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Leighton RE, Frontiera RR. Quantifying Bacteriorhodopsin Activity as a Function of its Local Environment with a Raman-Based Assay. J Phys Chem B 2023; 127:8833-8841. [PMID: 37812499 DOI: 10.1021/acs.jpcb.3c04802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Bacteriorhodopsin (bR) is a transmembrane protein that functions as a light-driven proton pump in halophilic archaea. The bR photocycle has been well-characterized; however, these measurements almost exclusively measured purified bR, outside of its native membrane. To investigate what effect the cellular environment has on the bR photocycle, we have developed a Raman-based assay that can monitor the activity of the bR in a variety of conditions, including in its native membrane. The assay uses two continuous-wave lasers, one to initiate photochemistry and one to monitor bR activity. The excitation leads to the steady-state depletion of ground-state bR, which directly relates to the population of photocycle intermediate states. We have used this assay to monitor bR activity both in vitro and in vivo. Our in vitro measurements confirm that our assay is sensitive to bulk environmental changes reported in the literature. Our in vivo measurements show a decrease in bR activity with increasing extracellular pH for bR in its native membrane. The difference in activity with increasing pH indicates that the native membrane environment affects the function of bR. This assay opens the door to future measurements into understanding how the local environment of this transmembrane protein affects function.
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Affiliation(s)
- Ryan E Leighton
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Renee R Frontiera
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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2
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Kaur J, Kriebel CN, Eberhardt P, Jakdetchai O, Leeder AJ, Weber I, Brown LJ, Brown RC, Becker-Baldus J, Bamann C, Wachtveitl J, Glaubitz C. Solid-state NMR analysis of the sodium pump Krokinobacter rhodopsin 2 and its H30A mutant. J Struct Biol 2019; 206:55-65. [DOI: 10.1016/j.jsb.2018.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/05/2018] [Accepted: 06/02/2018] [Indexed: 12/26/2022]
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3
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Mehler M, Eckert CE, Leeder AJ, Kaur J, Fischer T, Kubatova N, Brown LJ, Brown RCD, Becker-Baldus J, Wachtveitl J, Glaubitz C. Chromophore Distortions in Photointermediates of Proteorhodopsin Visualized by Dynamic Nuclear Polarization-Enhanced Solid-State NMR. J Am Chem Soc 2017; 139:16143-16153. [PMID: 29027800 DOI: 10.1021/jacs.7b05061] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Proteorhodopsin (PR) is the most abundant retinal protein on earth and functions as a light-driven proton pump. Despite extensive efforts, structural data for PR photointermediate states have not been obtained. On the basis of dynamic nuclear polarization (DNP)-enhanced solid-state NMR, we were able to analyze the retinal polyene chain between positions C10 and C15 as well as the Schiff base nitrogen in the ground state in comparison to light-induced, cryotrapped K- and M-states. A high M-state population could be achieved by preventing reprotonation of the Schiff base through a mutation of the primary proton donor (E108Q). Our data reveal unexpected large and alternating 13C chemical shift changes in the K-state propagating away from the Schiff base along the polyene chain. Furthermore, two different M-states have been observed reflecting the Schiff base reorientation after the deprotonation step. Our study provides novel insight into the photocycle of PR and also demonstrates the power of DNP-enhanced solid-state NMR to bridge the gap between functional and structural data and models.
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Affiliation(s)
- Michaela Mehler
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Carl Elias Eckert
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Alexander J Leeder
- Department of Chemistry, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Jagdeep Kaur
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Tobias Fischer
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Nina Kubatova
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Lynda J Brown
- Department of Chemistry, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Richard C D Brown
- Department of Chemistry, University of Southampton , Southampton SO17 1BJ, United Kingdom
| | - Johanna Becker-Baldus
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Josef Wachtveitl
- Institute for Physical and Theoretical Chemistry, Goethe-University Frankfurt , Frankfurt 60438, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry & Centre for Biomolecular Magnetic Resonance, Goethe-University Frankfurt , Frankfurt 60438, Germany
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4
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Affiliation(s)
- Benjamin J. Wylie
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Hoa Q. Do
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Collin G. Borcik
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Emily P. Hardy
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
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5
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Ding X, Wang H, Peng B, Cui H, Gao Y, Iuga D, Judge PJ, Li G, Watts A, Zhao X. Mediation mechanism of tyrosine 185 on the retinal isomerization equilibrium and the proton release channel in the seven-transmembrane receptor bacteriorhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1786-1795. [DOI: 10.1016/j.bbabio.2016.08.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 08/04/2016] [Accepted: 08/06/2016] [Indexed: 01/17/2023]
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Gebhard R, van der Hoef K, Lefeber AWM, Erkelens C, Lugtenburg J. Synthesis and spectroscopy of (14′-13C)- and (15′-13C)spheroidene. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19901090604] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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8
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Raap J, van der Wielen CM, Lugtenburg J. Enantioselective syntheses of isotopically labelled α-amino acids. Preparation of (ϵ-13C)-L-α-aminoadipic acid and five isotopomers of L-lysine with 13C, 15N and 2H in the δ- and ϵ-positions. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19901090404] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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9
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Curley RW, Sundaram AK, Fowble JW, Abildgaard F, Westler WM, Markley JL. NMR studies of retinoid-protein interactions: the conformation of [13C]-beta-ionones bound to beta-lactoglobulin B. Pharm Res 1999; 16:651-9. [PMID: 10350006 DOI: 10.1023/a:1018860221492] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
PURPOSE Vitamin A (retinol) and its metabolites comprise the natural retinoids. While the biological action of these molecules are thought to be primarily mediated by ca. 55 kDa nuclear retinoic acid receptors, a number of structurally similar 15-20 kDa proteins are involved in the transport, and possibly metabolism, of these compounds. The milk protein beta-lactoglobulin B (beta-LG) is an 18 kDa protein which binds retinol and may be involved in oral delivery of retinol to neonates. beta-LG also binds drugs and other natural products and is of potential interest as a protective delivery vehicle. METHODS To examine the conformation of the model retinoid beta-ionone both in solution and when bound to beta-LG, NMR and computational methods have been employed. RESULTS Taken together, NMR studies of beta-ionone in solution measuring scalar and dipolar coupling, as well as CHARMm calculations, suggest beta-ionone prefers a slightly twisted 6-s-cis conformation. Isotope-edited NMR studies of 13C-labeled beta-ionones bound to beta-LG, primarily employing the HMQC-NOE experiment, suggest beta-ionone also binds to beta-LG in its 6-s-cis conformation. CONCLUSIONS The methods employed here allow estimates of protein-bound ligand conformation. However, additional sites of ligand labeling will be necessary to aid in binding site localization.
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Affiliation(s)
- R W Curley
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus 43210, USA.
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10
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Roux B, Nina M, Pomès R, Smith JC. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study. Biophys J 1996; 71:670-81. [PMID: 8842206 PMCID: PMC1233524 DOI: 10.1016/s0006-3495(96)79267-6] [Citation(s) in RCA: 202] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The proton transfer activity of the light-driven proton pump, bacteriorhodopsin (bR) in the photochemical cycle might imply internal water molecules. The free energy of inserting water molecules in specific sites along the bR transmembrane channel has been calculated using molecular dynamics simulations based on a microscopic model. The existence of internal hydration is related to the free energy change on transfer of a water molecule from bulk solvent into a specific binding site. Thermodynamic integration and perturbation methods were used to calculate free energies of hydration for each hydrated model from molecular dynamics simulations of the creation of water molecules into specific protein-binding sites. A rigorous statistical mechanical formulation allowing the calculation of the free energy of transfer of water molecules from the bulk to a protein cavity is used to estimate the probabilities of occupancy in the putative bR proton channel. The channel contains a region lined primarily by nonpolar side-chains. Nevertheless, the results indicate that the transfer of four water molecules from bulk water to this apparently hydrophobic region is thermodynamically permitted. The column forms a continuous hydrogen-bonded chain over 12 A between a proton donor, Asp 96, and the retinal Schiff base acceptor. The presence of two water molecules in direct hydrogen-bonding association with the Schiff base is found to be strongly favorable thermodynamically. The implications of these results for the mechanism of proton transfer in bR are discussed.
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Affiliation(s)
- B Roux
- Départements de physique et chimie, Université de Montréal, Québec, Canada.
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11
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Houjou H, Sakurai M, Asakawa N, Inoue Y, Tamura Y. Ab InitioStudy of13C Shieldings for Linear π-Conjugated Systems. Theoretical Determination of the C12−C13 Conformation in the Chromophore of Rhodopsin. J Am Chem Soc 1996. [DOI: 10.1021/ja961023+] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Watts A, Ulrich AS, Middleton DA. Membrane protein structure: the contribution and potential of novel solid state NMR approaches. Mol Membr Biol 1995; 12:233-46. [PMID: 8520624 DOI: 10.3109/09687689509072423] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Alternative methods for describing molecular detail for large integral membrane proteins are required in the absence of routine crystallographic approaches. Novel solid state NMR methods, devised for the study of large molecular assemblies, are now finding applications in biological systems, including integral membrane proteins. Wild-type and genetically engineered proteins can be investigated and detailed information about side chains, prosthetic groups, ligands (e.g. drugs) and binding sites can be deduced. The molecular structure and dynamics of selected parts of the proteins are accessible by a range of different solid state NMR approaches. Inter- and intra-atomic distances can be determined rather accurately (within ångströms) and the orientation of molecular bonds (within 2 degrees) can be measured in ideal cases. Here, a brief description of the methods is given and then some specific examples described with an indication of the future potential for the approaches in studying membrane proteins. It is anticipated that this emerging NMR methodology will be more widely used in the future, not only for resolving local structure, but also for more expansive descriptions of membrane protein structure at atomic resolution.
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Affiliation(s)
- A Watts
- Department of Biochemistry, University of Oxford, UK
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Ulrich AS, Wallat I, Heyn MP, Watts A. Re-orientation of retinal in the M-photointermediate of bacteriorhodopsin. NATURE STRUCTURAL BIOLOGY 1995; 2:190-2. [PMID: 7773785 DOI: 10.1038/nsb0395-190] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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14
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Nina M, Roux B, Smith JC. Functional interactions in bacteriorhodopsin: a theoretical analysis of retinal hydrogen bonding with water. Biophys J 1995; 68:25-39. [PMID: 7711248 PMCID: PMC1281657 DOI: 10.1016/s0006-3495(95)80184-0] [Citation(s) in RCA: 88] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The light-driven proton pump, bacteriorhodopsin (bR) contains a retinal molecule with a Schiff base moiety that can participate in hydrogen-bonding interactions in an internal, water-containing channel. Here we combine quantum chemistry and molecular mechanics techniques to determine the geometries and energetics of retinal Schiff base-water interactions. Ab initio molecular orbital calculations are used to determine potential surfaces for water-Schiff base hydrogen-bonding and to characterize the energetics of rotation of the C-C single bond distal and adjacent to the Schiff base NH group. The ab initio results are combined with semiempirical quantum chemistry calculations to produce a data set used for the parameterization of a molecular mechanics energy function for retinal. Using the molecular mechanics force field the hydrated retinal and associated bR protein environment are energy-minimized and the resulting geometries examined. Two distinct sites are found in which water molecules can have hydrogen-bonding interactions with the Schiff base: one near the NH group of the Schiff base in a polar region directed towards the extracellular side, and the other near a retinal CH group in a relatively nonpolar region, directed towards the cytoplasmic side.
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Affiliation(s)
- M Nina
- Département de Biologie Cellulaire et Moléculaire, C.E.A., Centre d'Etudes Saclay, Gif-sur-Yvette, France
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15
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Fasman GD. The measurement of transmembrane helices by the deconvolution of CD spectra of membrane proteins: A review. Biopolymers 1995. [DOI: 10.1002/bip.360370505] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Haupts U, Eisfeld W, Stockburger M, Oesterhelt D. Sensory rhodopsin I photocycle intermediate SRI380 contains 13-cis retinal bound via an unprotonated Schiff base. FEBS Lett 1994; 356:25-9. [PMID: 7988713 DOI: 10.1016/0014-5793(94)01226-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Sensory rhodopsin I (SRI), the mutated derivative SRI-D76N and the complex of SRI with its transducer HtrI were overexpressed in Halobacterium salinarium and analyzed by resonance Raman spectroscopy. In the initial state SRI contains all-trans retinal bound via a protonated Schiff base as confirmed by retinal extraction which yields 95 +/- 3% all-trans retinal. The photocycle intermediate absorbing maximally at 380 nm (SRI380) contains a Schiff base linkage between the protein and 13-cis retinal. Extraction of illuminated SRI yields up to 93% 13-cis retinal. Neither the mutation D76N nor HtrI changed the vibrational pattern of the chromophore.
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Affiliation(s)
- U Haupts
- Max-Planck Institut für Biochemie, Martinsried, Germany
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17
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Hauss T, Büldt G, Heyn MP, Dencher NA. Light-induced isomerization causes an increase in the chromophore tilt in the M intermediate of bacteriorhodopsin: a neutron diffraction study. Proc Natl Acad Sci U S A 1994; 91:11854-8. [PMID: 7991546 PMCID: PMC45334 DOI: 10.1073/pnas.91.25.11854] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Bacteriorhodopsin (BR) was regenerated with two selectively deuterated retinals, one with 11 deuterons in the beta-ionone ring (D11) and the other with 5 deuterons (D5) at the end of the polyene chain closest to the Schiff base at carbon atoms C-14, C-15, and C-20. Both label positions (centers of deuteration) were obtained from difference Fourier maps of projections onto the plane of the membrane by neutron diffraction at 90 K, both in the light-adapted ground-state BR568 and in the photocycle intermediate M412. To retard the decay of M412, purple membrane films were soaked in 0.1 M or 1 M guanidine hydrochloride at pH 9.6. M412 was produced by illuminating oriented membrane films at physiological temperature (278 K), followed by rapid cooling to 90 K in the absence of light. The results show that in the projected structure the ring position is unaltered during the transition from BR568 to M412, whereas the position of the D5 label shifts by 1.4 +/- 0.9 A toward the ring. The shortened interlabel distance in the projected structure for the M412 state implies that as a result of the all-trans/13-cis isomerization, the C-5 to C-13 part of the polyene chain tilts out of the plane of the membrane toward the cytoplasm by about 11 degrees +/- 6 degrees. Pairwise comparison of data sets with the same retinal for the two photocycle states M412 and BR568 leads to four difference-density maps for the protein, which are in agreement with previous work. They show changes in the protein density near helices G and F.
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Affiliation(s)
- T Hauss
- Department of Physics, Freie Universität Berlin, Germany
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18
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Gat Y, Sheves M. THE ORIGIN OF THE RED-SHIFTED ABSORPTION MAXIMUM OF THE M412INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE. Photochem Photobiol 1994. [DOI: 10.1111/j.1751-1097.1994.tb05050.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Rath P, Marti T, Sonar S, Khorana H, Rothschild K. Hydrogen bonding interactions with the Schiff base of bacteriorhodopsin. Resonance Raman spectroscopy of the mutants D85N and D85A. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(17)46767-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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20
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Farrar MR, Lakshmi KV, Smith SO, Brown RS, Raap J, Lugtenburg J, Griffin RG, Herzfeld J. Solid state NMR study of [epsilon-13C]Lys-bacteriorhodopsin: Schiff base photoisomerization. Biophys J 1993; 65:310-5. [PMID: 8369438 PMCID: PMC1225725 DOI: 10.1016/s0006-3495(93)81065-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Previous solid state 13C-NMR studies of bacteriorhodopsin (bR) have inferred the C = N configuration of the retinal-lysine Schiff base linkage from the [14-13C]retinal chemical shift (1-3). Here we verify the interpretation of the [14-13C]-retinal data using the [epsilon-13C]lysine 216 resonance. The epsilon-Lys-216 chemical shifts in bR555 (48 ppm) and bR568 (53 ppm) are consistent with a C = N isomerization from syn in bR555 to anti in bR568. The M photointermediate was trapped at pH 10.0 and low temperatures by illumination of samples containing either 0.5 M guanidine-HCl or 0.1 M NaCl. In both preparations, the [epsilon-13C]Lys-216 resonance of M is 6 ppm downfield from that of bR568. This shift is attributed to deprotonation of the Schiff base nitrogen and is consistent with the idea that the M intermediate contains a C = N anti chromophore. M is the only intermediate trapped in the presence of 0.5 M guanidine-HCl, whereas a second species, X, is trapped in the presence of 0.1 M NaCl. The [epsilon-13C]Lys-216 resonance of X is coincident with the signal for bR568, indicating that X is either C = N anti and protonated or C = N syn and deprotonated.
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Affiliation(s)
- M R Farrar
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02254-9110
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21
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Takei H, Lewis A. BIPHASIC M DECAY OF HIGH pH DEHYDRATED PURPLE MEMBRANE STUDIED WITH FOURIER TRANSFORM INFRARED SPECTROSCOPY: A MODEL ACCOUNTING FOR FUNCTIONAL DIFFERENCES BETWEEN DIFFERENT M FORMS. Photochem Photobiol 1993. [DOI: 10.1111/j.1751-1097.1993.tb02942.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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22
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NMR and vibrational studies of a stable carbinolaminium chloride (CH3)2CHCH(OH)NH+2CH(CH3)2Cl− in the solid state. Influence of the solvation on carbinolaminium/iminium equilibrium. J Mol Struct 1992. [DOI: 10.1016/0022-2860(92)87091-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Park K, Perczel A, Fasman GD. Differentiation between transmembrane helices and peripheral helices by the deconvolution of circular dichroism spectra of membrane proteins. Protein Sci 1992; 1:1032-49. [PMID: 1338977 PMCID: PMC2142169 DOI: 10.1002/pro.5560010809] [Citation(s) in RCA: 99] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The interpretation of the circular dichroism (CD) spectra of proteins to date requires additional secondary structural information of the proteins to be analyzed, such as X-ray or NMR data. Therefore, these methods are inappropriate for a CD database whose secondary structures are unknown, as in the case of the membrane proteins. The convex constraint analysis algorithm (Perczel, A., Hollósi, M., Tusnády, G., & Fasman, G. D., 1991, Protein Eng. 4, 669-679), on the other hand, operates only on a collection of spectral data to extract the common spectral components with their spectral weights. The linear combinations of these derived "pure" CD curves can reconstruct the original data set with great accuracy. For a membrane protein data set, the five-component spectra so obtained from the deconvolution consisted of two different types of alpha helices (the alpha helix in the soluble domain and the alpha T helix, for the transmembrane alpha helix), a beta-pleated sheet, a class C-like spectrum related to beta turns, and a spectrum correlated with the unordered conformation. The deconvoluted CD spectrum for the alpha T helix was characterized by a positive red-shifted band in the range 195-200 nm (+95,000 deg cm2 dmol-1), with the intensity of the negative band at 208 nm being slightly less negative than that of the 222-nm band (-50,000 and -60,000 deg cm2 dmol-1, respectively) in comparison with the regular alpha helix, with a positive band at 190 nm and two negative bands at 208 and 222 nm with magnitudes of +70,000, -30,000, and -30,000 deg cm2 dmol-1, respectively.
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Affiliation(s)
- K Park
- Graduate Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02154
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24
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Metz G, Siebert F, Engelhard M. Asp85 is the only internal aspartic acid that gets protonated in the M intermediate and the purple-to-blue transition of bacteriorhodopsin. A solid-state 13C CP-MAS NMR investigation. FEBS Lett 1992; 303:237-41. [PMID: 1318849 DOI: 10.1016/0014-5793(92)80528-o] [Citation(s) in RCA: 116] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
High-resolution solid-state 13C NMR spectra of the ground state and M intermediate of the bacteriorhodopsin mutant D96N with the isotope label at [4-13C]Asp and [11-13C]Trp were recorded. The NMR spectra show that Asp85 is protonated in the M intermediate. The environment of Asp85 is quite hydrophobic. On the other hand, Asp212 remains deprotonated and a slight shift to lower field indicates a more hydrophilic environment. Asp85 also protonates in the purple-to-blue transition of bacteriorhodopsin in the deionized membrane, where it experiences a similar environment to M. The shift of Trp resonances in M reflect a conformational change of the protein in forming the M intermediate.
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Affiliation(s)
- G Metz
- Institut für Biophysik und Strahlenbiologie der Universität, Freiburg, Germany
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25
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Abstract
A review is given of the use of nuclear magnetic resonance (NMR) spectroscopy to study bacteriorhodopsin and bovine rhodopsin. Solution and solid-state approaches are included. The studies of the bacterial proton pump examine the chromophore, the peptide backbone, and the protein side chains. The studies of the bovine visual pigment are limited to the chromophore. Various forms of each pigment are considered. Both structural and dynamic features are addressed.
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Affiliation(s)
- L Zheng
- Department of Chemistry, Brandeis University, Waltham, Massachusetts 02254-9110
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26
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Vibrational spectroscopy of bacteriorhodopsin mutants. Evidence that Thr-46 and Thr-89 form part of a transient network of hydrogen bonds. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)45990-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Affiliation(s)
- P F Knowles
- Department of Biochemistry and Molecular Biology, University of Leeds, U.K
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Abstract
The photoreaction of bacteriorhodopsin was studied in moderately dehydrated films (relative humidities between 100 and 65%). Time-resolved difference spectra from a gated optical multichannel analyzer, between 100 ns and 100 ms after photoexcitation, were decomposed into sums of difference spectra of the intermediates K, L, M, N, and O, and the kinetics obtained were fitted to various alternative schemes. The data confirm the model of a single reaction sequence with reversible reactions we proposed recently for purple membrane suspensions (Váró, G., and J. K. Lanyi. Biochemistry. 1990. 29:2241-2250) but including reversibility also for the reaction K in equilibrium with L in addition to L in equilibrium with M, M in equilibrium with N, and N in equilibrium with O. With increasing dehydration the kinetics were increasingly dominated by the reverse reactions. As before, fitting the data required the existence of two M species in series: L in equilibrium with M1 in equilibrium with M2 in equilibrium with N. The M1 in equilibrium with M2 reaction was greatly slowed at lower humidities. This step might be the switch for the unidirectional transfer of protons. With increasing dehydration recovery of BR occurred less and less via the N intermediate and increasingly via direct shunts from the two M species. As indicated earlier by electrical measurements with similarly dried bacteriorhodopsin films (Váró, G., and L. Keszthelyi, 1983. Biophys. J. 43:47-51). The latter are pathways not necessarily associated with net proton translocation.
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Affiliation(s)
- G Váró
- Department of Physiology and Biophysics, University of California, Irvine 92717
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30
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Deber CM, Xu GY, Sorrell BJ. Proline residues in bacteriorhodopsin: Conformation and temperature dependence. Proteins 1991. [DOI: 10.1007/978-94-010-9063-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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31
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Abstract
Proline, noted as a hydrophilic residue with helix-breaking potential, nevertheless occurs widely in putatively alpha-helical transmembrane segments of many transport proteins. Ligand-activated or enzyme-assisted trans/cis isomerization of an X-proline peptide bond (where X = any amino acid)--a dynamic, reversible event which could alter the orientation of a transmembrane alpha-helix--may provide the molecular basis for a protein channel regulatory process. Further elucidation of such a function requires knowledge of the isomeric status of the X-Pro bonds in native conformations of membrane proteins. We have used 13C nuclear magnetic resonance (NMR) spectroscopy to examine the conformation of intramembranous X-Pro peptide bonds in biosynthetically-labelled samples of a model transport protein, bacteriorhodopsin (bR) (purple membrane). Spectra of 13C-Tyr-carbonyl labelled bR (in the solvent system CHCl3:CD3OD (1:1) + 0.1 M LiClO4) first established that all 11 bR Tyr residues were sufficiently mobile for their resonances to be detected and resolved, independent of their domain location within the bR sequence. By taking advantage of the known diagnostic chemical shifts of the isomers of Pro-C gamma carbon resonances, spectra of bR labelled with 13C gamma-Pro were then used to demonstrate that all 11 bR X-Pro peptide bonds--including those within the protein's membrane domain (Pro50, Pro91, Pro186)--are in the trans conformation in resting state bR.
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Affiliation(s)
- C M Deber
- Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
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32
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Dencher NA, Papadopoulos G, Dresselhaus D, Büldt G. Light- and dark-adapted bacteriorhodopsin, a time-resolved neutron diffraction study. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1026:51-6. [PMID: 2378881 DOI: 10.1016/0005-2736(90)90331-h] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recently, neutron diffraction experiments have revealed well-resolved and reversible changes in the protein conformation of bacteriorhodopsin (BR) between the light-adapted ground state and the M-intermediate of the proton pumping photocycle (Dencher, Dresselhaus, Zaccai and Büldt (1989) Proc. Natl. Acad. Sci. USA 86, 7876-7879). These changes are triggered by the light-induced isomerization of the chromophore retinal from the all-trans to the 13-cis configuration. Dark-adapted purple membranes contain a mixture of two pigment species with either the all-trans- or 13-cis-retinal isomer as chromophore. Employing a time-resolved neutron diffraction technique, no changes in protein conformation in the resolution regime of up to 7 A are observed during the transition between the two ground-state species 13-cis-BR and all-trans-BR. This is in line with the fact that the conversion of all-trans BR to 13-cis-BR involves an additional isomerization about the C15 = N Schiff's base bond, which in contrast to M formation minimizes retinal displacement and keeps the Schiff's base in the original protein environment. Furthermore, there is no indication for large-scale redistribution of water molecules in the purple membrane during light-dark adaptation.
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Affiliation(s)
- N A Dencher
- Department of Physics/Biophysics, Freie Universität Berlin, Germany
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33
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Herzfeld J, Das Gupta SK, Farrar MR, Harbison GS, McDermott AE, Pelletier SL, Raleigh DP, Smith SO, Winkel C, Lugtenburg J. Solid-state 13C NMR study of tyrosine protonation in dark-adapted bacteriorhodopsin. Biochemistry 1990; 29:5567-74. [PMID: 2167129 DOI: 10.1021/bi00475a022] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Solid-state 13C MAS NMR spectra were obtained for dark-adapted bacteriorhodopsin (bR) labeled with [4'-13C]Tyr. Difference spectra (labeled minus natural abundance) taken at pH values between 2 and 12, and temperatures between 20 and -90 degrees C, exhibit a single signal centered at 156 ppm, indicating that the 11 tyrosines are protonated over a wide pH range. However, at pH 13, a second line appears in the spectrum with an isotropic shift of 165 ppm. Comparisons with solution and solid-state spectra of model compounds suggest that this second line is due to the formation of tyrosinate. Integrated intensities indicate that about half of the tyrosines are deprotonated at pH 13. This result demonstrates that deprotonated tyrosines in a membrane protein are detectable with solid-state NMR and that neither the bR568 nor the bR555 form of bR present in the dark-adapted state contains a tyrosinate at pH values between 2 and 12. Deprotonation of a single tyrosine in bR568 would account for 3.6% of the total tyrosine signal, which would be detectable with the current signal-to-noise ratio. We observe a slight heterogeneity and subtle line-width changes in the tyrosine signal between pH 7 and pH 12, which we interpret to be due to protein environmental effects (such as changes in hydrogen bonding) rather than complete deprotonation of tyrosine residue(s).
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Affiliation(s)
- J Herzfeld
- Francis Bitter National Magnet Laboratory, Massachusetts Institute of Technology, Cambridge 02139
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Rothschild KJ, He YW, Gray D, Roepe PD, Pelletier SL, Brown RS, Herzfeld J. Fourier transform infrared evidence for proline structural changes during the bacteriorhodopsin photocycle. Proc Natl Acad Sci U S A 1989; 86:9832-5. [PMID: 2602377 PMCID: PMC298596 DOI: 10.1073/pnas.86.24.9832] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Structural changes involving bacteriohodopsin proline residues have been investigated by Fourier transform infrared difference spectroscopy. Bacteriohodopsin (bR)-producing Halobacteria halobium were grown on a stringent medium containing either ring-perdeuterated proline or 15N-labeled proline. Comparison of the difference spectra obtained from the photoreactions of these labeled bR samples with those for unlabeled bR has led to the assignment of peaks due to proline vibrations. [proline-N15]bR exhibited a 15-cm-1 isotopic downshift of peaks in the 1420- to 1440-cm-1 region of the bR----K and bR----M difference spectra as well as a similar downshift of peaks found in the absolute absorption spectrum of bR. In contrast, [proline-D7]bR did not cause shifts in this region of the difference spectra. These results indicate that one or more prolines undergo a structural rearrangement during the bR photocycle involving the Xaa-Pro C--N peptide bond. This change may be directly coupled to the light-induced isomerization of the retinal chromophore from all-trans-retinal to 13-cis-retinal.
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35
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Dencher NA, Dresselhaus D, Zaccai G, Büldt G. Structural changes in bacteriorhodopsin during proton translocation revealed by neutron diffraction. Proc Natl Acad Sci U S A 1989; 86:7876-9. [PMID: 2554293 PMCID: PMC298174 DOI: 10.1073/pnas.86.20.7876] [Citation(s) in RCA: 226] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A neutron diffraction study of spectroscopic states for the light-energized proton pump bacteriorhodopsin (BR) is presented. The photocycle states BR-568 and M were generated at temperatures above 4 degrees C and were measured after trapping at--180 degrees C. In the BR-568 to M-state transition, which is known to be a key step in transmembrane proton pumping, reversible structural changes of the protein were detected. These structural alterations occur in the neighborhood of the cyclohexene ring and at the Schiff's base end of the chromophore retinal. They are interpreted as a 1-2 degree tilt of three or four of the transmembrane alpha-helices or as positional changes of four or five amino acids. The structural changes observed are inherent in the transport mechanism of bacteriorhodopsin.
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Affiliation(s)
- N A Dencher
- Department of Physics/Biophysics, Freie Universität Berlin, Federal Republic of Germany
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