-mediated surface deformation on measurements of PM thickness were evaluated. The thickness of PM attached to mica and glass and the effect of papain on PM thickness were also examined. The apparent thickness of enzymatically modified PM increased after papain treatment. The mean thickness of both nitrogen-dried PM on mica and freeze-etched PM on glass was 4.6 nm. After papain treatment PM thickness on mica increased to 4.8 nm and on glass to 5.4 nm. These results demonstrate that STM analysis of metal-coated planar membrane monolayers can be used to measure changes in average membrane thickness at sub-nanometer resolution.
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Affiliation(s)
- K A Fisher
- Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0130
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36
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Duñach M, Padrós E, Muga A, Arrondo JL. Fourier-transform infrared studies on cation binding to native and modified purple membranes. Biochemistry 1989; 28:8940-5. [PMID: 2605235 DOI: 10.1021/bi00448a038] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Fourier-transform infrared spectroscopy has been used to examine the structural differences in the protein moiety between the native purple and the deionized blue membranes, both at pH 5.0. The spectra demonstrate that deionization of purple membrane decreases the content of the distorted alpha II-helices in favor of the more common alpha I-helices. Changes in the signals from beta-turns are also observed. The changes corresponding to the carboxyl groups suggest that deionization leads to a decrease in the strength of the hydrogen bonds involving carboxyl groups. Most of these effects are reversed progressively upon binding of one to five Mn2+ per bacteriorhodopsin to the deionized membrane. Binding of Hg2+ to the deionized membranes does not restore the purple color but induces global changes similar to, but less intense than, those brought about by Mn2+ binding. However, the effects attributed to the carboxyl groups are opposite to those found for Mn2+. Schiff base reduction or bleaching induces a decrease of the content of the alpha II-helix in favor of the alpha I-helix and a decrease in the strength of hydrogen bonds to carboxyl groups. Deionization of these modified membranes leads to a further loss in the alpha II content. These results indicate a conformational rearrangement of the protein structure between the native purple membrane and the deionized membrane, which could arise from surface potential changes elicited by bound cations. The changes observed in the carboxyl groups suggest that some of them are located structurally close to the retinal environment and may be involved in cation binding.
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Affiliation(s)
- M Duñach
- Departament de Bioquímica i Biologia Molecular, Facultat de Medicina, Universitat Autònoma de Barcelona, Spain
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37
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Abstract
Comparison of the primary structure of the chloride pump halorhodopsin with that of the proton pump bacteriorhodopsin provides insight into light-driven ion transport by retinal proteins. Several conserved amino acid residues in the membrane-spanning region of both proteins and their interaction with different isomerization states of retinal are suggested to be the key element for ion transport in both proteins.
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38
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Fimmel S, Choli T, Dencher NA, Büldt G, Wittmann-Liebold B. Topography of surface-exposed amino acids in the membrane protein bacteriorhodopsin determined by proteolysis and micro-sequencing. BIOCHIMICA ET BIOPHYSICA ACTA 1989; 978:231-40. [PMID: 2914138 DOI: 10.1016/0005-2736(89)90120-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The topography of membrane-surface-exposed amino acids in the light-driven proton pump bacteriorhodopsin (BR) was studied. By limited proteolysis of purple membrane with papain or proteinase K, domains were cleaved, separated by SDS-PAGE, and electroblotted onto polyvinylidene difluoride (PVDF) membranes. Fragments transferred were sequenced in a gas-phase sequencer. Papain cleavage sites at Gly-65, Gly-72, and Gly-231, previously only deduced from the apparent molecular weight of the digestion fragments, could be confirmed by N-terminal micro-sequencing. By proteinase K, cleavage occurred at Gln-3, Phe-71, Gly-72, Tyr-131, Tyr-133, and Ser-226, i.e., in regions previously suggested to be surface-exposed. Additionally, proteinase-K cleavage sites at Thr-121 and Leu-127 were identified, which are sites predicted to be in the alpha-helical membrane-spanning segment D. Our results, especially that the amino acids Gly-122 to Tyr-133 are protruding into the aqueous environment, place new constraints on the amino-acid folding of BR across the purple membrane. The validity of theoretical prediction methods of the secondary structure and polypeptide folding for membrane proteins is challenged. The results on BR show that micro-sequencing of peptides separated by SDS-PAGE and blotted to PVDF can be successfully applied to the study of membrane proteins.
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Affiliation(s)
- S Fimmel
- Department of Physics, Freie Universität Berlin, F.R.G
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39
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Tsetlin VI, Alyonycheva TN, Shemyakin VV, Neiman LA, Ivanov VT. Tritium thermal activation study of bacteriorhodopsin topography. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 178:123-9. [PMID: 3203683 DOI: 10.1111/j.1432-1033.1988.tb14437.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The action of thermally activated tritium on the purple membrane and delipidated bacteriorhodopsin fragments has been studied, tritium incorporation into specified amino acid residues being quantified by Edman degradation. The membrane environment was found to affect the accessibility of amino acid residues for tritium. Bacteriorhodopsin fragments 14-31, 45-63, 81-89, 171-179, and 210-225 were localized to the membrane interior while fragments 4-12, 32-44, 64-65, 73-80, and 156-170 should lie outside or close to membrane surface. It was demonstrated that the peptide fragments joining transmembrane rods are not fully exposed to the solution.
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Affiliation(s)
- V I Tsetlin
- Shemyakin Institute of Bioorganic Chemistry, USSR Academy of Sciences, Moscow
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40
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Influence of cations on the blue to purple transition of bacteriorhodopsin. Comparison of Ca2+ and Hg2+ binding and their effect on the surface potential. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(19)77846-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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41
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Lugtenburg J, Mathies RA, Griffin RG, Herzfeld J. Structure and function of rhodopsins from solid state NMR and resonance Raman spectroscopy of isotopic retinal derivatives. Trends Biochem Sci 1988; 13:388-93. [PMID: 3072701 DOI: 10.1016/0968-0004(88)90181-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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42
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Cladera J, Galisteo ML, Dun˜ach M, Mateo PL, Padrós E. Thermal denaturation of deionized and native purple membranes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 1988. [DOI: 10.1016/0005-2736(88)90546-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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43
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Stoeckenius W, Wolff EK, Hess B. A rapid population method for action spectra applied to Halobacterium halobium. J Bacteriol 1988; 170:2790-5. [PMID: 3372482 PMCID: PMC211204 DOI: 10.1128/jb.170.6.2790-2795.1988] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
We have developed a simple and rapid technique for measuring the action spectra for phototaxis of populations of microorganisms and applied it to halobacteria. A microscope with a dark-field condenser was used to illuminate the cell suspension in a sealed chamber with light of wavelength greater than 750 nm; in this region of the spectrum, the halobacteria show no phototactic response. A 150-micron spot of light from a xenon arc lamp, whose wavelength and intensity can be varied, was projected through the objective lens into the center of the dark field. The objective lens imaged this measuring spot through a 780-nm cut-off filter on an aperture in front of a photomultiplier. The intensity of the scattered 750-nm light, and therefore the photomultiplier current, is proportional to the number of cells in the measuring spot. A third lamp provided background light of variable wavelength and intensity through the dark-field condenser. To minimize secondary effects due to large changes in cell density, we recorded the initial changes in the photomultiplier current over 1 min after the actinic light had been switched on. By plotting the rate of change against wavelength, we obtained action spectra after the proper corrections for changes in light intensity with wavelength were applied and saturation effects were avoided.
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Affiliation(s)
- W Stoeckenius
- Cardiovascular Research Institute, University of California, San Francisco 94143
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44
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45
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46
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47
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Yarden Y, Schlessinger J. Self-phosphorylation of epidermal growth factor receptor: evidence for a model of intermolecular allosteric activation. Biochemistry 1987; 26:1434-42. [PMID: 3494472 DOI: 10.1021/bi00379a034] [Citation(s) in RCA: 374] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The membrane receptor for epidermal growth factor (EGF) is a 170,000-dalton glycoprotein composed of an extracellular EGF-binding domain and a cytoplasmic kinase domain connected by a stretch of 23 amino acids traversing the plasma membrane. The binding of EGF to the extracellular domain activates the cytoplasmic kinase function even in highly purified preparations of EGF receptor, suggesting that the activation occurs exclusively within the EGF receptor moiety. Conceivably, kinase activation may require the transfer of a conformational change through the single transmembrane region from the ligand binding domain to the cytoplasmic kinase region. Alternatively, ligand-induced receptor-receptor interactions may activate the kinase and thus bypass this requirement. Both mechanisms were contrasted by employing independent experimental approaches. The following lines of evidence support an intermolecular mechanism for the activation of the detergent-solubilized receptor: the EGF-induced receptor self-phosphorylation has a parabolic dependence on the concentration of EGF receptor, cross-linking of EGF receptors by antibodies or lectins stimulates receptor self-phosphorylation, immobilization of EGF receptor on various solid matrices prevents EGF from activating the kinase function, and cross-linking of EGF receptors increases their affinity toward EGF. On the basis of these results, an allosteric aggregation model is formulated for the activation of the cytoplasmic kinase function of the receptor by EGF. This model may be relevant to the mechanism by which the mitogenic signal of EGF is transferred across the membrane.
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48
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49
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Scherrer P, McGinnis K, Bogomolni RA. Biochemical and spectroscopic characterization of the blue-green photoreceptor in Halobacterium halobium. Proc Natl Acad Sci U S A 1987; 84:402-6. [PMID: 3467364 PMCID: PMC304215 DOI: 10.1073/pnas.84.2.402] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Spectroscopic evidence indicates the presence of a second sensory receptor sR-II in Halobacterium halobium, which causes a repellent response to blue-green light. Reactions with hydroxylamine and NaCNBH3 and reconstitution of the bleached pigment with retinal show that it is very similar to the other retinylidene pigments bacteriorhodopsin, halorhodopsin, and especially the earlier-discovered phototaxis receptor, sensory rhodopsin, renamed sR-I587. The second sensory receptor, sR-II480, has an absorbance maximum at 480 nm and undergoes a cyclic photoreaction with a half-time of approximately 200 msec. Its predominant photocycle intermediate absorbs maximally near 360 nm. The receptor can be detected spectroscopically in the presence of sR-I587 and quantitated through its transient response to 450-nm excitation. It is selectively bleached by low hydroxylamine concentrations that are insufficient to bleach sR-I587 significantly. Its photochemical and phototactic activities can be restored by addition of retinal. The mobility of the receptor, on NaDodSO4/polyacrylamide gels, was similar or identical to that of sR-I587 and slightly faster than bacteriorhodopsin, yielding an apparent molecular mass of 23-24 kDa.
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50
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Duñach M, Seigneuret M, Rigaud JL, Padrós E. The relationship between the chromophore moiety and the cation binding sites in bacteriorhodopsin. Biosci Rep 1986; 6:961-6. [PMID: 3580520 DOI: 10.1007/bf01114972] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Bleaching of the purple membrane strongly reduces the number of divalent cation binding sites as well as their affinities. Conversely, deionization of the bleached membrane drastically inhibits the chromophore regeneration. Proteolysis experiments using bromelain show that the bleached membrane has an additional cleavage site probably located at the fifth loop, whereas in the blue membrane, the C-terminal tail is no longer susceptible to proteolysis. It is suggested that there exists a close relationship between the retinal environment and one or more of the cation binding sites.
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