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Abdullin D, Schiemann O. Localization of metal ions in biomolecules by means of pulsed dipolar EPR spectroscopy. Dalton Trans 2021; 50:808-815. [PMID: 33416053 DOI: 10.1039/d0dt03596c] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Metal ions are important for the folding, structure, and function of biomolecules. Thus, knowing where their binding sites are located in proteins or oligonucleotides is a critical objective. X-ray crystallography and nuclear magnetic resonance are powerful methods in this respect, but both have their limitations. Here, a complementary method is highlighted in which paramagnetic metal ions are localized by means of trilateration using a combination of site-directed spin labeling and pulsed dipolar electron paramagnetic resonance spectroscopy. The working principle, the requirements, and the limitations of the method are critically discussed. Several applications of the method are outlined and compared with each other.
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Affiliation(s)
- Dinar Abdullin
- Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany.
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Yu Y, Petrik ID, Chacón KN, Hosseinzadeh P, Chen H, Blackburn NJ, Lu Y. Effect of circular permutation on the structure and function of type 1 blue copper center in azurin. Protein Sci 2017; 26:218-226. [PMID: 27759897 PMCID: PMC5275729 DOI: 10.1002/pro.3071] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 10/13/2016] [Accepted: 10/14/2016] [Indexed: 11/10/2022]
Abstract
Type 1 copper (T1Cu) proteins are electron transfer (ET) proteins involved in many important biological processes. While the effects of changing primary and secondary coordination spheres in the T1Cu ET function have been extensively studied, few report has explored the effect of the overall protein structural perturbation on active site configuration or reduction potential of the protein, even though the protein scaffold has been proposed to play a critical role in enforcing the entatic or "rack-induced" state for ET functions. We herein report circular permutation of azurin by linking the N- and C-termini and creating new termini in the loops between 1st and 2nd β strands or between 3rd and 4th β strands. Characterization by electronic absorption, electron paramagnetic spectroscopies, as well as crystallography and cyclic voltammetry revealed that, while the overall structure and the primary coordination sphere of the circular permutated azurins remain the same as those of native azurin, their reduction potentials increased by 18 and 124 mV over that of WTAz. Such increases in reduction potentials can be attributed to subtle differences in the hydrogen-bonding network in secondary coordination sphere around the T1Cu center.
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Affiliation(s)
- Yang Yu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjin300308China
| | - Igor D. Petrik
- Department of Chemistry, University of Illinois at Urbana‐ChampaignUrbanaIllinois61801
| | | | - Parisa Hosseinzadeh
- Department of BiochemistryUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois61801
| | - Honghui Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of SciencesTianjin300308China
- Tianjin University of Science and TechnologyTianjin300457China
| | - Ninian J. Blackburn
- Institute of Environmental Health, Oregon Health and Science UniversityPortlandOregon97239
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana‐ChampaignUrbanaIllinois61801
- Department of BiochemistryUniversity of Illinois at Urbana‐ChampaignUrbanaIllinois61801
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3
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Carter E, Sharples KM, Platts JA, Murphy DM. Structure determination of bound nitrogen-based adducts with copper(II) acetylacetonato; an EPR, ENDOR and DFT study. Phys Chem Chem Phys 2015; 17:11445-54. [PMID: 25854519 DOI: 10.1039/c5cp00559k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The adducts of bis(acetylacetonato)–copper(II), [Cu(acac)2], formed with a range of nitrogen heterocycles including pyridine (2), methylpyridines (3,4,5), amino-methylpyridines (6,7) and diazines (8,9,10) were investigated in frozen solution using X-band EPR and 1H ENDOR spectroscopy. The small perturbations to the EPR spin Hamiltonian parameters (g and CuA) were consistent with the axial coordination of the nitrogen bases to Cu(II), and found to be dependent on both the basicity and steric influence of the coordinating substrate. The detailed structure of two adducts was then investigated by angular selective (1)H ENDOR and DFT. For the [Cu(acac)2](pyridine) adduct, axial coordination of the substrate was found to occur via the pyridine nitrogen as expected, producing a characteristic (1)H hyperfine coupling ((H)Ai = −2.6, −2.04, 4.7 MHz; β = 36°; aiso = 0.2 MHz) arising from the ortho-(1)H in the ring 2 or 6 position. These results were confirmed by DFT. However, in the [Cu(acac)2](2-amino-6-methyl-pyridine) adduct, the ENDOR data revealed a substantially different (1)H hyperfine coupling ((H)Ai = −4.52, −3.35, 6.47 MHz; β = 14°; aiso = −0.47 MHz) arising from the –NH2 amino protons. Analysis of this experimentally derived tensor in conjunction with the calculated DFT tensors, revealed that the 2-amino-6-methyl-pyridine substrate binds to Cu(II) via the exocyclic amino pyridine nitrogen, but with a tilt angle of 20° of the pyridine ring away from the geometry optimised structure. These results reveal how important structural information on the coordination geometry of Cu(II) adducts can be obtained by (1)H ENDOR, but only when the complete angular dependency profile of the ENDOR data is thoroughly considered.
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Affiliation(s)
- Emma Carter
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK.
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Pievo R, Angerstein B, Fielding AJ, Koch C, Feussner I, Bennati M. A rapid freeze-quench setup for multi-frequency EPR spectroscopy of enzymatic reactions. Chemphyschem 2013; 14:4094-101. [PMID: 24323853 DOI: 10.1002/cphc.201300714] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/22/2013] [Indexed: 11/11/2022]
Abstract
Electron paramagnetic resonance (EPR) spectroscopy in combination with the rapid freeze-quench (RFQ) technique is a well-established method to trap and characterize intermediates in chemical or enzymatic reactions at the millisecond or even shorter time scales. The method is particularly powerful for mechanistic studies of enzymatic reactions when combined with high-frequency EPR (ν≥90 GHz), which permits the identification of substrate or protein radical intermediates by their electronic g values. In this work, we describe a new custom-designed micro-mix rapid freeze-quench apparatus, for which reagent volumes for biological samples as small as 20 μL are required. The apparatus was implemented with homemade sample collectors appropriate for 9, 34, and 94 GHz EPR capillaries (4, 2, and 0.87 mm outer diameter, respectively) and the performance was evaluated. We demonstrate the application potential of the RFQ apparatus by following the enzymatic reaction of PpoA, a fungal dioxygenase producing hydro(pero)xylated fatty acids. The larger spectral resolution at 94 GHz allows the discernment of structural changes in the EPR spectra, which are not detectable in the same samples at the standard 9 GHz frequency.
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Affiliation(s)
- Roberta Pievo
- Max Planck Institute for Biophysical Chemistry, Am Faßberg 11, 37077 Göttingen (Germany).
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Carter E, Hazeland EL, Murphy DM, Ward BD. Structure, EPR/ENDOR and DFT characterisation of a [Cu(II)(en)2](OTf)2 complex. Dalton Trans 2013; 42:15088-96. [PMID: 24000097 DOI: 10.1039/c3dt51694f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Jahn-Teller distorted Cu(II) complex [Cu(en)2](OTf)2 1 (en = 1,2-diaminoethane) has been reported and characterised using X-ray crystallography, EPR and ENDOR spectroscopy, and DFT calculations. The solid state structure shows an intra- and inter-molecular hydrogen-bonded network via the N-H groups and the coordinated triflate anions. CW and pulsed EPR/ENDOR were used to determine the spin Hamiltonian parameters of the Cu(II) complex, which were in excellent agreement with the DFT. The structure of the complex, as determined by angular selective ENDOR, is also in good agreement with the crystal structure, confirming the axial coordination of the counter-ion(s) in the frozen solution. The small (14)N superhyperfine couplings are also consistent with the sp(3) hybridised nature of the coordinating nitrogens. These results show that the correlation between the (14)N hyperfine coupling and hybridisation of donor nitrogens can be useful to determine not only the coordination around the Cu(ii) metal centre but also the nature of the donor in unknown Cu(II) systems.
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Affiliation(s)
- Emma Carter
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, UK.
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Fittipaldi M, Gatteschi D, Fornasiero P. The power of EPR techniques in revealing active sites in heterogeneous photocatalysis: The case of anion doped TiO2. Catal Today 2013. [DOI: 10.1016/j.cattod.2012.04.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Murphy DM, Caretti I, Carter E, Fallis IA, Göbel MC, Landon J, Doorslaer SV, Willock DJ. Visualizing Diastereomeric Interactions of Chiral Amine–Chiral Copper Salen Adducts by EPR Spectroscopy and DFT. Inorg Chem 2011; 50:6944-55. [DOI: 10.1021/ic200113u] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ruthstein S, Stone KM, Cunningham TF, Ji M, Cascio M, Saxena S. Pulsed electron spin resonance resolves the coordination site of Cu²(+) ions in α1-glycine receptor. Biophys J 2011; 99:2497-506. [PMID: 20959090 DOI: 10.1016/j.bpj.2010.08.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 08/09/2010] [Accepted: 08/26/2010] [Indexed: 11/19/2022] Open
Abstract
Herein, we identify the coordination environment of Cu²(+) in the human α1-glycine receptor (GlyR). GlyRs are members of the pentameric ligand-gated ion channel superfamily (pLGIC) that mediate fast signaling at synapses. Metal ions like Zn²(+) and Cu²(+) significantly modulate the activity of pLGICs, and metal ion coordination is essential for proper physiological postsynaptic inhibition by GlyR in vivo. Zn²(+) can either potentiate or inhibit GlyR activity depending on its concentration, while Cu²(+) is inhibitory. To better understand the molecular basis of the inhibitory effect we have used electron spin resonance to directly examine Cu²(+) coordination and stoichiometry. We show that Cu²(+) has one binding site per α1 subunit, and that five Cu²(+) can be coordinated per GlyR. Cu²(+) binds to E192 and H215 in each subunit of GlyR with a 40 μM apparent dissociation constant, consistent with earlier functional measurements. However, the coordination site does not include several residues of the agonist/antagonist binding site that were previously suggested to have roles in Cu²(+) coordination by functional measurements. Intriguingly, the E192/H215 site has been proposed as the potentiating Zn²(+) site. The opposing modulatory actions of these cations at a shared binding site highlight the sensitive allosteric nature of GlyR.
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Affiliation(s)
- Sharon Ruthstein
- Department of Chemistry, University of Pittsburgh, Pennsylvania, USA
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Lyubenova S, Maly T, Zwicker K, Brandt U, Ludwig B, Prisner T. Multifrequency pulsed electron paramagnetic resonance on metalloproteins. Acc Chem Res 2010; 43:181-9. [PMID: 19842617 DOI: 10.1021/ar900050d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metalloproteins often contain metal centers that are paramagnetic in some functional state of the protein; hence electron paramagnetic resonance (EPR) spectroscopy can be a powerful tool for studying protein structure and function. Dipolar spectroscopy allows the determination of the dipole-dipole interactions between metal centers in protein complexes, revealing the structural arrangement of different paramagnetic centers at distances of up to 8 nm. Hyperfine spectroscopy can be used to measure the interaction between an unpaired electron spin and nuclear spins within a distance of 0.8 nm; it therefore permits the characterization of the local structure of the paramagnetic center's ligand sphere with very high precision. In this Account, we review our laboratory's recent applications of both dipolar and hyperfine pulsed EPR methods to metalloproteins. We used pulsed dipolar relaxation methods to investigate the complex of cytochrome c and cytochrome c oxidase, a noncovalent protein-protein complex involved in mitochondrial electron-transfer reactions. Hyperfine sublevel correlation spectroscopy (HYSCORE) was used to study the ligand sphere of iron-sulfur clusters in complex I of the mitochondrial respiratory chain and substrate binding to the molybdenum enzyme polysulfide reductase. These examples demonstrate the potential of the two techniques; however, they also highlight the difficulties of data interpretation when several paramagnetic species with overlapping spectra are present in the protein. In such cases, further approaches and data are very useful to enhance the information content. Relaxation filtered hyperfine spectroscopy (REFINE) can be used to separate the individual components of overlapping paramagnetic species on the basis of differences in their longitudinal relaxation rates; it is applicable to any kind of pulsed hyperfine or dipolar spectroscopy. Here, we show that the spectra of the iron-sulfur clusters in complex I can be separated by this method, allowing us to obtain hyperfine (and dipolar) information from the individual species. Furthermore, performing pulsed EPR experiments at different magnetic fields is another important tool to disentangle the spectral components in such complex systems. Despite the fact that high magnetic fields do not usually lead to better spectral separation for metal centers, they provide additional information about the relative orientation of different paramagnetic centers. Our high-field EPR studies on cytochrome c oxidase reveal essential information regarding the structural arrangement of the binuclear Cu(A) center with respect to both the manganese ion within the enzyme and the cytochrome in the protein-protein complex with cytochrome c.
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Affiliation(s)
- Sevdalina Lyubenova
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Thorsten Maly
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Klaus Zwicker
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Ulrich Brandt
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Bernd Ludwig
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
| | - Thomas Prisner
- Cluster of Excellence Macromolecular Complexes, Goethe-University, Frankfurt am Main, Germany
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Schleicher E, Wenzel R, Ahmad M, Batschauer A, Essen LO, Hitomi K, Getzoff ED, Bittl R, Weber S, Okafuji A. The Electronic State of Flavoproteins: Investigations with Proton Electron-Nuclear Double Resonance. APPLIED MAGNETIC RESONANCE 2010; 37:339-352. [PMID: 26089595 PMCID: PMC4469238 DOI: 10.1007/s00723-009-0101-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Electron-nuclear double resonance (ENDOR) spectroscopy provides useful information on hyperfine interactions between nuclear magnetic moments and the magnetic moment of an unpaired electron spin. Because the hyperfine coupling constant reacts quite sensitively to polarity changes in the direct vicinity of the nucleus under consideration, ENDOR spectroscopy can be favorably used for the detection of subtle protein-cofactor interactions. A number of pulsed ENDOR studies on flavoproteins have been published during the past few years; most of them were designed to characterize the flavin cofactor by means of its protonation state, or to detect individual protein-cofactor interactions. The aim of this study is to compare the pulsed ENDOR spectra from different flavoproteins in terms of variations of characteristic proton hyperfine values. The general concept is to observe limits of possible influences on the cofactor's electronic state by surrounding amino acids. Furthermore, we compare ENDOR data obtained from in vivo experiments with in vitro data to emphasize the potential of the method for gaining molecular information in complex media.
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Affiliation(s)
- Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr.21, 79104 Freiburg, Germany
| | - Ringo Wenzel
- Institut für Experimentalphysik, Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | | | - Alfred Batschauer
- Fachbereich Biologie, Philipps-Universität Marburg, Marburg, Germany
| | | | - Kenichi Hitomi
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Elizabeth D Getzoff
- Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Robert Bittl
- Institut für Experimentalphysik, Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr.21, 79104 Freiburg, Germany
| | - Asako Okafuji
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstr.21, 79104 Freiburg, Germany
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Cruickshank PAS, Bolton DR, Robertson DA, Hunter RI, Wylde RJ, Smith GM. A kilowatt pulsed 94 GHz electron paramagnetic resonance spectrometer with high concentration sensitivity, high instantaneous bandwidth, and low dead time. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2009; 80:103102. [PMID: 19895049 DOI: 10.1063/1.3239402] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We describe a quasioptical 94 GHz kW pulsed electron paramagnetic resonance spectrometer featuring pi/2 pulses as short as 5 ns and an instantaneous bandwidth of 1 GHz in nonresonant sample holders operating in induction mode and at low temperatures. Low power pulses can be as short as 200 ps and kilowatt pulses as short as 1.5 ns with timing resolution of a few hundred picoseconds. Phase and frequency can be changed on nanosecond time scales and complex high power pulse sequences can be run at repetition rates up to 80 kHz with low dead time. We demonstrate that the combination of high power pulses at high frequencies and nonresonant cavities can offer excellent concentration sensitivity for orientation selective pulsed electron double resonance (double electron-electron resonance), where we demonstrate measurements at 1 microM concentration levels.
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Affiliation(s)
- Paul A S Cruickshank
- School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, United Kingdom
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Schleicher E, Bittl R, Weber S. New roles of flavoproteins in molecular cell biology: Blue-light active flavoproteins studied by electron paramagnetic resonance. FEBS J 2009; 276:4290-303. [DOI: 10.1111/j.1742-4658.2009.07141.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Niklas J, Epel B, Antonkine ML, Sinnecker S, Pandelia ME, Lubitz W. Electronic Structure of the Quinone Radical Anion A1•− of Photosystem I Investigated by Advanced Pulse EPR and ENDOR Techniques. J Phys Chem B 2009; 113:10367-79. [DOI: 10.1021/jp901890z] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jens Niklas
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, 45470 Mülheim/Ruhr, Germany, and Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Boris Epel
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, 45470 Mülheim/Ruhr, Germany, and Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Mikhail L. Antonkine
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, 45470 Mülheim/Ruhr, Germany, and Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Sebastian Sinnecker
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, 45470 Mülheim/Ruhr, Germany, and Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Maria-Eirini Pandelia
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, 45470 Mülheim/Ruhr, Germany, and Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Wolfgang Lubitz
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, 45470 Mülheim/Ruhr, Germany, and Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
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Advanced Pulse EPR Methods for the Characterization of Metalloproteins. HIGH RESOLUTION EPR 2009. [DOI: 10.1007/978-0-387-84856-3_2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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Shafaat HS, Leigh BS, Tauber MJ, Kim JE. Resonance Raman Characterization of a Stable Tryptophan Radical in an Azurin Mutant. J Phys Chem B 2008; 113:382-8. [PMID: 19072535 DOI: 10.1021/jp809329a] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hannah S. Shafaat
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Brian S. Leigh
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Michael J. Tauber
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California 92093
| | - Judy E. Kim
- Department of Chemistry & Biochemistry, University of California at San Diego, La Jolla, California 92093
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Dube H, Kasumaj B, Calle C, Saito M, Jeschke G, Diederich F. Direkter Nachweis einer Wasserstoffbrücke zu gebundenem Disauerstoff in einem Modellkomplex für Myoglobin/Hämoglobin und in Cobalt-Myoglobin durch Puls-EPR. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200705180] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Dube H, Kasumaj B, Calle C, Saito M, Jeschke G, Diederich F. Direct Evidence for a Hydrogen Bond to Bound Dioxygen in a Myoglobin/Hemoglobin Model System and in Cobalt Myoglobin by Pulse-EPR Spectroscopy. Angew Chem Int Ed Engl 2008; 47:2600-3. [DOI: 10.1002/anie.200705180] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Schinzel S, Müller R, Kaupp M. Structure and electron paramagnetic resonance parameters of the manganese site of concanavalin A studied by density functional methods. Theor Chem Acc 2008. [DOI: 10.1007/s00214-008-0420-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Sebastian ES, Matxain JM, Eriksson LA, Stote RH, Dejaegere A, Cossio FP, Lopez X. Metal Ion Dependent Adhesion Sites in Integrins: A Combined DFT and QMC Study on Mn2+. J Phys Chem B 2007; 111:9099-103. [PMID: 17608410 DOI: 10.1021/jp071065s] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The theoretical study of relative energies of different spin states of Mn2+ has been carried out for the isolated cation and for structures in which the cation is coordinated to ligands that represent the first coordination shell in a protein environment that contains a metal ion dependent adhesion site (MIDAS, found in the ligand binding domain of protein LFA-1). The calculations determine whether the ligand field generated by a prototype protein environment affects the relative energies between high, intermediate, and low spin states. Geometry optimizations and vibrational frequency calculations were carried out at the B3LYP/SKBJ+* level of theory. Single point calculations were performed at the B3LYP/6-311++G(2df,2p) and diffusion monte carlo (DMC) levels for the refinement of the electronic energies. These calculations reveal important differences in the relative energies between high/low spin complexes obtained by B3LYP and DMC and show that although both DFT and DMC show similar trends, a higher level method such as DMC is necessary for a quantitative description of the interactions between Mn2+ and its natural ligands. (G)s of acetate-type ligand binding reactions were calculated that show that the higher the spin of the manganese complex, the lower the affinity for the ligand.
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Affiliation(s)
- Eider San Sebastian
- Kimika Fakultatea, Euskal Herriko Unibertsitatea, P.K. 1072, 20080 Donostia, Spain
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Farver O, Hwang HJ, Lu Y, Pecht I. Reorganization Energy of the CuA Center in Purple Azurin: Impact of the Mixed Valence-to-Trapped Valence State Transition. J Phys Chem B 2007; 111:6690-4. [PMID: 17274649 DOI: 10.1021/jp0672555] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mixed valence (MV) coordination compounds play important roles in redox reactions in chemistry and biology. Details of the contribution of a mixed valence state to protein electron transfer (ET) reactivity such as reorganization energy, however, have not been experimentally defined. Herein we report measurements of reorganization energies of a binuclear CuA center engineered into Pseudomonas aeruginosa azurin that exhibits a reversible transition between a totally delocalized MV state at pH 8.0 and a trapped valence (TV) state at pH 4.0. The reorganization energy of a His120Ala variant of CuA azurin that displays a TV state at both the above pH values has also been determined. We found that the MV-to-TV state transition increases the reorganization energy by 0.18 eV, providing evidence that the MV state of the CuA center has lower reorganization energy than its TV counterpart. We have also shown that lowering the pH from 8.0 to 4.0 results in a similar (approximately 0.4 eV) decrease in reorganization energy for both blue (type 1) and purple (CuA) azurins, even though the reorganization energies of the two different copper centers are different at a given pH. These results suggest that the MV state plays only a secondary role in modulation of the ET reactivity via the reorganization energy, as compared to that of the driving force.
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Affiliation(s)
- Ole Farver
- Institute of Analytical and Pharmaceutical Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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Calle C, Sreekanth A, Fedin M, Forrer J, Garcia-Rubio I, Gromov I, Hinderberger D, Kasumaj B, Léger P, Mancosu B, Mitrikas G, Santangelo M, Stoll S, Schweiger A, Tschaggelar R, Harmer J. Pulse EPR Methods for Studying Chemical and Biological Samples Containing Transition Metals. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690229] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Utschig LM, Thurnauer MC, Tiede DM, Poluektov OG. Low-temperature interquinone electron transfer in photosynthetic reaction centers from Rhodobacter sphaeroides and Blastochloris viridis: characterization of Q(B)- states by high-frequency electron paramagnetic resonance (EPR) and electron-nuclear double resonance (ENDOR). Biochemistry 2006; 44:14131-42. [PMID: 16245929 DOI: 10.1021/bi051060q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
High-frequency electron paramagnetic resonance (HF EPR) techniques have been employed to look for localized light-induced conformational changes in the protein environments around the reduced secondary quinone acceptor (Q(B)(-)) in Rhodobacter sphaeroides and Blastochloris viridis RCs. The Q(A)(-) and Q(B)(-) radical species in Fe-removed/Zn-replaced protonated RCs substituted with deuterated quinones are distinguishable with pulsed D-band (130 GHz) EPR and provide native probes of both the low-temperature Q(A)(-)Q(B) --> Q(A)Q(B)(-) electron-transfer event and the structure of trapped conformational substates. We report here the first spectroscopic evidence that cryogenically trapped, light-induced changes enable low-temperature Q(A)(-)Q(B) --> Q(A)Q(B)(-) electron transfer in the B. viridis RC and the first observation of an inactive, trapped P(+)Q(B)(-) state in both R. sphaeroides and B. viridis RCs that does not recombine at 20 K. The high resolution and orientational selectivity of HF electron-nuclear double resonance (ENDOR) allows us to directly probe protein environments around Q(B)(-) for distinct P(+)Q(B)(-) kinetic RC states by spectrally selecting specific nuclei in isotopically labeled samples. No structural differences in the protein structure near Q(B)(-) or reorientation (within 5 degrees ) of Q(B)(-) was observed with HF ENDOR spectra of two states of P(+)Q(B)(-): "active" and "inactive" states with regards to low-temperature electron transfer. These results reveal a remarkably enforced local protein environment for Q(B) in its reduced semiquinone state and suggest that the conformational change that controls reactivity resides beyond the Q(B) local environment.
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Affiliation(s)
- Lisa M Utschig
- Chemistry Division, Argonne National Laboratory, Argonne, Illinois 60439, USA.
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Murphy DM, Farley RD. Principles and applications of ENDOR spectroscopy for structure determination in solution and disordered matrices. Chem Soc Rev 2006; 35:249-68. [PMID: 16505919 DOI: 10.1039/b500509b] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) spectroscopies are extremely powerful and versatile methods for the characterisation of paramagnetic systems in biology, chemistry, and physics. However, by comparison to EPR, ENDOR remains a less widely used technique. In this tutorial review the basic principles of continuous wave ENDOR are described. The theory of orientation selective ENDOR, for structure determination in frozen solutions and powders, is then described. A range of examples, illustrating the type of information obtained from the ENDOR spectrum, is finally presented.
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Affiliation(s)
- Damien M Murphy
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff, UKCF10 3AT
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