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Emmler T, Ayala I, Silverman D, Hafner S, Galstyan AS, Knapp EW, Buntkowsky G. Combined NMR and computational study for azide binding to human manganese superoxide dismutase. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2008; 34:6-13. [PMID: 18420387 DOI: 10.1016/j.ssnmr.2008.03.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2007] [Indexed: 05/26/2023]
Abstract
Human manganese superoxide dismutase (MnSOD) labeled with 3-fluorotyrosine (Tyf) was complexed with the (15)N-labeled inhibitor azide ([(15)N(3)(-)]). The sample was characterized by solid-state NMR (SSNMR) spectroscopy ((19)F-MAS and (15)N-CPMAS). Employing (19)F-(15)N-REDOR spectroscopy, we determined the distances between the fluorine label in Tyrosine-34 and the three (15)N-nuclei of the azide and the relative orientation of the azide in the binding pocket of the MnSOD. A distance of R(1)=4.85A between the (19)F-label of Tyf34 and the nearest (15)N of the azide and an azide-fluorotyrosine Tyf34 angle of 90 degrees were determined. These geometry data are employed as input for molecular modeling of the location of the inhibitor in the active site of the enzyme. In the computations, several possible binding geometries of the azide near the Mn-complex were assumed. Only when the azide replaces the water ligand at the Mn-complex we obtained a geometry of the azide-Mn-complex, which is consistent with the present NMR data. This indicates that the water molecule ligating to the Mn-complex is removed and the azide is placed at this position. As a consequence the azide forms an H bond with Gln143 instead with Tyf34, in contrast to non-(19)F-labeled MnSOD, where the azide is hydrogen bonded to the hydroxy group of Tyr34.
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Affiliation(s)
- Th Emmler
- Institut für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3,6 D-14195 Berlin, Germany
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Whittaker MM, Mizuno K, Bächinger HP, Whittaker JW. Kinetic analysis of the metal binding mechanism of Escherichia coli manganese superoxide dismutase. Biophys J 2005; 90:598-607. [PMID: 16258041 PMCID: PMC1367064 DOI: 10.1529/biophysj.105.071308] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The acquisition of a catalytic metal cofactor is an essential step in the maturation of every metalloenzyme, including manganese superoxide dismutase (MnSOD). In this study, we have taken advantage of the quenching of intrinsic protein fluorescence by bound metal ions to continuously monitor the metallation reaction of Escherichia coli MnSOD in vitro, permitting a detailed kinetic characterization of the uptake mechanism. Apo-MnSOD metallation kinetics are "gated", zero order in metal ion for both the native Mn2+ and a nonnative metal ion (Co2+) used as a spectroscopic probe to provide greater sensitivity to metal binding. Cobalt-binding time courses measured over a range of temperatures (35-50 degrees C) reveal two exponential kinetic processes (fast and slow phases) associated with metal binding. The amplitude of the fast phase increases rapidly as the temperature is raised, reflecting the fraction of Apo-MnSOD in an "open" conformation, and its temperature dependence allows thermodynamic parameters to be estimated for the "closed" to "open" conformational transition. The sensitivity of the metallated protein to exogenously added chelator decreases progressively with time, consistent with annealing of an initially formed metalloprotein complex (k anneal = 0.4 min(-1)). A domain-separation mechanism is proposed for metal uptake by apo-MnSOD.
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Affiliation(s)
- Mei M Whittaker
- Department of Environmental and Biomolecular Systems, OGI School of Science and Engineering, Oregon Health and Science University, Beaverton, Oregon 97006, USA
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Jackson TA, Karapetian A, Miller AF, Brunold TC. Probing the Geometric and Electronic Structures of the Low-Temperature Azide Adduct and the Product-Inhibited Form of Oxidized Manganese Superoxide Dismutase. Biochemistry 2005; 44:1504-20. [PMID: 15683235 DOI: 10.1021/bi048639t] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The geometric and electronic structures of the six-coordinate azide adduct of oxidized manganese superoxide dismutase (Mn3+ SOD) that is formed at low temperatures, LT N3-Mn3+ SOD, has been examined in detail through a combined spectroscopic/computational approach. Electronic absorption, circular dichroism (CD), magnetic CD (MCD) and variable-temperature, variable-field (VTVH) MCD spectroscopies were used to determine electronic transition energies and to obtain an estimate of zero-field splitting parameters for LT N3-Mn3+ SOD. These experimental data were utilized in conjunction with semiempirical intermediate neglect of differential overlap/spectroscopic parametrization-configuration interaction (INDO/S-CI) and time-dependent density functional theory (TD-DFT) computations to evaluate hypothetical active-site models of LT N3-Mn3+ SOD generated by constrained DFT geometry optimizations. Collectively, our spectroscopic/computational results indicate that N3- binding to Mn3+ SOD at low temperatures promotes neither protonation of the axial solvent ligand nor reorientation of the redox-active molecular orbital, both of which had been previously suggested. Using the same experimentally validated computational approach, models of the product-inhibited form of MnSOD were also developed and evaluated by their relative energies and TD-DFT-computed absorption spectra. On the basis of our computational results as well as previously published kinetic data, we propose that the product-inhibited form of MnSOD is best described as a side-on peroxo-Mn3+ adduct possessing an axial H2O ligand. Notably, attempts to generate a stable hydroperoxo-Mn3+ SOD species by protonation of the proximal O atom of the hydroperoxo ligand resulted in dissociation of HOO- and eventual H+ transfer from Tyr34 to HOO-, generating deprotonated Tyr34 and H2O2. The implications of these results with respect to the mechanism of O2*- dismutation by MnSOD are discussed.
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Affiliation(s)
- Timothy A Jackson
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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Whittaker MM, Whittaker JW. Thermally triggered metal binding by recombinant Thermus thermophilus manganese superoxide dismutase, expressed as the apo-enzyme. J Biol Chem 1999; 274:34751-7. [PMID: 10574944 DOI: 10.1074/jbc.274.49.34751] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Manganese superoxide dismutase from the extremely thermophilic eubacterium Thermus thermophilus has been cloned and expressed at high levels in a mesophilic host (Escherichia coli) as a soluble tetrameric protein mainly present as the metal-free apo-enzyme. Incubation of the purified apo-enzyme with manganese salts at ambient temperature did not restore superoxide dismutase activity, but reactivation could be achieved by heating the protein with Mn(II) at higher temperatures, approaching the physiological growth temperature for T. thermophilus. Heat annealing followed by incubation with manganese at lower temperature fails to reactivate the enzyme, demonstrating that a simple misfolding of the protein is not responsible for the observed behavior. The in vitro metal uptake is nonspecific, and manganese, iron, and vanadium all bind, but only manganese restores catalytic activity. Bound metal ions do not exchange during heat treatment, indicating that the formation of the metal complex is effectively irreversible under these conditions. The metallation process is strongly temperature-dependent, suggesting that substantial activation barriers to metal uptake at ambient temperature are overcome by a thermal transition in the apo-protein structure. A mechanism for SOD metallation is proposed, focusing on interactions at the domain interface.
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Affiliation(s)
- M M Whittaker
- Department of Biochemistry, Oregon Graduate Institute of Science and Technology, Beaverton, Oregon 97006, USA
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Li J, Fisher CL, Konecny R, Bashford D, Noodleman L. Density Functional and Electrostatic Calculations of Manganese Superoxide Dismutase Active Site Complexes in Protein Environments. Inorg Chem 1999; 38:929-939. [PMID: 11670865 DOI: 10.1021/ic980731o] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional and electrostatic methods have been applied to calculate active site geometries and the redox potential of manganese superoxide dismutase (MnSOD). The initial active site clusters were built up by including only first-shell side chain ligands and then augmented by second-shell ligands. The density functional optimized Mn-ligand bond lengths for the reduced complexes in general compared fairly well with protein crystallography data; however, large deviations for calculated Mn-OH distances were found for the oxidized active site clusters. Our calculations suggest that this deviation can be attributed to the redox heterogeneity of the oxidized protein in X-ray crystallography studies. The redox potential was calculated by treating the protein environment and the solvent bulk by a semimacroscopic electrostatic model. The protein structures were taken from the Thermus thermophilus enzyme. The calculated coupled redox potentials converge toward experimental values with increasing size of the active site cluster models, and the final calculated value was +0.06 V, compared to experimental values of +0.26 V determined for Bacillus stearothermophilus and +0.31 V in Escherichia coli enzymes. Using an energy decomposition scheme, the effects of the second-shell ligands and the protein and reaction fields have been analyzed.
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Affiliation(s)
- Jian Li
- Department of Molecular Biology, TPC-15, The Scripps Research Institute, La Jolla, California 92037
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Whittaker MM, Ekberg CA, Edwards RA, Baker EN, Jameson GB, Whittaker JW. Single Crystal Polarized Spectroscopy of Manganese Superoxide Dismutase and Electronic Structure of the Active Site Metal Complex. J Phys Chem B 1998. [DOI: 10.1021/jp980775i] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mei M. Whittaker
- Department of Biochemistry and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291-1000, School of Biological Sciences, University of Auckland, Auckland, New Zealand, and Department of Chemistry and Biochemistry, Protein Structural Laboratory, Massey University, Palmerston North, New Zealand
| | - Christopher A. Ekberg
- Department of Biochemistry and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291-1000, School of Biological Sciences, University of Auckland, Auckland, New Zealand, and Department of Chemistry and Biochemistry, Protein Structural Laboratory, Massey University, Palmerston North, New Zealand
| | - Ross A. Edwards
- Department of Biochemistry and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291-1000, School of Biological Sciences, University of Auckland, Auckland, New Zealand, and Department of Chemistry and Biochemistry, Protein Structural Laboratory, Massey University, Palmerston North, New Zealand
| | - Edward N. Baker
- Department of Biochemistry and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291-1000, School of Biological Sciences, University of Auckland, Auckland, New Zealand, and Department of Chemistry and Biochemistry, Protein Structural Laboratory, Massey University, Palmerston North, New Zealand
| | - Geoffrey B. Jameson
- Department of Biochemistry and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291-1000, School of Biological Sciences, University of Auckland, Auckland, New Zealand, and Department of Chemistry and Biochemistry, Protein Structural Laboratory, Massey University, Palmerston North, New Zealand
| | - James W. Whittaker
- Department of Biochemistry and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291-1000, School of Biological Sciences, University of Auckland, Auckland, New Zealand, and Department of Chemistry and Biochemistry, Protein Structural Laboratory, Massey University, Palmerston North, New Zealand
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Whittaker MM, Whittaker JW. Mutagenesis of a proton linkage pathway in Escherichia coli manganese superoxide dismutase. Biochemistry 1997; 36:8923-31. [PMID: 9220980 DOI: 10.1021/bi9704212] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Mutagenesis of Escherichia coli manganese superoxide dismutase (MnSD) demonstrates involvement of the strictly conserved gateway tyrosine (Y34) in exogenous ligand interactions. Conservative replacement of this residue by phenylalanine (Y34F) affects the pH sensitivity of the active-site metal ion and perturbs ligand binding, stabilizing a temperature-independent six-coordinate azide complex. Mutant complexes characterized by optical and electron paramagnetic resonance (EPR) spectroscopy are distinct from the corresponding wild-type forms and the anion affinities are altered, consistent with modified basicity of the metal ligands. However, dismutase activity is only slightly reduced by mutagenesis, implying that tyrosine-34 is not essential for catalysis and may function indirectly as a proton donor for turnover, coupled to a protonation cycle of the metal ligands. In vivo substitution of Fe for Mn in the MnSD wild-type and mutant proteins leads to increased affinity for azide and altered active-site properties, shifting the pH-dependent transition of the active site from 9.7 (Mn) to 6.4 (Fe) for wt enzyme. This pH-coupled transition shifts once more to a higher effective pKa for Y34F Fe2-MnSD, allowing the mutant to be catalytically active well into the physiological pH range and decreasing the metal selectivity of the enzyme. Peroxide sensitivities of the Fe complexes are distinct for the wild-type and mutant proteins, indicating a role for Y34 in peroxide interactions. These results provide evidence for a conserved peroxide-protonation linkage pathway in superoxide dismutases, analogous to the proton relay chains of peroxidases, and suggests that the selectivity of Mn and Fe superoxide dismutases is determined by proton coupling with metal ligands.
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Affiliation(s)
- M M Whittaker
- Department of Biochemistry and Molecular Biology, Oregon Graduate Institute of Science and Technology, P.O. Box 91000, Portland, Oregon 97291-1000, USA
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