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Van Stappen C, Decamps L, Cutsail GE, Bjornsson R, Henthorn JT, Birrell JA, DeBeer S. The Spectroscopy of Nitrogenases. Chem Rev 2020; 120:5005-5081. [PMID: 32237739 PMCID: PMC7318057 DOI: 10.1021/acs.chemrev.9b00650] [Citation(s) in RCA: 117] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Indexed: 01/08/2023]
Abstract
Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.
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Affiliation(s)
- Casey Van Stappen
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Laure Decamps
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - George E. Cutsail
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Justin T. Henthorn
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - James A. Birrell
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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2
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Horitani M, Grubel K, McWilliams SF, Stubbert BD, Mercado BQ, Yu Y, Gurubasavaraj PM, Lees NS, Holland PL, Hoffman BM. ENDOR characterization of an iron-alkene complex provides insight into a corresponding organometallic intermediate of nitrogenase. Chem Sci 2017; 8:5941-5948. [PMID: 28989623 PMCID: PMC5620524 DOI: 10.1039/c7sc01602f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/17/2017] [Indexed: 12/16/2022] Open
Abstract
Comparison of an iron(I)–alkene complex to a nitrogenase intermediate using ENDOR reveals details of the binding geometry.
A bio-organometallic intermediate, denoted PA, was previously trapped during the reduction of propargyl alcohol to allyl alcohol (AA) by nitrogenase, and a similar one was trapped during acetylene reduction, representing foundational examples of alkene binding to a metal center in biology. ENDOR spectroscopy led to the conclusion that these intermediates have η2 binding of the alkene, with the hydrogens on the terminal carbon structurally/magnetically equivalent and related by local mirror symmetry. However, our understanding of both the PA intermediate, and of the dependability of the ENDOR analysis on which this understanding was based, was constrained by the absence of reference iron–alkene complexes for EPR/ENDOR comparison. Here, we report an ENDOR study of the crystallographically characterized biomimetic iron(i) complex 1, which exhibits η2 coordination of styrene, thus connecting hyperfine and structural parameters of an Fe-bound alkene fragment for the first time. A tilt of the alkene plane of 1 from normal to the crystallographic Fe–C2–C1 plane causes substantial differences in the dipolar couplings of the two terminal vinylic protons. Comparison of the hyperfine couplings of 1 and PA confirms the proposed symmetry of PA, and that the η2 interaction forms a scalene Fe–C–C triangle, rather than an isosceles triangle. This spectroscopic study of a structurally characterized complex thus shows the exceptional sensitivity of ENDOR spectroscopy to structural details, while enhancing our understanding of the geometry of a key nitrogenase adduct.
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Affiliation(s)
- Masaki Horitani
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , USA . .,Department of Applied Biochemistry and Food Science , Saga University , Saga , 840-8502 , Japan
| | - Katarzyna Grubel
- Department of Chemistry , Yale University , New Haven , CT 06520 , USA .
| | - Sean F McWilliams
- Department of Chemistry , Yale University , New Haven , CT 06520 , USA .
| | - Bryan D Stubbert
- Department of Chemistry , University of Rochester , Rochester , New York 14627 , USA
| | - Brandon Q Mercado
- Department of Chemistry , Yale University , New Haven , CT 06520 , USA .
| | - Ying Yu
- Department of Chemistry , University of Rochester , Rochester , New York 14627 , USA
| | | | - Nicholas S Lees
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , USA .
| | - Patrick L Holland
- Department of Chemistry , Yale University , New Haven , CT 06520 , USA .
| | - Brian M Hoffman
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , USA .
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3
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Sharma A, Roemelt M, Reithofer M, Schrock RR, Hoffman BM, Neese F. EPR/ENDOR and Theoretical Study of the Jahn-Teller-Active [HIPTN 3N]Mo VL Complexes (L = N -, NH). Inorg Chem 2017; 56:6906-6919. [PMID: 28571321 DOI: 10.1021/acs.inorgchem.7b00364] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The molybdenum trisamidoamine (TAA) complex [Mo] {[3,5-(2,4,6-i-Pr3C6H2)2C6H3NCH2CH2N]Mo} carries out catalytic reduction of N2 to ammonia (NH3) by protons and electrons at room temperature. A key intermediate in the proposed [Mo] nitrogen reduction cycle is nitridomolybdenum(VI), [Mo(VI)]N. The addition of [e-/H+] to [Mo(VI)]N to generate [Mo(V)]NH might, in principle, follow one of three possible pathways: direct proton-coupled electron transfer; H+ first and then e-; e- and then H+. In this study, the paramagnetic Mo(V) intermediate {[Mo]N}- and the [Mo]NH transfer product were generated by irradiating the diamagnetic [Mo]N and {[Mo]NH}+ Mo(VI) complexes, respectively, with γ-rays at 77 K, and their electronic and geometric structures were characterized by electron paramagnetic resonance and electron nuclear double resonance spectroscopies, combined with quantum-chemical computations. In combination with previous X-ray studies, this creates the rare situation in which each one of the four possible states of [e-/H+] delivery has been characterized. Because of the degeneracy of the electronic ground states of both {[Mo(V)]N}- and [Mo(V)]NH, only multireference-based methods such as the complete active-space self-consistent field (CASSCF) and related methods provide a qualitatively correct description of the electronic ground state and vibronic coupling. The molecular g values of {[Mo]N}- and [Mo]NH exhibit large deviations from the free-electron value ge. Their actual values reflect the relative strengths of vibronic and spin-orbit coupling. In the course of the computational treatment, the utility and limitations of a formal two-state model that describes this competition between couplings are illustrated, and the implications of our results for the chemical reactivity of these states are discussed.
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Affiliation(s)
- Ajay Sharma
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Michael Roemelt
- Max-Planck Institut für Chemische Energiekonversion , Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany.,Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum , D-44780 Bochum, Germany.,Max-Planck Institut für Kohlenforschung , Kaiser-Wilhelm Platz1, D-45470 Mülheim an der Ruhr, Germany
| | - Michael Reithofer
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Richard R Schrock
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University , Evanston, Illinois 60208, United States
| | - Frank Neese
- Max-Planck Institut für Chemische Energiekonversion , Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
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4
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Horitani M, Offenbacher AR, Carr CAM, Yu T, Hoeke V, Cutsail GE, Hammes-Schiffer S, Klinman JP, Hoffman BM. 13C ENDOR Spectroscopy of Lipoxygenase-Substrate Complexes Reveals the Structural Basis for C-H Activation by Tunneling. J Am Chem Soc 2017; 139:1984-1997. [PMID: 28121140 PMCID: PMC5322796 DOI: 10.1021/jacs.6b11856] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Indexed: 12/20/2022]
Abstract
In enzymatic C-H activation by hydrogen tunneling, reduced barrier width is important for efficient hydrogen wave function overlap during catalysis. For native enzymes displaying nonadiabatic tunneling, the dominant reactive hydrogen donor-acceptor distance (DAD) is typically ca. 2.7 Å, considerably shorter than normal van der Waals distances. Without a ground state substrate-bound structure for the prototypical nonadiabatic tunneling system, soybean lipoxygenase (SLO), it has remained unclear whether the requisite close tunneling distance occurs through an unusual ground state active site arrangement or by thermally sampling conformational substates. Herein, we introduce Mn2+ as a spin-probe surrogate for the SLO Fe ion; X-ray diffraction shows Mn-SLO is structurally faithful to the native enzyme. 13C ENDOR then reveals the locations of 13C10 and reactive 13C11 of linoleic acid relative to the metal; 1H ENDOR and molecular dynamics simulations of the fully solvated SLO model using ENDOR-derived restraints give additional metrical information. The resulting three-dimensional representation of the SLO active site ground state contains a reactive (a) conformer with hydrogen DAD of ∼3.1 Å, approximately van der Waals contact, plus an inactive (b) conformer with even longer DAD, establishing that stochastic conformational sampling is required to achieve reactive tunneling geometries. Tunneling-impaired SLO variants show increased DADs and variations in substrate positioning and rigidity, confirming previous kinetic and theoretical predictions of such behavior. Overall, this investigation highlights the (i) predictive power of nonadiabatic quantum treatments of proton-coupled electron transfer in SLO and (ii) sensitivity of ENDOR probes to test, detect, and corroborate kinetically predicted trends in active site reactivity and to reveal unexpected features of active site architecture.
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Affiliation(s)
- Masaki Horitani
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Adam R. Offenbacher
- Department of Chemistry and California Institute for Quantitative
Biosciences (QB3), Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Cody A. Marcus Carr
- Department of Chemistry and California Institute for Quantitative
Biosciences (QB3), Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Tao Yu
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Veronika Hoeke
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - George E. Cutsail
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Sharon Hammes-Schiffer
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Judith P. Klinman
- Department of Chemistry and California Institute for Quantitative
Biosciences (QB3), Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Brian M. Hoffman
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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5
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Cutsail GE, Telser J, Hoffman BM. Advanced paramagnetic resonance spectroscopies of iron-sulfur proteins: Electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM). BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1853:1370-94. [PMID: 25686535 DOI: 10.1016/j.bbamcr.2015.01.025] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 01/29/2015] [Accepted: 01/29/2015] [Indexed: 12/20/2022]
Abstract
The advanced electron paramagnetic resonance (EPR) techniques, electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) spectroscopies, provide unique insights into the structure, coordination chemistry, and biochemical mechanism of nature's widely distributed iron-sulfur cluster (FeS) proteins. This review describes the ENDOR and ESEEM techniques and then provides a series of case studies on their application to a wide variety of FeS proteins including ferredoxins, nitrogenase, and radical SAM enzymes. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.
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Affiliation(s)
- George E Cutsail
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Joshua Telser
- Department of Biological, Chemical and Physical Sciences, Roosevelt University, Chicago, IL 60605, USA
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA.
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6
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Tseitlin M, Yu Z, Quine RW, Rinard GA, Eaton SS, Eaton GR. Digitally generated excitation and near-baseband quadrature detection of rapid scan EPR signals. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2014; 249:126-134. [PMID: 25462956 PMCID: PMC4416072 DOI: 10.1016/j.jmr.2014.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 10/15/2014] [Accepted: 10/15/2014] [Indexed: 05/26/2023]
Abstract
The use of multiple synchronized outputs from an arbitrary waveform generator (AWG) provides the opportunity to perform EPR experiments differently than by conventional EPR. We report a method for reconstructing the quadrature EPR spectrum from periodic signals that are generated with sinusoidal magnetic field modulation such as continuous wave (CW), multiharmonic, or rapid scan experiments. The signal is down-converted to an intermediate frequency (IF) that is less than the field scan or field modulation frequency and then digitized in a single channel. This method permits use of a high-pass analog filter before digitization to remove the strong non-EPR signal at the IF, that might otherwise overwhelm the digitizer. The IF is the difference between two synchronized X-band outputs from a Tektronix AWG 70002A, one of which is for excitation and the other is the reference for down-conversion. To permit signal averaging, timing was selected to give an exact integer number of full cycles for each frequency. In the experiments reported here the IF was 5kHz and the scan frequency was 40kHz. To produce sinusoidal rapid scans with a scan frequency eight times IF, a third synchronized output generated a square wave that was converted to a sine wave. The timing of the data acquisition with a Bruker SpecJet II was synchronized by an external clock signal from the AWG. The baseband quadrature signal in the frequency domain was reconstructed. This approach has the advantages that (i) the non-EPR response at the carrier frequency is eliminated, (ii) both real and imaginary EPR signals are reconstructed from a single physical channel to produce an ideal quadrature signal, and (iii) signal bandwidth does not increase relative to baseband detection. Spectra were obtained by deconvolution of the reconstructed signals for solid BDPA (1,3-bisdiphenylene-2-phenylallyl) in air, 0.2mM trityl OX63 in water, 15N perdeuterated tempone, and a nitroxide with a 0.5G partially-resolved proton hyperfine splitting.
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Affiliation(s)
- Mark Tseitlin
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Zhelin Yu
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Richard W Quine
- School of Engineering and Computer Science, University of Denver, Denver, CO 80210, USA
| | - George A Rinard
- School of Engineering and Computer Science, University of Denver, Denver, CO 80210, USA
| | - Sandra S Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA
| | - Gareth R Eaton
- Department of Chemistry and Biochemistry, University of Denver, Denver, CO 80210, USA.
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7
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Cutsail III G, Stein BW, Subedi D, Smith JM, Kirk ML, Hoffman BM. EPR, ENDOR, and electronic structure studies of the Jahn-Teller distortion in an Fe(V) nitride. J Am Chem Soc 2014; 136:12323-36. [PMID: 25137531 PMCID: PMC4156863 DOI: 10.1021/ja505403j] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Indexed: 01/26/2023]
Abstract
The recently synthesized and isolated low-coordinate Fe(V) nitride complex has numerous implications as a model for high-oxidation states in biological and industrial systems. The trigonal [PhB((t)BuIm)3Fe(V)≡N](+) (where (PhB((t)BuIm)3(-) = phenyltris(3-tert-butylimidazol-2-ylidene)), (1) low-spin d(3) (S = 1/2) coordination compound is subject to a Jahn-Teller (JT) distortion of its doubly degenerate (2)E ground state. The electronic structure of this complex is analyzed by a combination of extended versions of the formal two-orbital pseudo Jahn-Teller (PJT) treatment and of quantum chemical computations of the PJT effect. The formal treatment is extended to incorporate mixing of the two e orbital doublets (30%) that results from a lowering of the idealized molecular symmetry from D3h to C3v through strong "doming" of the Fe-C3 core. Correspondingly we introduce novel DFT/CASSCF computational methods in the computation of electronic structure, which reveal a quadratic JT distortion and significant e-e mixing, thus reaching a new level of synergism between computational and formal treatments. Hyperfine and quadrupole tensors are obtained by pulsed 35 GHz ENDOR measurements for the (14/15)N-nitride and the (11)B axial ligands, and spectra are obtained from the imidazole-2-ylidene (13)C atoms that are not bound to Fe. Analysis of the nitride ENDOR tensors surprisingly reveals an essentially spherical nitride trianion bound to Fe, with negative spin density and minimal charge density anisotropy. The four-coordinate (11)B, as expected, exhibits negligible bonding to Fe. A detailed analysis of the frontier orbitals provided by the electronic structure calculations provides insight into the reactivity of 1: JT-induced symmetry lowering provides an orbital selection mechanism for proton or H atom transfer reactivity.
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Affiliation(s)
- George
E. Cutsail III
- Department
of Chemistry Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Benjamin W. Stein
- Department
of Chemistry and Chemical Biology The University
of New Mexico, MSC03 2060, 300 Terrace St. NE, Albuquerque, New Mexico 87131-0001, United States
| | - Deepak Subedi
- Department
of Chemistry and Biochemistry MSC 3C, New
Mexico State University, 1175 North Horseshoe Drive, Las Cruces, New Mexico 88003, United States
| | - Jeremy M. Smith
- Department
of Chemistry and Biochemistry MSC 3C, New
Mexico State University, 1175 North Horseshoe Drive, Las Cruces, New Mexico 88003, United States
| | - Martin L. Kirk
- Department
of Chemistry and Chemical Biology The University
of New Mexico, MSC03 2060, 300 Terrace St. NE, Albuquerque, New Mexico 87131-0001, United States
| | - Brian M. Hoffman
- Department
of Chemistry and Biochemistry MSC 3C, New
Mexico State University, 1175 North Horseshoe Drive, Las Cruces, New Mexico 88003, United States
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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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9
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Lukoyanov D, Dikanov SA, Yang ZY, Barney BM, Samoilova RI, Narasimhulu KV, Dean DR, Seefeldt LC, Hoffman BM. ENDOR/HYSCORE studies of the common intermediate trapped during nitrogenase reduction of N2H2, CH3N2H, and N2H4 support an alternating reaction pathway for N2 reduction. J Am Chem Soc 2011; 133:11655-64. [PMID: 21744838 DOI: 10.1021/ja2036018] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymatic N(2) reduction proceeds along a reaction pathway composed of a sequence of intermediate states generated as a dinitrogen bound to the active-site iron-molybdenum cofactor (FeMo-co) of the nitrogenase MoFe protein undergoes six steps of hydrogenation (e(-)/H(+) delivery). There are two competing proposals for the reaction pathway, and they invoke different intermediates. In the 'Distal' (D) pathway, a single N of N(2) is hydrogenated in three steps until the first NH(3) is liberated, and then the remaining nitrido-N is hydrogenated three more times to yield the second NH(3). In the 'Alternating' (A) pathway, the two N's instead are hydrogenated alternately, with a hydrazine-bound intermediate formed after four steps of hydrogenation and the first NH(3) liberated only during the fifth step. A recent combination of X/Q-band EPR and (15)N, (1,2)H ENDOR measurements suggested that states trapped during turnover of the α-70(Ala)/α-195(Gln) MoFe protein with diazene or hydrazine as substrate correspond to a common intermediate (here denoted I) in which FeMo-co binds a substrate-derived [N(x)H(y)] moiety, and measurements reported here show that turnover with methyldiazene generates the same intermediate. In the present report we describe X/Q-band EPR and (14/15)N, (1,2)H ENDOR/HYSCORE/ESEEM measurements that characterize the N-atom(s) and proton(s) associated with this moiety. The experiments establish that turnover with N(2)H(2), CH(3)N(2)H, and N(2)H(4) in fact generates a common intermediate, I, and show that the N-N bond of substrate has been cleaved in I. Analysis of this finding leads us to conclude that nitrogenase reduces N(2)H(2), CH(3)N(2)H, and N(2)H(4) via a common A reaction pathway, and that the same is true for N(2) itself, with Fe ion(s) providing the site of reaction.
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Affiliation(s)
- Dmitriy Lukoyanov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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10
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Hunsicker-Wang L, Vogt M, Derose VJ. EPR methods to study specific metal-ion binding sites in RNA. Methods Enzymol 2009; 468:335-67. [PMID: 20946777 DOI: 10.1016/s0076-6879(09)68016-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The properties of metal-ion interactions with RNA can be explored by spectroscopic methods. In this chapter, we describe the use of paramagnetic Mn(2+) ions and electron paramagnetic resonance (EPR)-based techniques to monitor the association of Mn(2+) with RNA and related nucleotides. Solution EPR methods are used to determine the numbers of Mn(2+) ions associating with RNA. For RNA poised with a single-bound Mn(2+), low-temperature EPR characteristics provide information about the asymmetry of the Mn(2+) coordination site. To identify the RNA groups coordinating to the Mn(2+) ion, ENDOR (electron nuclear double resonance) and ESEEM (electron spin echo envelope modulation) methods are applied. Both continuous-wave (CW) and electron spin echo (ESE)-detected ENDOR methods are described. This chapter includes practical details for RNA sample preparation, including isotope substitution and cryoprotection, and an overview of data acquisition and analysis methods used in these techniques, as well as examples from the current literature.
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11
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Lees NS, McNaughton RL, Gregory WV, Holland PL, Hoffman BM. ENDOR Characterization of a Synthetic Diiron Hydrazido Complex as a Model for Nitrogenase Intermediates. J Am Chem Soc 2007; 130:546-55. [DOI: 10.1021/ja073934x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nicholas S. Lees
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 and Department of Chemistry, University of Rochester, RC Box 270216, Rochester, New York 14627-0216
| | - Rebecca L. McNaughton
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 and Department of Chemistry, University of Rochester, RC Box 270216, Rochester, New York 14627-0216
| | - Wilda Vargas Gregory
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 and Department of Chemistry, University of Rochester, RC Box 270216, Rochester, New York 14627-0216
| | - Patrick L. Holland
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 and Department of Chemistry, University of Rochester, RC Box 270216, Rochester, New York 14627-0216
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208 and Department of Chemistry, University of Rochester, RC Box 270216, Rochester, New York 14627-0216
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12
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Lukoyanov D, Pelmenschikov V, Maeser N, Laryukhin M, Yang TC, Noodleman L, Dean DR, Case DA, Seefeldt LC, Hoffman BM. Testing if the Interstitial Atom, X, of the Nitrogenase Molybdenum−Iron Cofactor Is N or C: ENDOR, ESEEM, and DFT Studies of the S = 3/2 Resting State in Multiple Environments. Inorg Chem 2007; 46:11437-49. [DOI: 10.1021/ic7018814] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dmitriy Lukoyanov
- Department of Chemistry, Northwestern University, 2145 N. Sheridan Road, Evanston, Illinois 60208-3113, Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322-0300, and The Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0002
| | - Vladimir Pelmenschikov
- Department of Chemistry, Northwestern University, 2145 N. Sheridan Road, Evanston, Illinois 60208-3113, Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322-0300, and The Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0002
| | - Nathan Maeser
- Department of Chemistry, Northwestern University, 2145 N. Sheridan Road, Evanston, Illinois 60208-3113, Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322-0300, and The Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0002
| | - Mikhail Laryukhin
- Department of Chemistry, Northwestern University, 2145 N. Sheridan Road, Evanston, Illinois 60208-3113, Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322-0300, and The Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0002
| | - Tran Chin Yang
- Department of Chemistry, Northwestern University, 2145 N. Sheridan Road, Evanston, Illinois 60208-3113, Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322-0300, and The Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0002
| | - Louis Noodleman
- Department of Chemistry, Northwestern University, 2145 N. Sheridan Road, Evanston, Illinois 60208-3113, Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322-0300, and The Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0002
| | - Dennis R. Dean
- Department of Chemistry, Northwestern University, 2145 N. Sheridan Road, Evanston, Illinois 60208-3113, Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322-0300, and The Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0002
| | - David A. Case
- Department of Chemistry, Northwestern University, 2145 N. Sheridan Road, Evanston, Illinois 60208-3113, Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322-0300, and The Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0002
| | - Lance C. Seefeldt
- Department of Chemistry, Northwestern University, 2145 N. Sheridan Road, Evanston, Illinois 60208-3113, Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322-0300, and The Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0002
| | - Brian M. Hoffman
- Department of Chemistry, Northwestern University, 2145 N. Sheridan Road, Evanston, Illinois 60208-3113, Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322-0300, and The Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061-0002
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13
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Lees NS, Chen D, Walsby CJ, Behshad E, Frey PA, Hoffman BM. How an Enzyme Tames Reactive Intermediates: Positioning of the Active-Site Components of Lysine 2,3-Aminomutase during Enzymatic Turnover As Determined by ENDOR Spectroscopy. J Am Chem Soc 2006; 128:10145-54. [PMID: 16881644 DOI: 10.1021/ja061282r] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lysine 2,3-aminomutase (LAM) utilizes a [4Fe-4S] cluster, S-adenosyl-L-methionine (SAM), and pyridoxal 5'-phosphate (PLP) to isomerize L-alpha-lysine to L-beta-lysine. LAM is a member of the radical-SAM enzyme superfamily in which a [4Fe-4S]+ cluster reductively cleaves SAM to produce the 5'-deoxyadenosyl radical, which abstracts an H-atom from substrate to form 5'-deoxyadenosine (5'-Ado) and the alpha-Lys* radical (state 3 (Lys*)). This radical isomerizes to the beta-Lys* radical (state 4(Lys*)), which then abstracts an H-atom from 5'-Ado to form beta-lysine and the 5'-deoxyadenosyl radical; the latter then regenerates SAM. We use 13C, 1,2H, 31P, and 14N ENDOR to characterize the active site of LAM in intermediate states that contain the isomeric substrate radicals or analogues. With L-alpha-lysine as substrate, we monitor the state with beta-Lys*. In parallel, we use two substrate analogues that generate stable analogues of the alpha-Lys* radical: trans-4,5-dehydro-L-lysine (DHLys) and 4-thia-L-lysine (SLys). This first glimpse of the motions of active-site components during catalytic turnover suggests a possible major movement of PLP during catalysis. However, the principal focus of this work is on the relative positions of the carbons involved in H-atom transfer. We conclude that the active site facilitates hydrogen atom transfer by enforcing van der Waals contact between radicals and their reacting partners. This constraint enables the enzyme to minimize and even eliminate side reactions of highly reactive species such as the 5'-deoxyadensosyl radical.
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Affiliation(s)
- Nicholas S Lees
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, USA
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14
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Yang TC, Wolfe MD, Neibergall MB, Mekmouche Y, Lipscomb JD, Hoffman BM. Substrate binding to NO-ferro-naphthalene 1,2-dioxygenase studied by high-resolution Q-band pulsed 2H-ENDOR spectroscopy. J Am Chem Soc 2003; 125:7056-66. [PMID: 12783560 DOI: 10.1021/ja0214126] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The active site of naphthalene 1,2-dioxygenase (NDO) contains a Rieske Fe-S cluster and a mononuclear non-heme iron, which are contributed by different alpha-subunits in the (alphabeta)(3) structure. The enzyme catalyzes cis-dihydroxylation of aromatic substrates, in addition to numerous other adventitious oxidation reactions. High-resolution Mims (2)H-ENDOR (electron nuclear double resonance) spectra have been recorded for the NO-ferrous center of NDO bound with the substrates d(8)-naphthalene, d(2)-naphthalene, d(8)-toluene, d(3)-toluene, and d(6)-benzene; samples were prepared in a D(2)O buffer to test for solvent-derived ligands; spectra were collected for enzymes with the Rieske diiron center in both its oxidized and reduced states. A sharp quartet ENDOR pattern from a nearby deuteron of the substrate in a major binding geometry (denoted as A) was detected for all perdeuterated substrates. Examination of the sample prepared with 1,4-di-deutero-naphthalene shows that the signal arises from D1. Analysis of two-dimensional (2-D) orientation-selective ENDOR patterns collected for this sample defined the location of the D1 deuteron, with respect to the g-frame of the iron center and the orientation of the C-D1 bond. Consideration of the orientations of naphthalene that are permitted within the constraints of these results, as supported by a novel approach to simulations of orientation-selective, 2-D ENDOR patterns for the perdeuterated naphthalene sample, which summed contributions from D1/D2/D8, disclose the geometry of the naphthalene and the Fe-NO fragment. The two deuterons of the reactive carbons, D1 and D2, are closest to the Fe atom (r(Fe)(-)(D1) approximately 4.3 A, r(Fe)(-)(D2) approximately 5.0 A), whereas D8 is farther away (r(Fe)(-)(D8) approximately 5.3 A). Perhaps more instructive, D1-N and D2-N distances to the O(2) surrogate, NO, are approximately 2.4 and approximately 3.3 A, respectively, whereas the D8-N distance is approximately 3.7 A. The data show that benzene and the aromatic ring of toluene also sit within the substrate-binding pocket adjacent to the mononuclear Fe atom. These rings occupy a position similar to that of the "proximal" ring of naphthalene, with the closest ring deuteron being located at a distance of approximately 4.3-4.4 A from the Fe atom and with the Fe-D vector being slightly off the Fe-N(O) direction. In particular, comparison of the data for d(8)-toluene and methyl-d(3)-toluene shows that the methyl group of toluene points away from the Fe atom, despite observations that the oxidation of toluene occurs at the methyl group during catalysis. The Rieske cluster is reduced during both steady-state and single-turnover catalysis; therefore, the effect of its oxidation state on the geometry of substrate binding was examined. The spectra from the NDO-naphthalene complex also revealed a second binding conformation (denoted as B), in which the substrate is located approximately 0.5 A farther from the Fe atom. The relative populations of A- and B-sites are allosterically changed when the Rieske cluster is reduced. ENDOR of exchangeable protons shows that the water/hydroxide of Fe-NDO is retained upon binding NO.
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Affiliation(s)
- Tran Chin Yang
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, USA
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15
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Hoffman BM. Electron-nuclear double resonance spectroscopy (and electron spin-echo envelope modulation spectroscopy) in bioinorganic chemistry. Proc Natl Acad Sci U S A 2003; 100:3575-8. [PMID: 12642664 PMCID: PMC152963 DOI: 10.1073/pnas.0636464100] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This perspective discusses the ways that advanced paramagnetic resonance techniques, namely electron-nuclear double resonance (ENDOR) and electron spin-echo envelope modulation (ESEEM) spectroscopies, can help us understand how metal ions function in biological systems.
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Affiliation(s)
- Brian M Hoffman
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, USA.
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16
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Katterle B, Gvozdev RI, Abudu N, Ljones T, Andersson KK. A continuous-wave electron-nuclear double resonance (X-band) study of the Cu2+ sites of particulate methane mono-oxygenase of Methylococcus capsulatus (strain M) in membrane and pure dopamine beta-mono-oxygenase of the adrenal medulla. Biochem J 2002; 363:677-86. [PMID: 11964168 PMCID: PMC1222520 DOI: 10.1042/0264-6021:3630677] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
All methanotrophic bacteria express a membrane-bound (particulate) methane mono-oxygenase (pMMO). In the present study, we have investigated pMMO in membrane fragments from Methylococcus capsulatus (strain M). pMMO contains a typical type-2 Cu(2+) centre with the following EPR parameters: g(z) 2.24, g(x,y) 2.06, A(Cu)(z) 19.0 mT and A(Cu)(x,y) 1.0 mT. Simulation of the Cu(2+) spectrum yielded a best match by using four equivalent nitrogens (A(N)=1.5 mT, 42 MHz). Incubation with ferricyanide neither changed nor increased the amount of EPR-active Cu(2+), in contrast with other reports. The EPR visible copper seems not to be part of any cluster, as judged from the microwave power saturation behaviour. Continuous-wave electron-nuclear double resonance (CW ENDOR; 9.4 GHz, 5-20 K) experiments at g( perpendicular) of the Cu(II) spectrum show a weak coupling to protons with an A(H) of 2.9 MHz that corresponds to a distance of 3.8 A (1 A identical with 0.1 nm), assuming that it is a purely dipolar coupling. Incubation in (2)H(2)O leads to a significant decrease in these (1)H-ENDOR intensities, showing that these protons are exchangeable. This result strongly suggests that the EPR visible copper site of pMMO is accessible to solvent, which was confirmed by the chelation of the Cu(2+) by diethyldithiocarbamic acid. The (1)H and (14)N hyperfine coupling constants confirm a histidine ligation of the EPR visible copper site in pMMO. The hyperfine structure in the ENDOR or EPR spectra of pMMO is not influenced by the inhibitors azide, cyanide or ammonia, indicating that they do not bind to the EPR visible copper. We compared pMMO with the type-2 Cu(2+) enzyme, dopamine beta-mono-oxygenase (DbetaM). For DbetaM, it is assumed that the copper site is solvent-accessible. CW ENDOR shows similar weakly coupled and (2)H(2)O-exchangeable protons (2.9 MHz), as observed in pMMO, as well as the strongly coupled nitrogens (40 MHz) from the co-ordinating N of the histidines in DbetaM. In conclusion, the resting EPR visible Cu in pMMO is not part of a trinuclear cluster, as has been suggested previously.
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Affiliation(s)
- Bettina Katterle
- Department of Biochemistry, University of Oslo, P.O. Box 1041 Blindern, N-0316 Oslo, Norway
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17
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Smoukov SK, Kopp DA, Valentine AM, Davydov R, Lippard SJ, Hoffman BM. Product binding to the diiron(III) and mixed-valence diiron centers of methane monooxygenase hydroxylase studied by (1,2)H and (19)F ENDOR spectroscopy. J Am Chem Soc 2002; 124:2657-63. [PMID: 11890816 DOI: 10.1021/ja010123z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The binding of ethanol and 1,1,1-trifluoroethanol (TFE) to both the H(mv) and H(ox) forms of soluble methane monooxygenase (sMMO) in solution has been studied by Q-band (35 GHz) CW and pulsed ENDOR spectroscopy of (1)H, (2)H and (19)F nuclei of exogenous ligands. As part of this investigation we introduce (19)F, in this case from bound TFE, as a new probe for the binding of small molecules to a metalloenzyme active site. The H(mv) form was prepared in solution by chemical reduction of H(ox). For study of H(ox) itself, frozen solutions were subjected to gamma-irradiation in the frozen solution state at 77 K, which affords an EPR-visible mixed-valent diiron center, denoted (H(ox))(mv), held in the geometry of the diiron(III) state. The (19)F and (2)H ENDOR spectra of bound TFE together with (1,2)H ENDOR spectra of bound ethanol indicate that the alcohols bind close to the Fe(II) ion of the mixed-valence cluster in H(mv) and in a bridging or semi-bridging fashion to H(ox). DMSO does not affect the binding of either of the ethanols or of methanol to H(ox), nor of ethanol or methanol to H(mv). It does, however, displace TFE from the diiron site in H(mv). These results provide the first evidence that crystal structures of sMMO hydroxylase into which product alcohols were introduced by diffusion represent the structures in solution.
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Affiliation(s)
- Stoyan K Smoukov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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18
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Smoukov SK, Quaroni L, Wang X, Doan PE, Hoffman BM, Que L. Electro-nuclear double resonance spectroscopic evidence for a hydroxo-bridge nucleophile involved in catalysis by a dinuclear hydrolase. J Am Chem Soc 2002; 124:2595-603. [PMID: 11890810 DOI: 10.1021/ja003169l] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite the current availability of several crystal structures of purple acid phosphatases, to date there is no direct evidence for solvent-derived ligands occupying terminal positions in the active enzyme. This is of central importance, because catalysis has been shown to proceed through the direct attack on a metal-bound phosphate ester by a metal-activated solvent-derived moiety, which has been proposed to be either (i) a hydroxide ligand terminally bound to the ferric center or (ii) a bridging hydroxide. In this work we use (2)H Q-band (35 GHz) pulsed electron-nuclear double resonance (ENDOR) spectroscopy to identify solvent molecules coordinated to the active mixed-valence (Fe(3+)Fe(2+)) form of the dimetal center of uteroferrin (Uf), as well as to its complexes with the anions MoO(4), AsO(4), and PO(4). The solvent-derived coordination of the dinuclear center of Uf as deduced from ENDOR data includes a bridging hydroxide and a terminal water/hydroxide bound to Fe(2+) but no terminal water/hydroxide bound to Fe(3+). The terminal water is lost upon anion binding while the hydroxyl bridge remains. These results are not compatible with a hydrolysis mechanism involving a terminal Fe(3+)-bound nucleophile, but they are consistent with a mechanism that relies on the bridging hydroxide as the nucleophile.
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Affiliation(s)
- Stoyan K Smoukov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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19
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Eaton SS, Eaton GR. Relaxation Times of Organic Radicals and Transition Metal Ions. DISTANCE MEASUREMENTS IN BIOLOGICAL SYSTEMS BY EPR 2002. [DOI: 10.1007/0-306-47109-4_2] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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20
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Nissen LR, Månsson L, Bertelsen G, Huynh-Ba T, Skibsted LH. Protection of dehydrated chicken meat by natural antioxidants as evaluated by electron spin resonance spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2000; 48:5548-5556. [PMID: 11087517 DOI: 10.1021/jf0003552] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Dehydrated chicken meat (a(w) = 0.20-0.35) made from mechanically deboned chicken necks can be protected against oxidative deterioration during storage by rosemary extract (at a sensory acceptable level of 1000 ppm, incorporated prior to drying). The efficiency of the rosemary extract was similar to that obtained by synthetic antioxidants in a reference product (70 ppm butylated hydroxyanisole and 70 ppm octyl gallate). Tea extract and coffee extract were less efficient than rosemary and synthetic antioxidants. Among the natural antioxidants tested, grape skin extract provided the least protection against oxidative changes in dehydrated chicken meat. Radicals in the product, quantified by direct measurement by electron spin resonance (ESR) spectrometry, developed similarly to headspace ethane, pentane, and hexanal, and to oxygen depletion both in unprotected and protected products. The ESR signal intensity and headspace hexanal both correlated with the sensory descriptor "rancidity" as evaluated by a trained sensory panel. Hexanal, as a secondary lipid oxidation product, showed an exponential dependence on the level of radicals in the product in agreement with a chain reaction mechanism for autoxidation, and direct ESR measurement may be used in quality control of dehydrated food products.
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Affiliation(s)
- L R Nissen
- Food Chemistry, Department of Dairy and Food Science, Royal Veterinary and Agricultural University, Rolighedsvej 30, DK-1958 Frederiksberg C, Denmark
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21
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Jeschke G. Structure Characterization of the Copper(II) Complex of Poly(4-vinylpyridine) by a Combination of EPR, ENDOR, and Molecular Modeling Techniques. J Phys Chem B 2000. [DOI: 10.1021/jp000256r] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gunnar Jeschke
- Max-Planck-Institut für Polymerforschung, Postfach 3148, D-55021 Mainz, Germany
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22
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Davydov RM, Yoshida T, Ikeda-Saito M, Hoffman BM. Hydroperoxy-Heme Oxygenase Generated by Cryoreduction Catalyzes the Formation of α-meso-Hydroxyheme as Detected by EPR and ENDOR. J Am Chem Soc 1999. [DOI: 10.1021/ja992425v] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Lee HI, Doan PE, Hoffman BM. General analysis of (14)N (I = 1) electron spin echo envelope modulation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1999; 140:91-107. [PMID: 10479552 DOI: 10.1006/jmre.1999.1803] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The analysis methods described to date for (14)N electron spin echo envelope modulation (ESEEM) mostly deal with isotropic g- and (14)N hyperfine coupling tensors. However, many cases of rhombic tensors are encountered. In the present report we present general equations for analyzing orientation-selective ESEEM and illustrate their use. (i) We present general equations for the nuclear interactions in an electron spin system where the EPR signal arises from an isolated Kramers doublet, then give the nuclear (electron-nuclear double resonance) frequencies for I = 1 associated with such a system. (ii) These are incorporated into equations for single-crystal ESEEM amplitudes, which in turn are incorporated into general equations for the orientation-selective ESEEM that arises when the EPR envelope of a frozen-solution (powder) sample is determined by g anisotropy. (iii) This development is first used in the simplest limit of an isotropic g-tensor and leads to a more general picture of the response of the I = 1 modulation amplitude to variations in the nuclear hyperfine and quadrupole coupling constants, relative to the nuclear Zeeman interaction, than had been presented previously. We find that strong modulation occurs not only in the well-known regime where the "exact/near cancellation" condition (A/2 approximately nu(N)) is satisfied, but also when the nuclear hyperfine interaction is much larger than the nuclear Zeeman interaction (A/nu(N) > 3) with A/K = 4 approximately 5. (iv) We then describe the orientation-selective (14)N ESEEM frequency-domain patterns (g vs frequency) in the presence of anisotropic (rhombic) hyperfine and electron Zeeman interactions for both coaxial and noncoaxial cases. We derive analytical solutions when the g-, hyperfine, and nuclear quadrupole tensors are coaxial. (v) The method is applied to the ESEEM of the nitrogenase MoFe protein (Av1) to determine the full hyperfine and nuclear quadrupole tensors of (14)N nuclei interacting with the S = 32 FeMo-cofactor (Fe(7)S(8)Mo: homocitrate).
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Affiliation(s)
- H I Lee
- Department of Chemistry, Northwestern University, Evanston, Illinois, 60208, USA
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24
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Jeschke G, Mandelshtam VA, Shaka AJ. Pure absorption electron spin echo envelope modulation spectra by using the filter-diagonalization method for harmonic inversion. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 1999; 137:221-230. [PMID: 10053151 DOI: 10.1006/jmre.1998.1658] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Harmonic inversion of electron spin echo envelope (ESEEM) time-domain signals by filter diagonalization is investigated as an alternative to Fourier transformation. It is demonstrated that this method features enhanced resolution compared to Fourier-transform magnitude spectra, since it can eliminate dispersive contributions to the line shape, even if no linear phase correction is possible. Furthermore, instrumental artifacts can be easily removed from the spectra if they are narrow either in time or frequency domain. This applies to echo crossings that are only incompletely eliminated by phase cycling and to spurious spectrometer frequencies, respectively. The method is computationally efficient and numerically stable and does not require extensive parameter adjustments or advance knowledge of the number of spectral lines. Experiments on gamma-irradiated methyl-alpha-d-glucopyranoside show that more information can be obtained from typical ESEEM time-domain signals by filter-diagonalization than by Fourier transformation.
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Affiliation(s)
- G Jeschke
- Max-Planck-Institut für Polymerforschung, Mainz, 55028, Germany.
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25
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Willems JP, Valentine AM, Gurbiel R, Lippard SJ, Hoffman BM. Small Molecule Binding to the Mixed-Valent Diiron Center of Methane Monooxygenase Hydroxylase from Methylococcus capsulatus (Bath) as Revealed by ENDOR Spectroscopy. J Am Chem Soc 1998. [DOI: 10.1021/ja980795y] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jean-Paul Willems
- Contribution from the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307
| | - Ann M. Valentine
- Contribution from the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307
| | - Ryszard Gurbiel
- Contribution from the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307
| | - Stephen J. Lippard
- Contribution from the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307
| | - Brian M. Hoffman
- Contribution from the Department of Chemistry, Northwestern University, Evanston, Illinois 60208-3113, and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307
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26
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DeRose VJ, Telser J, Anderson ME, Lindahl PA, Hoffman BM. A Multinuclear ENDOR Study of the C-Cluster in CO Dehydrogenase from Clostridium thermoaceticum: Evidence for HxO and Histidine Coordination to the [Fe4S4] Center. J Am Chem Soc 1998. [DOI: 10.1021/ja9731480] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Victoria J. DeRose
- Contribution from the Departments of Chemistry, Texas A&M University, College Station, Texas 77842-3012, and Northwestern University, Evanston, Illinois 60208-3113
| | - Joshua Telser
- Contribution from the Departments of Chemistry, Texas A&M University, College Station, Texas 77842-3012, and Northwestern University, Evanston, Illinois 60208-3113
| | - Mark E. Anderson
- Contribution from the Departments of Chemistry, Texas A&M University, College Station, Texas 77842-3012, and Northwestern University, Evanston, Illinois 60208-3113
| | - Paul A. Lindahl
- Contribution from the Departments of Chemistry, Texas A&M University, College Station, Texas 77842-3012, and Northwestern University, Evanston, Illinois 60208-3113
| | - Brian M. Hoffman
- Contribution from the Departments of Chemistry, Texas A&M University, College Station, Texas 77842-3012, and Northwestern University, Evanston, Illinois 60208-3113
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27
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Huyett JE, Carepo M, Pamplona A, Franco R, Moura I, Moura JJG, Hoffman BM. 57Fe Q-Band Pulsed ENDOR of the Hetero-Dinuclear Site of Nickel Hydrogenase: Comparison of the NiA, NiB, and NiC States. J Am Chem Soc 1997. [DOI: 10.1021/ja9700919] [Citation(s) in RCA: 73] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. E. Huyett
- Department of Chemistry, Northwestern University Evanston, Illinois 60208-3113 Departamento de Química and Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia Universidade Nova de Lisboa, 2825 Monte de Caparica, Portugal
| | - M. Carepo
- Department of Chemistry, Northwestern University Evanston, Illinois 60208-3113 Departamento de Química and Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia Universidade Nova de Lisboa, 2825 Monte de Caparica, Portugal
| | - A. Pamplona
- Department of Chemistry, Northwestern University Evanston, Illinois 60208-3113 Departamento de Química and Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia Universidade Nova de Lisboa, 2825 Monte de Caparica, Portugal
| | - R. Franco
- Department of Chemistry, Northwestern University Evanston, Illinois 60208-3113 Departamento de Química and Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia Universidade Nova de Lisboa, 2825 Monte de Caparica, Portugal
| | - I. Moura
- Department of Chemistry, Northwestern University Evanston, Illinois 60208-3113 Departamento de Química and Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia Universidade Nova de Lisboa, 2825 Monte de Caparica, Portugal
| | - J. J. G. Moura
- Department of Chemistry, Northwestern University Evanston, Illinois 60208-3113 Departamento de Química and Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia Universidade Nova de Lisboa, 2825 Monte de Caparica, Portugal
| | - B. M. Hoffman
- Department of Chemistry, Northwestern University Evanston, Illinois 60208-3113 Departamento de Química and Centro de Química Fina e Biotecnologia, Faculdade de Ciências e Tecnologia Universidade Nova de Lisboa, 2825 Monte de Caparica, Portugal
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Holm RH, Kennepohl P, Solomon EI. Structural and Functional Aspects of Metal Sites in Biology. Chem Rev 1996; 96:2239-2314. [PMID: 11848828 DOI: 10.1021/cr9500390] [Citation(s) in RCA: 1870] [Impact Index Per Article: 66.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Richard H. Holm
- Departments of Chemistry, Harvard University, Cambridge, Massachusetts 02138, and Stanford University, Stanford, California 94305
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Jeschke G, Schweiger A. Matched two‐pulse electron spin echo envelope modulation spectroscopy. J Chem Phys 1996. [DOI: 10.1063/1.472087] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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