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Lux J, Azarkh M, Fitzner L, Keppler JK, Schwarz K, Drescher M, Steffen-Heins A. Amyloid aggregation of spin-labeled β-lactoglobulin. Part II: Identification of spin-labeled protein and peptide sequences after amyloid aggregation. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2020.106174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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2
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Syryamina VN, De Zotti M, Toniolo C, Formaggio F, Dzuba SA. Alamethicin self-assembling in lipid membranes: concentration dependence from pulsed EPR of spin labels. Phys Chem Chem Phys 2018; 20:3592-3601. [DOI: 10.1039/c7cp07298h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The antimicrobial action of the peptide antibiotic alamethicin (Alm) is commonly related to peptide self-assembling resulting in the formation of voltage-dependent channels in bacterial membranes, which induces ion permeation.
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Affiliation(s)
- Victoria N. Syryamina
- Institute of Chemical Kinetics and Combustion
- RAS
- Novosibirsk 630090
- Russian Federation
- Novosibirsk State University
| | - Marta De Zotti
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
| | - Claudio Toniolo
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
- Institute of Biomolecular Chemistry
| | - Fernando Formaggio
- Department of Chemical Sciences
- University of Padova
- 35131 Padova
- Italy
- Institute of Biomolecular Chemistry
| | - Sergei A. Dzuba
- Institute of Chemical Kinetics and Combustion
- RAS
- Novosibirsk 630090
- Russian Federation
- Novosibirsk State University
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3
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Localization of dexamethasone within dendritic core-multishell (CMS) nanoparticles and skin penetration properties studied by multi-frequency electron paramagnetic resonance (EPR) spectroscopy. Eur J Pharm Biopharm 2017; 116:94-101. [DOI: 10.1016/j.ejpb.2016.10.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 09/30/2016] [Accepted: 10/12/2016] [Indexed: 12/27/2022]
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4
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Klare JP, Ortiz de Orué Lucana D. Conformational changes in the novel redox sensor protein HbpS studied by site-directed spin labeling and its turnover in dependence on the catalase-peroxidase CpeB. Antioxid Redox Signal 2012; 16:639-48. [PMID: 21846213 PMCID: PMC3277929 DOI: 10.1089/ars.2011.4080] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
AIMS To establish conditions to study the oligomeric assembly of heme-binding protein (HbpS) in solution by applying the tools of site-directed spin labeling combined with pulse electron paramagnetic resonance (SDSL EPR) spectroscopy, as well as to analyze redox stress-based conformational changes in HbpS subunits within the oligomer in solution. In vivo elucidation of molecular mechanisms that control the downregulation of the novel redox-system HbpS-SenS-SenR. RESULTS Using a set of specifically generated HbpS mutants, and SDSL EPR spectroscopy, we show the octomeric assembly of HbpS in solution, and demonstrate that iron-mediated stress induces conformational changes in HbpS subunits within the octamer. We further demonstrate that the catalase-peroxidase CpeB protects HbpS from hydrogen peroxide (H(2)O(2))-mediated oxidative attack in vivo. Moreover, chromosomal inactivation of cpeB results in an enhanced sensitivity of the mutant to redox-cycling compounds. INNOVATION SDSL EPR has been used in this work for the first time to monitor redox-mediated conformational changes in a redox-sensing protein in solution. This work substantially explains redox-dependent dynamics in HbpS at the atomic level, and presents novel molecular mechanisms supporting downregulation of a signaling cascade. CONCLUSION Iron-mediated stress induces movements of subunits within the HbpS octomeric assembly. We suggest a motion of the C-terminal α-helix toward the preceding helical segment. These events upregulate the activity of the HbpS-SenS-SenR system, in which HbpS acts as an accessory element. The mycelia-associated CpeB, under the control of HbpS-SenS-SenR, protects the extracellular HbpS from oxidation in vivo. Thus, de novo synthesized HbpS proteins downregulate the HbpS-SenS-SenR signaling cascade.
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Affiliation(s)
- Johann P Klare
- Department of Physics, University of Osnabrueck, Osnabrueck, Germany
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5
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Krishnamani V, Hegde BG, Langen R, Lanyi JK. Secondary and Tertiary Structure of Bacteriorhodopsin in the SDS Denatured State. Biochemistry 2012; 51:1051-60. [DOI: 10.1021/bi201769z] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Venkatramanan Krishnamani
- Department
of Physiology and Biophysics, University of California, Irvine, Irvine, California 92697, United States
| | - Balachandra G. Hegde
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California
90033, United States
| | - Ralf Langen
- Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, California
90033, United States
| | - Janos K. Lanyi
- Department
of Physiology and Biophysics, University of California, Irvine, Irvine, California 92697, United States
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6
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Verhoefen MK, Lenz MO, Amarie S, Klare JP, Tittor J, Oesterhelt D, Engelhard M, Wachtveitl J. Primary Reaction of Sensory Rhodopsin II Mutant D75N and the Influence of Azide. Biochemistry 2009; 48:9677-83. [DOI: 10.1021/bi901197c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mirka-Kristin Verhoefen
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Martin O. Lenz
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Sergiu Amarie
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Johann P. Klare
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44139 Dortmund, Germany
| | - Jörg Tittor
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Dieter Oesterhelt
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Martin Engelhard
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44139 Dortmund, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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7
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El Alaoui Faris MD, Lacoste D, Pécréaux J, Joanny JF, Prost J, Bassereau P. Membrane tension lowering induced by protein activity. PHYSICAL REVIEW LETTERS 2009; 102:038102. [PMID: 19257398 DOI: 10.1103/physrevlett.102.038102] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Indexed: 05/27/2023]
Abstract
Using videomicroscopy we present measurements of the fluctuation spectrum of giant vesicles containing bacteriorhodopsin pumps. When the pumps are activated, we observe a significant increase of the fluctuations in the low wave vector region, which we interpret as due to a lowering of the effective tension of the membrane.
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Affiliation(s)
- M D El Alaoui Faris
- Institut Curie, Centre de Recherche; CNRS, UMR 168; Université Pierre et Marie Curie, Paris, F-75248 France
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8
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Hayakawa N, Kasahara T, Hasegawa D, Yoshimura K, Murakami M, Kouyama T. Effect of Xenon Binding to a Hydrophobic Cavity on the Proton Pumping Cycle in Bacteriorhodopsin. J Mol Biol 2008; 384:812-23. [PMID: 18930734 DOI: 10.1016/j.jmb.2008.09.075] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Revised: 09/21/2008] [Accepted: 09/25/2008] [Indexed: 11/25/2022]
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9
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Abstract
In oxygenic photosynthesis, photosystem II (PSII) is the multisubunit membrane protein responsible for the oxidation of water to O2 and the reduction of plastoquinone to plastoquinol. One electron charge separation in the PSII reaction center is coupled to sequential oxidation reactions at the oxygen-evolving complex (OEC), which is composed of four manganese ions and one calcium ion. The sequentially oxidized forms of the OEC are referred to as the S(n) states. S(1) is the dark-adapted state of the OEC. Flash-induced oxygen production oscillates with period four and occurs during the S(3) to S(0) transition. Chloride plays an important, but poorly understood role in photosynthetic water oxidation. Chloride removal is known to block manganese oxidation during the S(2) to S(3) transition. In this work, we have used azide as a probe of proton transfer reactions in PSII. PSII was sulfate-treated to deplete chloride and then treated with azide. Steady state oxygen evolution measurements demonstrate that azide inhibits oxygen evolution in a chloride-dependent manner and that azide is a mixed or noncompetitive inhibitor. This result is consistent with two azide binding sites, one at which azide competes with chloride and one at which azide and chloride do not compete. At pH 7.5, the K(i) for the competing site was estimated as 1 mM, and the K(i)' for the uncompetitive site was estimated as 8 mM. Vibrational spectroscopy was then used to monitor perturbations in the frequency and amplitude of the azide antisymmetric stretching band. These changes were induced by laser-induced charge separation in the PSII reaction center. The results suggest that azide is involved in proton transfer reactions, which occur before manganese oxidation, on the donor side of chloride-depleted PSII.
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10
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Marsh D, Toniolo C. Polarity dependence of EPR parameters for TOAC and MTSSL spin labels: correlation with DOXYL spin labels for membrane studies. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 190:211-221. [PMID: 18042415 DOI: 10.1016/j.jmr.2007.11.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2007] [Revised: 11/05/2007] [Accepted: 11/05/2007] [Indexed: 05/25/2023]
Abstract
TOAC (2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid) is a nitroxyl amino acid that can be incorporated in the backbone of peptides. DOXYL (4,4-dimethyl-oxazolidine-1-oxyl) is a nitroxyl ring that can be attached rigidly at specific C-atom positions in the acyl chains of phospholipids. Spin-labelled phosphatidylcholines of the DOXYL type have been used previously to establish the transmembrane polarity profile in biological lipid bilayers [D. Marsh, Polarity and permeation profiles in lipid membranes, Proc. Natl. Acad. Sci. USA 87 (2001) 7777-7782]. Here, we determine the polarity dependence of the isotropic (14)N-hyperfine couplings, a(o)(N), and g-values, g(o), in a wide range of protic and aprotic media, for a TOAC-containing dipeptide (Fmoc-TOAC-Aib-OMe) and for a DOXYL-containing fatty acid (12-DOXYL-stearic acid). The correlation between datasets for TOAC and DOXYL nitroxides in the various solvents is used to establish the polarity profile for isotropic hyperfine couplings of TOAC in a transmembrane peptide. This calibration can be used to determine the location of TOAC at selected residue positions in a transmembrane or surface-active peptide. A similar calibration procedure is also applied to a(o)(N) and g(o) for the pyrroline methanethiosulphonate nitroxide (MTSSL) that is used in site-directed spin-labelling studies of membrane proteins.
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Affiliation(s)
- Derek Marsh
- Max-Planck-Institut für biophysikalische Chemie, Abt. Spektroskopie, 37077 Göttingen, Germany.
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11
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Marsh D. Reaction fields and solvent dependence of the EPR parameters of nitroxides: the microenvironment of spin labels. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 190:60-67. [PMID: 17977036 DOI: 10.1016/j.jmr.2007.10.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2007] [Revised: 10/02/2007] [Accepted: 10/08/2007] [Indexed: 05/25/2023]
Abstract
The sensitivity of nitroxide spin-label EPR to the polarity of aprotic environments arises from the reaction field produced by polarisation of the surrounding dielectric by the nitroxide electric dipole moment. The performances of three different reaction fields that have been proposed as improvements on the original Onsager model are compared for representative spin-label nitroxides in a range of apolar and dipolar aprotic solvents. Explicit allowance is made for the polarisability of the nitroxide, which effectively renormalises the reaction field but has been neglected in previous analyses of nitroxide hyperfine couplings when using the improved reaction fields. It is found that the model of Block and Walker, which incorporates an exponential dependence of the dielectric permittivity on inverse radial distance from the nitroxide, gives the best description of the solvent dependence of the isotropic (14)N-hyperfine couplings. These results should be useful not only for calibration of environmental polarity using homogeneous solvents, but also for transferring polarity scales and polarity profiles (e.g., in membranes) between different nitroxide spin labels (e.g., of the TEMPO and DOXYL variety).
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Affiliation(s)
- Derek Marsh
- Max-Planck-Institut für biophysikalische Chemie, Abteilung Spektroskopie, 37077 Göttingen, Germany.
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12
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Chen D, Wang JM, Lanyi JK. Electron paramagnetic resonance study of structural changes in the O photointermediate of bacteriorhodopsin. J Mol Biol 2006; 366:790-805. [PMID: 17196982 PMCID: PMC1850110 DOI: 10.1016/j.jmb.2006.12.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 12/04/2006] [Accepted: 12/06/2006] [Indexed: 10/23/2022]
Abstract
The structural changes of bacteriorhodopsin during its photochemical cycle, as revealed by crystal structures of trapped intermediates, have provided insights to the proton translocation mechanism. Because accumulation of the last photointermediate, O, appears to be hindered by lattice forces in the crystals, the only information about the structure of this state is from suggested analogies with the determined structures of the non-illuminated D85S mutant and wild-type bacteriorhodopsin at low pH. We used electron paramagnetic resonance spectroscopy of site-directed spin labels at the extracellular protein surface in membranes to test these models. Spin-spin dipolar interactions in the authentic O state compared to the non-illuminated state revealed that the distance between helices C and F increases by ca 4 Angstroms, there is no distance change between helices D and F, and the distance between helix D and helix B of the adjacent monomer increases. Further, the mobility changes of single labels indicate that helices E and F move outward from the proton channel at the center of the protein, and helix D tilts inward. The overall pattern of movements suggests that the model at acid pH is a better representation of the O state than D85S. However, the mobility analysis of spin-labels on the B-C interhelical loop indicates that the antiparallel beta-sheet maintains its ordered secondary structure in O, instead of the predicted disorder in the two structural models. During decay of the O state, the last step of the photocycle, a proton is transferred from Asp85 to proton release complex in the extracellular proton channel. The structural changes in O suggest the need of large conformational changes to drive the Arg82 side-chain back to its initial orientation towards Asp85, and to rearrange the numerous water molecules in this region in order to conduct the proton away from Asp85.
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Affiliation(s)
- Deliang Chen
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
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13
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Noethig-Laslo V, Šentjurc M. Chapter 13 Transmembrane Polarity Profile of Lipid Membranes. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/s1554-4516(06)05013-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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14
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Savitsky A, Kühn M, Duché D, Möbius K, Steinhoff HJ. Spontaneous Refolding of the Pore-Forming Colicin A Toxin upon Membrane Association As Studied by X-Band and W-Band High-Field Electron Paramagnetic Resonance Spectroscopy. J Phys Chem B 2004. [DOI: 10.1021/jp036397l] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anton Savitsky
- Fachbereich Physik, Freie Universität Berlin, Arnimalle 14, D-14195 Berlin, Germany, Fachbereich Physik, Universität Osnabrück, Barbarastrasse 7, D-49069 Osnabrück, Germany, and Laboratoire d'Ingéniérie des Systèmes Macromoléculaires, Institut de Biologie Structurale et Microbiologie, CNRS, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, France
| | - Martin Kühn
- Fachbereich Physik, Freie Universität Berlin, Arnimalle 14, D-14195 Berlin, Germany, Fachbereich Physik, Universität Osnabrück, Barbarastrasse 7, D-49069 Osnabrück, Germany, and Laboratoire d'Ingéniérie des Systèmes Macromoléculaires, Institut de Biologie Structurale et Microbiologie, CNRS, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, France
| | - Denis Duché
- Fachbereich Physik, Freie Universität Berlin, Arnimalle 14, D-14195 Berlin, Germany, Fachbereich Physik, Universität Osnabrück, Barbarastrasse 7, D-49069 Osnabrück, Germany, and Laboratoire d'Ingéniérie des Systèmes Macromoléculaires, Institut de Biologie Structurale et Microbiologie, CNRS, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, France
| | - Klaus Möbius
- Fachbereich Physik, Freie Universität Berlin, Arnimalle 14, D-14195 Berlin, Germany, Fachbereich Physik, Universität Osnabrück, Barbarastrasse 7, D-49069 Osnabrück, Germany, and Laboratoire d'Ingéniérie des Systèmes Macromoléculaires, Institut de Biologie Structurale et Microbiologie, CNRS, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, France
| | - Heinz-Jürgen Steinhoff
- Fachbereich Physik, Freie Universität Berlin, Arnimalle 14, D-14195 Berlin, Germany, Fachbereich Physik, Universität Osnabrück, Barbarastrasse 7, D-49069 Osnabrück, Germany, and Laboratoire d'Ingéniérie des Systèmes Macromoléculaires, Institut de Biologie Structurale et Microbiologie, CNRS, 31 chemin Joseph Aiguier F-13402, Marseille Cedex 20, France
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15
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Onufriev A, Smondyrev A, Bashford D. Proton affinity changes driving unidirectional proton transport in the bacteriorhodopsin photocycle. J Mol Biol 2003; 332:1183-93. [PMID: 14499620 DOI: 10.1016/s0022-2836(03)00903-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Bacteriorhodopsin is the smallest autonomous light-driven proton pump. Proposals as to how it achieves the directionality of its trans-membrane proton transport fall into two categories: accessibility-switch models in which proton transfer pathways in different parts of the molecule are opened and closed during the photocycle, and affinity-switch models, which focus on changes in proton affinity of groups along the transport chain during the photocycle. Using newly available structural data, and adapting current methods of protein protonation-state prediction to the non-equilibrium case, we have calculated the relative free energies of protonation microstates of groups on the transport chain during key conformational states of the photocycle. Proton flow is modeled using accessibility limitations that do not change during the photocycle. The results show that changes in affinity (microstate energy) calculable from the structural models are sufficient to drive unidirectional proton transport without invoking an accessibility switch. Modeling studies for the N state relative to late M suggest that small structural re-arrangements in the cytoplasmic side may be enough to produce the crucial affinity change of Asp96 during N that allows it to participate in the reprotonation of the Schiff base from the cytoplasmic side. Methodologically, the work represents a conceptual advance compared to the usual calculations of pK(a) using macroscopic electrostatic models. We operate with collective states of protonation involving all key groups, rather than the individual-group pK(a) values traditionally used. When combined with state-to-state transition rules based on accessibility considerations, a model for non-equilibrium proton flow is obtained. Such methods should also be applicable to other active proton-transport systems.
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Affiliation(s)
- Alexey Onufriev
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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16
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Engström M, Vaara J, Schimmelpfennig B, Ågren H. Density Functional Theory Calculations of Electron Paramagnetic Resonance Parameters of a Nitroxide Spin Label in Tissue Factor and Factor VIIa Protein Complex. J Phys Chem B 2002. [DOI: 10.1021/jp022070t] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Maria Engström
- Institute of Physics and Measurement Technology, Linköping University, S-58183 Linköping, Sweden
| | - Juha Vaara
- Department of Chemistry, P.O.B. 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland
| | - Bernd Schimmelpfennig
- Department of Biotechnology, Laboratory of Theoretical Chemistry, Royal Institute of Technology, S-10691 Stockholm, Sweden
| | - Hans Ågren
- Department of Biotechnology, Laboratory of Theoretical Chemistry, Royal Institute of Technology, S-10691 Stockholm, Sweden
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17
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Porschke D. Reaction Coupling, Acceptor pK, and Diffusion Control in Light Induced Proton Release of Bacteriorhodopsin. J Phys Chem B 2002. [DOI: 10.1021/jp0261004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dietmar Porschke
- Max Planck Institut für biophysikalische Chemie, 37077 Göttingen, Germany
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18
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Nachliel E, Gutman M, Tittor J, Oesterhelt D. Proton transfer dynamics on the surface of the late M state of bacteriorhodopsin. Biophys J 2002; 83:416-26. [PMID: 12080130 PMCID: PMC1302157 DOI: 10.1016/s0006-3495(02)75179-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The cytoplasmic surface of the BR (initial) state of bacteriorhodopsin is characterized by a cluster of three carboxylates that function as a proton-collecting antenna. Systematic replacement of most of the surface carboxylates indicated that the cluster is made of D104, E161, and E234 (Checover, S., Y. Marantz, E. Nachliel, M. Gutman, M. Pfeiffer, J. Tittor, D. Oesterhelt, and N. Dencher. 2001. Biochemistry. 40:4281-4292), yet the BR state is a resting configuration; thus, its proton-collecting antenna can only indicate the presence of its role in the photo-intermediates where the protein is re-protonated by protons coming from the cytoplasmic matrix. In the present study we used the D96N and the triple (D96G/F171C/F219L) mutant for monitoring the proton-collecting properties of the protein in its late M state. The protein was maintained in a steady M state by continuous illumination and subjected to reversible pulse protonation caused by repeated excitation of pyranine present in the reaction mixture. The re-protonation dynamics of the pyranine anion was subjected to kinetic analysis, and the rate constants of the reaction of free protons with the surface groups and the proton exchange reactions between them were calculated. The reconstruction of the experimental signal indicated that the late M state of bacteriorhodopsin exhibits an efficient mechanism of proton delivery to the unoccupied-most basic-residue on its cytoplasmic surface (D38), which exceeds that of the BR configuration of the protein. The kinetic analysis was carried out in conjunction with the published structure of the M state (Sass, H., G. Büldt, R. Gessenich, D. Hehn, D. Neff, R. Schlesinger, J. Berendzen, and P. Ormos. 2000. Nature. 406:649-653), the model that resolves most of the cytoplasmic surface. The combination of the kinetic analysis and the structural information led to identification of two proton-conducting tracks on the protein's surface that are funneling protons to D38. One track is made of the carboxylate moieties of residues D36 and E237, while the other is made of D102 and E232. In the late M state the carboxylates of both tracks are closer to D38 than in the BR (initial) state, accounting for a more efficient proton equilibration between the bulk and the protein's proton entrance channel. The triple mutant resembles in the kinetic properties of its proton conducting surface more the BR-M state than the initial state confirming structural similarities with the BR-M state and differences to the BR initial state.
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Affiliation(s)
- Esther Nachliel
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, Tel Aviv University, Tel Aviv 69978, Israel
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19
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Owenius R, Engström M, Lindgren M, Huber M. Influence of Solvent Polarity and Hydrogen Bonding on the EPR Parameters of a Nitroxide Spin Label Studied by 9-GHz and 95-GHz EPR Spectroscopy and DFT Calculations. J Phys Chem A 2001. [DOI: 10.1021/jp0116914] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rikard Owenius
- IFM-Departments of Chemical Physics and Computational Physics, Linköping University, SE-581 83 Linköping, Sweden
| | - Maria Engström
- IFM-Departments of Chemical Physics and Computational Physics, Linköping University, SE-581 83 Linköping, Sweden
| | - Mikael Lindgren
- IFM-Departments of Chemical Physics and Computational Physics, Linköping University, SE-581 83 Linköping, Sweden
| | - Martina Huber
- Huygens Laboratory, MAT Group, Leiden University, P.O. Box 9504, 2300 RA Leiden, The Netherlands
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20
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Kaulen AD. Electrogenic processes and protein conformational changes accompanying the bacteriorhodopsin photocycle. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1460:204-19. [PMID: 10984601 DOI: 10.1016/s0005-2728(00)00140-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The possible mechanisms of electrogenic processes accompanying proton transport in bacteriorhodopsin are discussed on the basis of recent structural data of the protein. Apparent inconsistencies between experimental data and their interpretation are considered. Special emphasis is placed on the protein conformational changes accompanying the reprotonation of chromophore and proton uptake stage in the bacteriorhodopsin photocycle.
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Affiliation(s)
- A D Kaulen
- Department of Photobiochemistry, A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119899, Moscow, Russia
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21
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Steinhoff H, Savitsky A, Wegener C, Pfeiffer M, Plato M, Möbius K. High-field EPR studies of the structure and conformational changes of site-directed spin labeled bacteriorhodopsin. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1457:253-62. [PMID: 10773169 DOI: 10.1016/s0005-2728(00)00106-7] [Citation(s) in RCA: 135] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cw and pulsed high-field EPR (95 GHz, 3.4 T) are performed on site-directed spin labeled bacteriorhodopsin (BR) mutants. The enhanced Zeeman splitting leads to spectra with resolved g-tensor components of the nitroxide spin label. The g(xx) component shift determined for 10 spin labels located in the cytoplasmic loop region and in the protein interior along the BR proton channel reveals a maximum close to position 46 between the proton donor D96 and the retinal. A plot of g(xx) versus A(zz) of the nitrogen discloses grouping of 12 spin labeled sites in protic and aprotic sites. Spin labels at positions 46, 167 and 171 show the aprotic character of the cytoplasmic moiety of the proton channel whereas nitroxides at positions 53, 194 and 129 reveal the protic environment in the extracellular channel. The enhanced sensitivity of high-field EPR with respect to anisotropic reorientational motion of nitroxides allows the characterization of different motional modes for spin labels bound to positions 167 and 170. The motional restriction of the nitroxide at position 167 of the double mutant V167C/D96N is decreased in the M(N) photo-intermediate. An outward shift of the cytoplasmic moiety of helix F in the M(N) intermediate would account for the high-field EPR results and is in agreement with diffraction and recent X-band EPR data.
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Affiliation(s)
- H Steinhoff
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, 44780, Bochum, Germany.
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22
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Alonso A, Gonçalves dos Santos J, Tabak M. Stratum corneum protein mobility as evaluated by a spin label maleimide derivative. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1478:89-101. [PMID: 10719178 DOI: 10.1016/s0167-4838(00)00011-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The molecular dynamics in the vicinity of sulfhydryl groups of stratum corneum (SC) proteins has been studied by electron paramagnetic resonance (EPR) spectroscopy of maleimide spin labels covalently bound to the proteins. The total amount of bound maleimide was around 4 nmol per mg of SC. We have interpreted the coexistence of two spectral components in the EPR spectra by a two-state model with a fraction of label hydrogen bonded to proteins and another fraction exposed to the aqueous environment. We showed that the relative populations among these two states, determined by spectral simulation, are in thermodynamic equilibrium. The calculated energetic gain for the nitroxide to form hydrogen bond with SC proteins rather than to be dissolved in the buffer was approximately 12 kcal/mol in the temperature range of 2-30 degrees C and approximately 5 kcal/mol in the range of 30-86 degrees C. Temperature profiles of other EPR parameters related to the rotational diffusion of the probe also showed changes in the temperature interval of 26-42 degrees C, suggesting alterations in the vibration modes of SC proteins which are sensitive to higher motional freedom above 26-42 degrees C. We also compared samples of intact and lipid-depleted SC and we found that the delipidization process does not alter significantly the backbone mobility in the SH group regions, but the data suggest that the protein cavity is more open in the case of the delipidized samples. These results contribute to the understanding of the protein participation in the barrier function of SC, and can be useful to improve the spectral analysis of site-directed spin labeling, particularly for a more quantitative description of the dynamic modes of the nitroxide side chains.
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Affiliation(s)
- A Alonso
- Instituto de Física, Universidade Federal de Goiás, Goiânia, Brazil
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23
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Rink T, Pfeiffer M, Oesterhelt D, Gerwert K, Steinhoff HJ. Unraveling photoexcited conformational changes of bacteriorhodopsin by time resolved electron paramagnetic resonance spectroscopy. Biophys J 2000; 78:1519-30. [PMID: 10692336 PMCID: PMC1300749 DOI: 10.1016/s0006-3495(00)76704-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
By means of time-resolved electron paramagnetic resonance (EPR) spectroscopy, the photoexcited structural changes of site-directed spin-labeled bacteriorhodopsin are studied. A complete set of cysteine mutants of the C-D loop, positions 100-107, and of the E-F loop, including the first alpha-helical turns of helices E and F, positions 154-171, was modified with a methanethiosulfonate spin label. The EPR spectral changes occurring during the photocycle are consistent with a small movement of helix C and an outward tilt of helix F. These helix movements are accompanied by a rearrangement of the E-F loop and of the C-terminal turn of helix E. The kinetic analysis of the transient EPR data and the absorbance changes in the visible spectrum reveals that the conformational change occurs during the lifetime of the M intermediate. Prominent rearrangements of nitroxide side chains in the vicinity of D96 may indicate the preparation of the reprotonation of the Schiff base. All structural changes reverse with the recovery of the bacteriorhodopsin initial state.
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Affiliation(s)
- T Rink
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, 44801 Bochum, Germany
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