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Van Stappen C, Dai H, Jose A, Tian S, Solomon EI, Lu Y. Primary and Secondary Coordination Sphere Effects on the Structure and Function of S-Nitrosylating Azurin. J Am Chem Soc 2023; 145:20610-20623. [PMID: 37696009 PMCID: PMC10539042 DOI: 10.1021/jacs.3c07399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023]
Abstract
Much progress has been made in understanding the roles of the secondary coordination sphere (SCS) in tuning redox potentials of metalloproteins. In contrast, the impact of SCS on reactivity is much less understood. A primary example is how copper proteins can promote S-nitrosylation (SNO), which is one of the most important dynamic post-translational modifications, and is crucial in regulating nitric oxide storage and transportation. Specifically, the factors that instill CuII with S-nitrosylating capabilities and modulate activity are not well understood. To address this issue, we investigated the influence of the primary and secondary coordination sphere on CuII-catalyzed S-nitrosylation by developing a series of azurin variants with varying catalytic capabilities. We have employed a multidimensional approach involving electronic absorption, S and Cu K-edge XAS, EPR, and resonance Raman spectroscopies together with QM/MM computational analysis to examine the relationships between structure and molecular mechanism in this reaction. Our findings have revealed that kinetic competency is correlated with three balancing factors, namely Cu-S bond strength, Cu spin localization, and relative S(ps) vs S(pp) contributions to the ground state. Together, these results support a reaction pathway that proceeds through the attack of the Cu-S bond rather than electrophilic addition to CuII or radical attack of SCys. The insights gained from this work provide not only a deeper understanding of SNO in biology but also a basis for designing artificial and tunable SNO enzymes to regulate NO and prevent diseases due to SNO dysregulation.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 E 24th St., Austin, Texas 78712, United States
| | - Huiguang Dai
- Department of Chemistry, University of Texas at Austin, 105 E 24th St., Austin, Texas 78712, United States
- Department of Chemistry, University of Urbana-Champaign, Champaign, Illinois 61801, United States
| | - Anex Jose
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States
| | - Shiliang Tian
- Department of Chemistry, University of Urbana-Champaign, Champaign, Illinois 61801, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, United States
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 E 24th St., Austin, Texas 78712, United States
- Department of Chemistry, University of Urbana-Champaign, Champaign, Illinois 61801, United States
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2
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Steiner RA, Dzul SP, Stemmler TL, Harrop TC. Synthesis and Speciation-Dependent Properties of a Multimetallic Model Complex of NiSOD That Exhibits Unique Hydrogen-Bonding. Inorg Chem 2017; 56:2849-2862. [PMID: 28212040 DOI: 10.1021/acs.inorgchem.6b02997] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The complex Na3[{NiII(nmp)}3S3BTAalk)] (1) (nmp2- = deprotonated form of N-(2-mercaptoethyl)picolinamide; H3S3BTAalk = N1,N3,N5-tris(2-mercaptoethyl)benzene-1,3,5-tricarboxamide, where H = dissociable protons), supported by the thiolate-benzenetricarboxamide scaffold (S3BTAalk), has been synthesized as a trimetallic model of nickel-containing superoxide dismutase (NiSOD). X-ray absorption spectroscopy (XAS) and 1H NMR measurements on 1 indicate that the NiII centers are square-planar with N2S2 coordination, and Ni-N and Ni-S distances of 1.95 and 2.16 Å, respectively. Additional evidence from IR indicates the presence of H-bonds in 1 from the approximately -200 cm-1 shift in νNH from free ligand. The presence of H-bonds allows for speciation that is temperature-, concentration-, and solvent-dependent. In unbuffered water and at low temperature, a dimeric complex (1A; λ = 410 nm) that aggregates through intermolecular NH···O═C bonds of BTA units is observed. Dissolution of 1 in pH 7.4 buffer or in unbuffered water at temperatures above 50 °C results in monomeric complex (1M; λ = 367 nm) linked through intramolecular NH···S bonds. DFT computations indicate a low energy barrier between 1A and 1M with nearly identical frontier MOs and Ni-ligand metrics. Notably, 1A and 1M exhibit remarkable stability in protic solvents such as MeOH and H2O, in stark contrast to monometallic [NiII(nmp)(SR)]- complexes. The reactivity of 1 with excess O2, H2O2, and O2•- is species-dependent. IR and UV-vis reveal that 1A in MeOH reacts with excess O2 to yield an S-bound sulfinate, but does not react with O2•-. In contrast, 1M is stable to O2 in pH 7.4 buffer, but reacts with O2•- to yield a putative [NiII(nmp)(O2)]- complex from release of the BTA-thiolate based on EPR.
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Affiliation(s)
- Ramsey A Steiner
- Department of Chemistry and Center for Metalloenzyme Studies, The University of Georgia , 140 Cedar St, Athens, Georgia 30602, United States
| | - Stephen P Dzul
- Departments of Pharmaceutical Sciences, and Biochemistry and Molecular Biology, Wayne State University , Detroit, Michigan 48201, United States
| | - Timothy L Stemmler
- Departments of Pharmaceutical Sciences, and Biochemistry and Molecular Biology, Wayne State University , Detroit, Michigan 48201, United States
| | - Todd C Harrop
- Department of Chemistry and Center for Metalloenzyme Studies, The University of Georgia , 140 Cedar St, Athens, Georgia 30602, United States
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3
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Mittra K, Sengupta K, Singha A, Bandyopadhyay S, Chatterjee S, Rana A, Samanta S, Dey A. Second sphere control of spin state: Differential tuning of axial ligand bonds in ferric porphyrin complexes by hydrogen bonding. J Inorg Biochem 2016; 155:82-91. [DOI: 10.1016/j.jinorgbio.2015.11.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Revised: 10/02/2015] [Accepted: 11/10/2015] [Indexed: 11/16/2022]
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4
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Umadevi P, Senthilkumar L. Metal-interacted histidine dimer: an ETS-NOCV and XANES study. RSC Adv 2016. [DOI: 10.1039/c6ra01264g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have analyzed the metal coordination in a histidine dimer, hydrated with a water molecule, based on the extended transition state scheme with the theory of natural orbitals for chemical valence (ETS-NOCV).
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Affiliation(s)
- P. Umadevi
- Department of Physics
- Bharathiar University
- Coimbatore
- India
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5
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Shearer J, Peck KL, Schmitt JC, Neupane KP. Cysteinate protonation and water hydrogen bonding at the active-site of a nickel superoxide dismutase metallopeptide-based mimic: implications for the mechanism of superoxide reduction. J Am Chem Soc 2014; 136:16009-22. [PMID: 25322331 DOI: 10.1021/ja5079514] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nickel-containing superoxide dismutase (NiSOD) is a mononuclear cysteinate-ligated nickel metalloenzyme that catalyzes the disproportionation of superoxide into dioxygen and hydrogen peroxide by cycling between Ni(II) and Ni(III) oxidation states. All of the ligating residues to nickel are found within the first six residues from the N-terminus, which has prompted several research groups to generate NiSOD metallopeptide-based mimics derived from the first several residues of the NiSOD sequence. To assess the viability of using these metallopeptide-based mimics (NiSOD maquettes) to probe the mechanism of SOD catalysis facilitated by NiSOD, we computationally explored the initial step of the O2(-) reduction mechanism catalyzed by the NiSOD maquette {Ni(II)(SOD(m1))} (SOD(m1) = HCDLP CGVYD PA). Herein we use spectroscopic (S K-edge X-ray absorption spectroscopy, electronic absorption spectroscopy, and circular dichroism spectroscopy) and computational techniques to derive the detailed active-site structure of {Ni(II)(SOD(m1))}. These studies suggest that the {Ni(II)(SOD(m1))} active-site possesses a Ni(II)-S(H(+))-Cys(6) moiety and at least one associated water molecule contained in a hydrogen-bonding interaction to the coordinated Cys(2) and Cys(6) sulfur atoms. A computationally derived mechanism for O2(-) reduction using the formulated active-site structure of {Ni(II)(SOD(m1))} suggests that O2(-) reduction takes place through an apparent initial outersphere hydrogen atom transfer (HAT) from the Ni(II)-S(H(+))-Cys(6) moiety to the O2(-) molecule. It is proposed that the water molecule aids in driving the reaction forward by lowering the Ni(II)-S(H(+))-Cys(6) pK(a). Such a mechanism is not possible in NiSOD itself for structural reasons. These results therefore strongly suggest that maquettes derived from the primary sequence of NiSOD are mechanistically distinct from NiSOD itself despite the similarities in the structure and physical properties of the metalloenzyme vs the NiSOD metallopeptide-based models.
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Affiliation(s)
- Jason Shearer
- Department of Chemistry, University of Nevada, Reno , Reno, Nevada 89557, United States
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6
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Hadt RG, Sun N, Marshall NM, Hodgson KO, Hedman B, Lu Y, Solomon EI. Spectroscopic and DFT studies of second-sphere variants of the type 1 copper site in azurin: covalent and nonlocal electrostatic contributions to reduction potentials. J Am Chem Soc 2012; 134:16701-16. [PMID: 22985400 PMCID: PMC3506006 DOI: 10.1021/ja306438n] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reduction potentials (E(0)) of type 1 (T1) or blue copper (BC) sites in proteins and enzymes with identical first coordination spheres around the redox active copper ion can vary by ~400 mV. Here, we use a combination of low-temperature electronic absorption and magnetic circular dichroism, electron paramagnetic resonance, resonance Raman, and S K-edge X-ray absorption spectroscopies to investigate a series of second-sphere variants--F114P, N47S, and F114N in Pseudomonas aeruginosa azurin--which modulate hydrogen bonding to and protein-derived dipoles nearby the Cu-S(Cys) bond. Density functional theory calculations correlated to the experimental data allow for the fractionation of the contributions to tuning E(0) into covalent and nonlocal electrostatic components. These are found to be significant, comparable in magnitude, and additive for active H-bonds, while passive H-bonds are mostly nonlocal electrostatic in nature. For dipoles, these terms can be additive to or oppose one another. This study provides a methodology for uncoupling covalency from nonlocal electrostatics, which, when coupled to X-ray crystallographic data, distinguishes specific local interactions from more long-range protein/active interactions, while affording further insight into the second-sphere mechanisms available to the protein to tune the E(0) of electron-transfer sites in biology.
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Affiliation(s)
- Ryan G. Hadt
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Ning Sun
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Nicholas M. Marshall
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801
| | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
| | - Yi Lu
- Department of Chemistry, University of Illinois, Urbana-Champaign, Illinois 61801
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA 94025
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7
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Daly SR, Keith JM, Batista ER, Boland KS, Clark DL, Kozimor SA, Martin RL. Sulfur K-edge X-ray Absorption Spectroscopy and Time-Dependent Density Functional Theory of Dithiophosphinate Extractants: Minor Actinide Selectivity and Electronic Structure Correlations. J Am Chem Soc 2012; 134:14408-22. [DOI: 10.1021/ja303999q] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Scott R. Daly
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Jason M. Keith
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Enrique R. Batista
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Kevin S. Boland
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - David L. Clark
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Stosh A. Kozimor
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
| | - Richard L. Martin
- Los Alamos National Laboratory, Los Alamos,
New Mexico 87545, United States
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8
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Lopes LJS, Guerra ACO, Comerlato NM, Turci CC, Ferreira GB. Vibrational and Electronic Spectroscopy of Neutral Antimony Coordination Compounds of the 1,3-Dithiole-2-thione-4,5-dithiolate (dmit). J Phys Chem A 2012; 116:2244-60. [DOI: 10.1021/jp208881g] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Laura J. S. Lopes
- Instituto de Química, Universidade Federal do Rio de Janeiro, CP 68563, 21945-970
Rio de Janeiro, RJ, Brazil
| | - Antonio C. O. Guerra
- Instituto de Química, Universidade Federal do Rio de Janeiro, CP 68563, 21945-970
Rio de Janeiro, RJ, Brazil
| | - Nadia M. Comerlato
- Instituto de Química, Universidade Federal do Rio de Janeiro, CP 68563, 21945-970
Rio de Janeiro, RJ, Brazil
| | - Cássia C. Turci
- Instituto de Química, Universidade Federal do Rio de Janeiro, CP 68563, 21945-970
Rio de Janeiro, RJ, Brazil
| | - Glaucio B. Ferreira
- Instituto de Química, Departamento de Química
Inorgânica, Universidade Federal Fluminense, 24020-150 Niterói, RJ, Brazil
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9
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Gennari M, Gerey B, Hall N, Pécaut J, Vezin H, Collomb MN, Orio M, Duboc C. Structural, spectroscopic and redox properties of a mononuclear CoII thiolate complex – the reactivity toward S-alkylation: an experimental and theoretical study. Dalton Trans 2012; 41:12586-94. [DOI: 10.1039/c2dt31222k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Gennari M, Retegan M, DeBeer S, Pécaut J, Neese F, Collomb MN, Duboc C. Experimental and Computational Investigation of Thiolate Alkylation in NiII and ZnII Complexes: Role of the Metal on the Sulfur Nucleophilicity. Inorg Chem 2011; 50:10047-55. [DOI: 10.1021/ic200899w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Marcello Gennari
- Université Joseph Fourier Grenoble 1/CNRS, Département de Chimie Moléculaire, UMR-5250, Laboratoire de Chimie Inorganique Redox, Institut de Chimie Moléculaire de Grenoble FR, CNRS-2607, BP-53, 38041 Grenoble Cedex 9, France
| | - Marius Retegan
- Université Joseph Fourier Grenoble 1/CNRS, Département de Chimie Moléculaire, UMR-5250, Laboratoire de Chimie Inorganique Redox, Institut de Chimie Moléculaire de Grenoble FR, CNRS-2607, BP-53, 38041 Grenoble Cedex 9, France
| | - Serena DeBeer
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Jacques Pécaut
- Laboratoire de Reconnaissance Ionique et Chimie de Coordination, Service de Chimie Inorganique et Biologique, UMR E-3 CEA/UJF, CNRS, CEA-Grenoble, INAC, 17 Rue des Martyrs 38054 Grenoble Cedex 9, France
| | - Frank Neese
- Institute for Physical and Theoretical Chemistry, Universität Bonn, Wegelerstrasse 12, D-53113 Bonn, Germany
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Marie-Noëlle Collomb
- Université Joseph Fourier Grenoble 1/CNRS, Département de Chimie Moléculaire, UMR-5250, Laboratoire de Chimie Inorganique Redox, Institut de Chimie Moléculaire de Grenoble FR, CNRS-2607, BP-53, 38041 Grenoble Cedex 9, France
| | - Carole Duboc
- Université Joseph Fourier Grenoble 1/CNRS, Département de Chimie Moléculaire, UMR-5250, Laboratoire de Chimie Inorganique Redox, Institut de Chimie Moléculaire de Grenoble FR, CNRS-2607, BP-53, 38041 Grenoble Cedex 9, France
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11
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Gennari M, Orio M, Pécaut J, Bothe E, Neese F, Collomb MN, Duboc C. Influence of Mixed Thiolate/Thioether versus Dithiolate Coordination on the Accessibility of the Uncommon +I and +III Oxidation States for the Nickel Ion: An Experimental and Computational Study. Inorg Chem 2011; 50:3707-16. [DOI: 10.1021/ic200063d] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marcello Gennari
- Université Joseph Fourier Grenoble 1/CNRS, Département de Chimie Moléculaire, UMR-5250, Laboratoire de Chimie Inorganique Redox, Institut de Chimie Moléculaire de Grenoble FR-CNRS-2607, BP-53, 38041 Grenoble Cedex 9, France
| | - Maylis Orio
- Institute for Physical and Theoretical Chemistry Universität Bonn, Wegelerstrasse 12, D-53113 Bonn, Germany
| | - Jacques Pécaut
- Laboratoire de Reconnaissance Ionique et Chimie de Coordination, Service de Chimie Inorganique et Biologique, (UMR E-3 CEA/UJF, FRE3200 CNRS), CEA-Grenoble, INAC, 17 rue des Martyrs 38054, Grenoble cedex 9, France
| | - Eberhard Bothe
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Institute for Physical and Theoretical Chemistry Universität Bonn, Wegelerstrasse 12, D-53113 Bonn, Germany
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstr. 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Marie-Noëlle Collomb
- Université Joseph Fourier Grenoble 1/CNRS, Département de Chimie Moléculaire, UMR-5250, Laboratoire de Chimie Inorganique Redox, Institut de Chimie Moléculaire de Grenoble FR-CNRS-2607, BP-53, 38041 Grenoble Cedex 9, France
| | - Carole Duboc
- Université Joseph Fourier Grenoble 1/CNRS, Département de Chimie Moléculaire, UMR-5250, Laboratoire de Chimie Inorganique Redox, Institut de Chimie Moléculaire de Grenoble FR-CNRS-2607, BP-53, 38041 Grenoble Cedex 9, France
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12
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Hsieh CH, Chupik RB, Brothers SM, Hall MB, Darensbourg MY. cis-Dithiolatonickel as metalloligand to dinitrosyl iron units: the di-metallic structure of Ni(μ-SR)[Fe(NO)2] and an unexpected, abbreviated metalloadamantyl cluster, Ni2(μ-SR)4[Fe(NO)2]3. Dalton Trans 2011; 40:6047-53. [DOI: 10.1039/c1dt10438a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Gale EM, Narendrapurapu BS, Simmonett AC, Schaefer HF, Harrop TC. Exploring the Effects of H-Bonding in Synthetic Analogues of Nickel Superoxide Dismutase (Ni-SOD): Experimental and Theoretical Implications for Protection of the Ni−SCys Bond. Inorg Chem 2010; 49:7080-96. [DOI: 10.1021/ic1009187] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Eric M. Gale
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, 1001 Cedar Street, Athens, Georgia 30602
| | - Beulah S. Narendrapurapu
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, 1001 Cedar Street, Athens, Georgia 30602
| | - Andrew C. Simmonett
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, 1001 Cedar Street, Athens, Georgia 30602
| | - Henry F. Schaefer
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, 1001 Cedar Street, Athens, Georgia 30602
| | - Todd C. Harrop
- Department of Chemistry and Center for Computational Chemistry, University of Georgia, 1001 Cedar Street, Athens, Georgia 30602
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