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Rajbongshi J, Das DK, Mazumdar S. Spectroscopic and electrochemical studies of the pH-Induced transition in the CuA centre from Thermus thermophilus. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2021.120749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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2
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Zhang L, Bill E, Kroneck PMH, Einsle O. Histidine-Gated Proton-Coupled Electron Transfer to the CuA Site of Nitrous Oxide Reductase. J Am Chem Soc 2020; 143:830-838. [DOI: 10.1021/jacs.0c10057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg im Breisgau, Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34-36, D-45470 Mülheim an der Ruhr, Germany
| | | | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104 Freiburg im Breisgau, Germany
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3
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Mirts EN, Dikanov SA, Jose A, Solomon EI, Lu Y. A Binuclear Cu A Center Designed in an All α-Helical Protein Scaffold. J Am Chem Soc 2020; 142:13779-13794. [PMID: 32662996 DOI: 10.1021/jacs.0c04226] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The primary and secondary coordination spheres of metal binding sites in metalloproteins have been investigated extensively, leading to the creation of high-performing functional metalloproteins; however, the impact of the overall structure of the protein scaffold on the unique properties of metalloproteins has rarely been studied. A primary example is the binuclear CuA center, an electron transfer cupredoxin domain of photosynthetic and respiratory complexes and, recently, a protein coregulated with particulate methane and ammonia monooxygenases. The redox potential, Cu-Cu spectroscopic features, and a valence delocalized state of CuA are difficult to reproduce in synthetic models, and every artificial protein CuA center to-date has used a modified cupredoxin. Here, we present a fully functional CuA center designed in a structurally nonhomologous protein, cytochrome c peroxidase (CcP), by only two mutations (CuACcP). We demonstrate with UV-visible absorption, resonance Raman, and magnetic circular dichroism spectroscopy that CuACcP is valence delocalized. Continuous wave and pulsed (HYSCORE) X-band EPR show it has a highly compact gz area and small Az hyperfine principal value with g and A tensors that resemble axially perturbed CuA. Stopped-flow kinetics found that CuA formation proceeds through a single T2Cu intermediate. The reduction potential of CuACcP is comparable to native CuA and can transfer electrons to a physiological redox partner. We built a structural model of the designed Cu binding site from extended X-ray absorption fine structure spectroscopy and validated it by mutation of coordinating Cys and His residues, revealing that a triad of residues (R48C, W51C, and His52) rigidly arranged on one α-helix is responsible for chelating the first Cu(II) and that His175 stabilizes the binuclear complex by rearrangement of the CcP heme-coordinating helix. This design is a demonstration that a highly conserved protein fold is not uniquely necessary to induce certain characteristic physical and chemical properties in a metal redox center.
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Affiliation(s)
- Evan N Mirts
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Sergei A Dikanov
- Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Anex Jose
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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4
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Dikanov SA, Berry SM, Lu Y. HYSCORE Insights into the Distribution of the Unpaired Spin Density in an Engineered Cu A Site in Azurin and Its His120Gly Variant. Inorg Chem 2019; 58:4437-4445. [PMID: 30869885 DOI: 10.1021/acs.inorgchem.8b03604] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A comparative study of the 1H and 14N hyperfine interactions between the CuA site in an engineered CuA center in azurin (WT-CuAAz) and its His120Gly variant (H120G-CuAAz) using the two-dimensional ESEEM technique, HYSCORE, is reported. HYSCORE spectroscopy has clarified conflicting results in previous electron paramagnetic resonance (EPR) and electron nuclear double resonance (ENDOR) studies and found clear differences between the two CuA azurins. Specifically, a hyperfine coupling AN⊥ of 15.3 MHz was determined for the first time from the frequencies of double-quantum transitions of 14N histidine nitrogens coordinated to CuA in WT-CuAAz. In contrast, such coupling was not observed in the spectra of H120G-CuAAz, indicating at least a several megahertz increase in AN⊥ for the coordinated nitrogen in this variant. In addition, 14N HYSCORE spectra of WT-CuAAz show interaction with only one type of weakly coupled nitrogen assigned to the remote Nε atom of coordinated imidazole residues based on the quadrupole coupling constant ( e2 Qq/4 h) of ∼0.4 MHz. The spectrum of H120G-CuAAz resolves additional features typical for backbone peptide nitrogens with larger e2 Qq/4 h values of ∼0.7 MHz. Hyperfine couplings with these nitrogens vary between ∼0.4 and 0.7 MHz. In addition, the two resolved cross-peaks from Cβ protons in H120G-CuAAz display only ∼1 MHz shifts relative to the corresponding peaks in WT-CuAAz. These new findings have provided the first experimental evidence of the previous density functional theory analysis that predicted changes in the delocalized electron spin population of ∼0.02-0.03 (i.e., ∼10%) on copper and sulfur atoms of the CuA center in H120 variants relative to WT-CuAAz and resolved contradicting results between EPR and ENDOR studies of the valence distribution in CuAAz and its variants.
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Affiliation(s)
- Sergei A Dikanov
- Department of Veterinary Clinical Medicine , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Steven M Berry
- Department of Chemistry and Biochemistry , University of Minnesota Duluth , Duluth , Minnesota 55812 , United States
| | - Yi Lu
- Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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5
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Zitare UA, Szuster J, Santalla MC, Llases ME, Morgada MN, Vila AJ, Murgida DH. Fine Tuning of Functional Features of the Cu A Site by Loop-Directed Mutagenesis. Inorg Chem 2019; 58:2149-2157. [PMID: 30644741 DOI: 10.1021/acs.inorgchem.8b03244] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we report the spectroscopic and electrochemical characterization of three novel chimeric CuA proteins in which either one or the three loops surrounding the metal ions in the Thermus thermophilus protein have been replaced by homologous human and plant sequences while preserving the set of coordinating amino acids. These conservative modifications mimic basic differences between CuA sites from different organisms and allow for fine tuning the energy gap between alternative electronic ground states of CuA.. This results in a systematic modulation of thermodynamic and kinetic electron transfer (ET) parameters and in the selection of one of two possible redox-active molecular orbitals, which differ in the ET reorganization energy by a factor of 2. Moreover, the ET mechanism is found to be frictionally controlled, and the modifications introduced into the different chimeras do not affect the frictional activation parameter.
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Affiliation(s)
- Ulises A Zitare
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE) , Universidad de Buenos Aires and CONICET, 1428 Buenos Aires , Argentina
| | - Jonathan Szuster
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE) , Universidad de Buenos Aires and CONICET, 1428 Buenos Aires , Argentina
| | - María C Santalla
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE) , Universidad de Buenos Aires and CONICET, 1428 Buenos Aires , Argentina
| | - María E Llases
- Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas , Instituto de Biología Molecular y Celular de Rosario (IBR) , Universidad Nacional de Rosario and CONICET, 2000 Rosario , Argentina
| | - Marcos N Morgada
- Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas , Instituto de Biología Molecular y Celular de Rosario (IBR) , Universidad Nacional de Rosario and CONICET, 2000 Rosario , Argentina
| | - Alejandro J Vila
- Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas , Instituto de Biología Molecular y Celular de Rosario (IBR) , Universidad Nacional de Rosario and CONICET, 2000 Rosario , Argentina
| | - Daniel H Murgida
- Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales , Instituto de Química Física de los Materiales, Medio Ambiente y Energía (INQUIMAE) , Universidad de Buenos Aires and CONICET, 1428 Buenos Aires , Argentina
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6
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Devlin T, Hofman CR, Acevedo ZPV, Kohler KR, Tao L, Britt RD, Hoke KR, Hunsicker-Wang LM. DEPC modification of the Cu A protein from Thermus thermophilus. J Biol Inorg Chem 2018; 24:117-135. [PMID: 30523412 DOI: 10.1007/s00775-018-1632-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/28/2018] [Indexed: 11/28/2022]
Abstract
The CuA center is the initial electron acceptor in cytochrome c oxidase, and it consists of two copper ions bridged by two cysteines and ligated by two histidines, a methionine, and a carbonyl in the peptide backbone of a nearby glutamine. The two ligating histidines are of particular interest as they may influence the electronic and redox properties of the metal center. To test for the presence of reactive ligating histidines, a portion of cytochrome c oxidase from the bacteria Thermus thermophilus that contains the CuA site (the TtCuA protein) was treated with the chemical modifier diethyl pyrocarbonate (DEPC) and the reaction followed through UV-visible, circular dichroism, and electron paramagnetic resonance spectroscopies at pH 5.0-9.0. A mutant protein (H40A/H117A) with the non-ligating histidines removed was similarly tested. Introduction of an electron-withdrawing DEPC-modification onto the ligating histidine 157 of TtCuA increased the reduction potential by over 70 mV, as assessed by cyclic voltammetry. Results from both proteins indicate that DEPC reacts with one of the two ligating histidines, modification of a ligating histidine raises the reduction potential of the CuA site, and formation of the DEPC adduct is reversible at room temperature. The existence of the reactive ligating histidine suggests that this residue may play a role in modulating the electronic and redox properties of TtCuA through kinetically-controlled proton exchange with the solvent. Lack of reactivity by the metalloproteins Sco and azurin, both of which contain a mononuclear copper center, indicate that reactivity toward DEPC is not a characteristic of all ligating histidines.
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Affiliation(s)
- Taylor Devlin
- Department of Chemistry, Trinity University, San Antonio, TX, 78212-7200, USA
- Department of Biophysics, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21218, USA
| | - Cristina R Hofman
- Department of Chemistry, Trinity University, San Antonio, TX, 78212-7200, USA
| | - Zachary P V Acevedo
- Department of Chemistry, Trinity University, San Antonio, TX, 78212-7200, USA
| | - Kelsey R Kohler
- Department of Chemistry, Trinity University, San Antonio, TX, 78212-7200, USA
| | - Lizhi Tao
- Department of Chemistry, University of California at Davis, Davis, CA, 95616, USA
| | - R David Britt
- Department of Chemistry, University of California at Davis, Davis, CA, 95616, USA
| | - Kevin R Hoke
- Department of Chemistry and Biochemistry, Berry College, Mount Berry, GA, 30149, USA
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7
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Clark KM, Tian S, van der Donk WA, Lu Y. Probing the role of the backbone carbonyl interaction with the Cu A center in azurin by replacing the peptide bond with an ester linkage. Chem Commun (Camb) 2016; 53:224-227. [PMID: 27918029 PMCID: PMC5253137 DOI: 10.1039/c6cc07274g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The role of a backbone carbonyl interaction with an engineered CuA center in azurin was investigated by developing a method of synthesis and incorporation of a depsipeptide where one of the amide bonds in azurin is replaced by an ester bond using expressed protein ligation. Studies by electronic absorption and electron paramagnetic resonance spectroscopic techniques indicate that, while the substitution does not significantly alter the geometry of the site, it weakens the axial interaction to the CuA center and strengthens the Cu-Cu bond, as evidenced by the blue shift of the near-IR absorption that has been assigned to the Cu-Cu ψ → ψ* transition. Interestingly, the changes in the electronic structure from the replacement did not result in a change in the reduction potential of the CuA center, suggesting that the diamond core structure of Cu2SCys2 is resistant to variations in axial interactions.
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Affiliation(s)
- Kevin M Clark
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue Urbana, IL 61801, USA.
| | - Shiliang Tian
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue Urbana, IL 61801, USA
| | - Wilfred A van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue Urbana, IL 61801, USA. and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue Urbana, IL 61801, USA
| | - Yi Lu
- Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue Urbana, IL 61801, USA. and Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue Urbana, IL 61801, USA
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8
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Le Fur M, Beyler M, Le Poul N, Lima LMP, Le Mest Y, Delgado R, Platas-Iglesias C, Patinec V, Tripier R. Improving the stability and inertness of Cu(ii) and Cu(i) complexes with methylthiazolyl ligands by tuning the macrocyclic structure. Dalton Trans 2016; 45:7406-20. [PMID: 27041505 DOI: 10.1039/c6dt00385k] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A tacn based ligand bearing two methylthiazolyl arms (no2th) was synthesized with the aim to find ligands forming very stable and inert complexes with Cu(ii) and Cu(i) in aqueous medium for radiopharmaceutical applications. The no2th ligand was efficiently prepared following the orthoamide intermediate synthesis. The complexes with Cu(2+) and Zn(2+) were obtained and analyzed by X-ray diffraction. The [Cu(no2th)](2+) complex presents a pentacoordinated distorted square pyramidal coordination geometry, while the metal ion in [Zn(no2th)](2+) adopts a hexacoordinated distorted trigonal prismatic geometry involving the coordination of a perchlorate counter ion. The acid-base properties of no2th have been studied using potentiometric titrations, and the stability constants of Cu(2+) and Zn(2+) complexes were determined by potentiometric and UV-vis titrations using H4edta as a competitor ligand. The stability constant determined for the Cu(2+) complex is rather high (log KCuL = 20.77 and pCu = 17.15), and moreover no2th exhibits a high selectivity for copper(ii) in relation to zinc(ii). The kinetics of the copper(ii) complexation process is very fast even in acidic medium. In addition, the [Cu(no2th)](2+) complex was found to be inert under rather harsh conditions (up to 2 M HCl and 60 °C), displaying a very high half-life time of about 15 days in 2 M HCl at 90 °C. The electrochemical reduction of the copper(ii) complex in water leads to the reversible formation of a stable copper(i) species. Spectroscopic studies performed by NMR, UV-vis and EPR, assisted by theoretical calculations, show that the [Cu(no2th)](2+) complex presents a structure in solution similar to that observed in the solid state. When compared to its cyclam di-N-methylthiazolyl counterpart, the results reported in this paper unambiguously show that replacing the cyclam unit by a tacn moiety improves the stability and inertness of its Cu(ii) and Cu(i) complexes.
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Affiliation(s)
- Mariane Le Fur
- Université de Bretagne Occidentale, UMR-CNRS 6521, SFR ScInBioS, Faculté des Sciences et Techniques, 6 avenue Victor le Gorgeu, C.S. 93837, 29238 Brest Cedex 3, France.
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9
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Calcium ions inhibit reduction of heme a in bovine cytochrome c oxidase. FEBS Lett 2015; 589:3853-8. [PMID: 26611345 DOI: 10.1016/j.febslet.2015.11.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 11/15/2015] [Accepted: 11/16/2015] [Indexed: 01/14/2023]
Abstract
The effect of Ca(2+) on the rate of heme a reduction by dithionite and hexaammineruthenium (RuAm) was studied in the cyanide-complexed bovine cytochrome oxidase (CcO). The rate of heme a reduction is proportional to RuAm concentration below 300 μM with kv of 0.53×10(6) M(-1) s(-1). Ca(2+) inhibits the rate of heme a reduction by dithionite by ∼25%. As the reaction speeds up with increased concentrations of RuAm, the inhibition by Ca(2+) disappears. The inhibition of heme a reduction may contribute to recently described partial inhibition of CcO by Ca(2+) in the enzymatic assays. The inhibitory effect of Ca(2+) on heme a reduction indicates that ET through heme a may be coupled to proton movement in the exit part of the proton channel H.
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10
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Lane AC, Barnes CL, Antholine WE, Wang D, Fiedler AT, Walensky JR. Di- and Trinuclear Mixed-Valence Copper Amidinate Complexes from Reduction of Iodine. Inorg Chem 2015; 54:8509-17. [PMID: 26252561 PMCID: PMC4733884 DOI: 10.1021/acs.inorgchem.5b01161] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular examples of mixed-valence copper complexes through chemical oxidation are rare but invoked in the mechanism of substrate activation, especially oxygen, in copper-containing enzymes. To examine the cooperative chemistry between two metals in close proximity to each other we began studying the reactivity of a dinuclear Cu(I) amidinate complex. The reaction of [(2,6-Me2C6H3N)2C(H)]2Cu2, 1, with I2 in tetrahydrofuran (THF), CH3CN, and toluene affords three new mixed-valence copper complexes [(2,6-Me2C6H3N)2C(H)]2Cu2(μ2-I3)(THF)2, 2, [(2,6-Me2C6H3N)2C(H)]2Cu2(μ2-I) (NCMe)2, 3, and [(2,6-Me2C6H3N)2C(H)]3Cu3(μ3-I)2, 4, respectively. The first two compounds were characterized by UV-vis and electron paramagnetic resonance spectroscopies, and their molecular structure was determined by X-ray crystallography. Both di- and trinuclear mixed-valence intermediates were characterized for the reaction of compound 1 to compound 4, and the molecular structure of 4 was determined by X-ray crystallography. The electronic structure of each of these complexes was also investigated using density functional theory.
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Affiliation(s)
- Andrew C. Lane
- Department of Chemistry, University of Missouri, 601 S. College Avenue, Columbia, Missouri 65211
| | - Charles L. Barnes
- Department of Chemistry, University of Missouri, 601 S. College Avenue, Columbia, Missouri 65211
| | - William E. Antholine
- Department of Biophysics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, Wisconsin 53226
| | - Denan Wang
- Department of Chemistry, Marquette University, 535 North 14 Street, Milwaukee, Wisconsin 53233
| | - Adam T. Fiedler
- Department of Chemistry, Marquette University, 535 North 14 Street, Milwaukee, Wisconsin 53233
| | - Justin R. Walensky
- Department of Chemistry, University of Missouri, 601 S. College Avenue, Columbia, Missouri 65211
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11
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Zitare U, Alvarez-Paggi D, Morgada MN, Abriata LA, Vila AJ, Murgida DH. Reversible Switching of Redox-Active Molecular Orbitals and Electron Transfer Pathways in CuASites of Cytochrome cOxidase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201504188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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12
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Zitare U, Alvarez-Paggi D, Morgada MN, Abriata LA, Vila AJ, Murgida DH. Reversible Switching of Redox-Active Molecular Orbitals and Electron Transfer Pathways in Cu(A) Sites of Cytochrome c Oxidase. Angew Chem Int Ed Engl 2015; 54:9555-9. [PMID: 26118421 DOI: 10.1002/anie.201504188] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 11/06/2022]
Abstract
The Cu(A) site of cytochrome c oxidase is a redox hub that participates in rapid electron transfer at low driving forces with two redox cofactors in nearly perpendicular orientations. Spectroscopic and electrochemical characterizations performed on first and second-sphere mutants have allowed us to experimentally detect the reversible switching between two alternative electronic states that confer different directionalities to the redox reaction. Specifically, the M160H variant of a native Cu(A) shows a reversible pH transition that allows to functionally probe both states in the same protein species. Alternation between states exerts a dramatic impact on the kinetic redox parameters, thereby suggesting this effect as the mechanism underlying the efficiency and directionality of Cu(A) electron transfer in vivo. These findings may also prove useful for the development of molecular electronics.
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Affiliation(s)
- Ulises Zitare
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET (Argentina)
| | - Damián Alvarez-Paggi
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET (Argentina)
| | - Marcos N Morgada
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and CONICET (Argentina)
| | - Luciano A Abriata
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and CONICET (Argentina)
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR), Departamento de Química Biológica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario and CONICET (Argentina)
| | - Daniel H Murgida
- Instituto de Química Física de los Materiales, Medio Ambiente y Energía, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires and CONICET (Argentina).
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13
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Ording-Wenker ECM, van der Plas M, Siegler MA, Fonseca Guerra C, Bouwman E. Protonation of a Biologically Relevant CuIIμ-Thiolate Complex: Ligand Dissociation or Formation of a Protonated CuIDisulfide Species? Chemistry 2014; 20:16913-21. [DOI: 10.1002/chem.201403918] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Indexed: 11/06/2022]
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14
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Culpepper MA, Cutsail GE, Gunderson WA, Hoffman BM, Rosenzweig AC. Identification of the valence and coordination environment of the particulate methane monooxygenase copper centers by advanced EPR characterization. J Am Chem Soc 2014; 136:11767-75. [PMID: 25059917 PMCID: PMC4140498 DOI: 10.1021/ja5053126] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Particulate methane monooxygenase (pMMO) catalyzes the oxidation of methane to methanol in methanotrophic bacteria. As a copper-containing enzyme, pMMO has been investigated extensively by electron paramagnetic resonance (EPR) spectroscopy, but the presence of multiple copper centers has precluded correlation of EPR signals with the crystallographically identified monocopper and dicopper centers. A soluble recombinant fragment of the pmoB subunit of pMMO, spmoB, like pMMO itself, contains two distinct copper centers and exhibits methane oxidation activity. The spmoB protein, spmoB variants designed to disrupt one or the other or both copper centers, as well as native pMMO have been investigated by EPR, ENDOR, and ESEEM spectroscopies in combination with metal content analysis. The data are remarkably similar for spmoB and pMMO, validating the use of spmoB as a model system. The results indicate that one EPR-active Cu(II) ion is present per pMMO and that it is associated with the active-site dicopper center in the form of a valence localized Cu(I)Cu(II) pair; the Cu(II), however, is scrambled between the two locations within the dicopper site. The monocopper site observed in the crystal structures of pMMO can be assigned as Cu(I). (14)N ENDOR and ESEEM data are most consistent with one of these dicopper-site signals involving coordination of the Cu(II) ion by residues His137 and His139, the other with Cu(II) coordinated by His33 and the N-terminal amino group. (1)H ENDOR measurements indicate there is no aqua (HxO) ligand bound to the Cu(II), either terminally or as a bridge to Cu(I).
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Affiliation(s)
- Megen A Culpepper
- Departments of ‡Molecular Biosciences and of §Chemistry, Northwestern University , Evanston, Illinois 60208, United States
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15
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Liu J, Chakraborty S, Hosseinzadeh P, Yu Y, Tian S, Petrik I, Bhagi A, Lu Y. Metalloproteins containing cytochrome, iron-sulfur, or copper redox centers. Chem Rev 2014; 114:4366-469. [PMID: 24758379 PMCID: PMC4002152 DOI: 10.1021/cr400479b] [Citation(s) in RCA: 574] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 02/07/2023]
Affiliation(s)
- Jing Liu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Saumen Chakraborty
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Parisa Hosseinzadeh
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yang Yu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shiliang Tian
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Igor Petrik
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ambika Bhagi
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, Department of Biochemistry, and Center for Biophysics
and Computational
Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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16
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Solomon EI, Heppner DE, Johnston EM, Ginsbach JW, Cirera J, Qayyum M, Kieber-Emmons MT, Kjaergaard CH, Hadt RG, Tian L. Copper active sites in biology. Chem Rev 2014; 114:3659-853. [PMID: 24588098 PMCID: PMC4040215 DOI: 10.1021/cr400327t] [Citation(s) in RCA: 1157] [Impact Index Per Article: 115.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
| | - David E. Heppner
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | - Jake W. Ginsbach
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Jordi Cirera
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Munzarin Qayyum
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | | | | | - Ryan G. Hadt
- Department of Chemistry, Stanford University, Stanford, CA, 94305
| | - Li Tian
- Department of Chemistry, Stanford University, Stanford, CA, 94305
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17
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Yu F, Cangelosi VM, Zastrow ML, Tegoni M, Plegaria JS, Tebo AG, Mocny CS, Ruckthong L, Qayyum H, Pecoraro VL. Protein design: toward functional metalloenzymes. Chem Rev 2014; 114:3495-578. [PMID: 24661096 PMCID: PMC4300145 DOI: 10.1021/cr400458x] [Citation(s) in RCA: 329] [Impact Index Per Article: 32.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Fangting Yu
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | | | | | | | - Alison G. Tebo
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Leela Ruckthong
- University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hira Qayyum
- University of Michigan, Ann Arbor, Michigan 48109, United States
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18
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Alvarez-Paggi D, Zitare U, Murgida DH. The role of protein dynamics and thermal fluctuations in regulating cytochrome c/cytochrome c oxidase electron transfer. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:1196-207. [PMID: 24502917 DOI: 10.1016/j.bbabio.2014.01.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/22/2014] [Accepted: 01/28/2014] [Indexed: 01/06/2023]
Abstract
In this overview we present recent combined electrochemical, spectroelectrochemical, spectroscopic and computational studies from our group on the electron transfer reactions of cytochrome c and of the primary electron acceptor of cytochrome c oxidase, the CuA site, in biomimetic complexes. Based on these results, we discuss how protein dynamics and thermal fluctuations may impact on protein ET reactions, comment on the possible physiological relevance of these results, and finally propose a regulatory mechanism that may operate in the Cyt/CcO electron transfer reaction in vivo. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.
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Affiliation(s)
- Damian Alvarez-Paggi
- INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, pab. 2, piso 3, C1428EHA Buenos Aires, Argentina
| | - Ulises Zitare
- INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, pab. 2, piso 3, C1428EHA Buenos Aires, Argentina
| | - Daniel H Murgida
- INQUIMAE-CONICET, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, pab. 2, piso 3, C1428EHA Buenos Aires, Argentina.
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19
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Alvarez-Paggi D, Abriata LA, Murgida DH, Vila AJ. Native Cu(A) redox sites are largely resilient to pH variations within a physiological range. Chem Commun (Camb) 2013; 49:5381-3. [PMID: 23652317 DOI: 10.1039/c3cc40457a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Previous studies on engineered CuA centres have shown that one of the histidine ligands is protonated and dissociated from the metal site at physiological pH values, thus suggesting a role in regulating proton-coupled electron transfer of cytochrome c oxidases in vivo. Here we report that for native CuA such protonation does not take place at physiologically relevant pH values and, furthermore, no significant changes in the spectroscopic and redox properties of the metal site occur at low pH.
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Affiliation(s)
- Damián Alvarez-Paggi
- INQUIMAE-CONICET and Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria Pab. 2, C1428EHA Buenos Aires, Argentina
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20
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Abriata LA, Vila AJ. Redox-state sensing by hydrogen bonds in the CuA center of cytochrome c oxidase. J Inorg Biochem 2013; 132:18-20. [PMID: 24012017 DOI: 10.1016/j.jinorgbio.2013.07.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 07/18/2013] [Accepted: 07/23/2013] [Indexed: 11/25/2022]
Abstract
Cytochrome c oxidases (CcO) couple electron transfer to active proton translocation through a gated mechanism that minimizes energy losses by preventing protons from flowing backwards or leaking. Such a complex mechanism requires that information about the redox and protonation states of the different centers be transmitted between different parts of the oxidase. Here we report a network of residues located around the electron entry point of CcO, the CuA site in subunit II, that experience collective pH equilibria around neutral pH. This network starts at the occluded side of the CuA site and extends to the interface between subunits I and II of the CcO, where the proton exit is located and through which electrons flow into subunit I. One of the residues in this network is directly involved in a hydrogen bond to one of the CuA ligands, whose strength is highly sensitive to the redox state of the metal center. We propose that this interaction mediates the transmission of redox changes from ET centers to other functional regions of the oxidase, and possibly also in other similar machineries, as part of their gating and regulatory mechanisms.
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Affiliation(s)
- Luciano A Abriata
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) and Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Alejandro J Vila
- Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR) and Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina.
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21
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Wilson TD, Yu Y, Lu Y. Understanding copper-thiolate containing electron transfer centers by incorporation of unnatural amino acids and the CuA center into the type 1 copper protein azurin. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.06.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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22
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De la Mora E, Lovett JE, Blanford CF, Garman EF, Valderrama B, Rudino-Pinera E. Structural changes caused by radiation-induced reduction and radiolysis: the effect of X-ray absorbed dose in a fungal multicopper oxidase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:564-77. [PMID: 22525754 PMCID: PMC3335286 DOI: 10.1107/s0907444912005343] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 02/07/2012] [Indexed: 02/20/2023]
Abstract
X-ray radiation induces two main effects at metal centres contained in protein crystals: radiation-induced reduction and radiolysis and a resulting decrease in metal occupancy. In blue multicopper oxidases (BMCOs), the geometry of the active centres and the metal-to-ligand distances change depending on the oxidation states of the Cu atoms, suggesting that these alterations are catalytically relevant to the binding, activation and reduction of O(2). In this work, the X-ray-determined three-dimensional structure of laccase from the basidiomycete Coriolopsis gallica (Cg L), a high catalytic potential BMCO, is described. By combining spectroscopic techniques (UV-Vis, EPR and XAS) and X-ray crystallography, structural changes at and around the active copper centres were related to pH and absorbed X-ray dose (energy deposited per unit mass). Depletion of two of the four active Cu atoms as well as low occupancies of the remaining Cu atoms, together with different conformations of the metal centres, were observed at both acidic pH and high absorbed dose, correlating with more reduced states of the active coppers. These observations provide additional evidence to support the role of flexibility of copper sites during O(2) reduction. This study supports previous observations indicating that interpretations regarding redox state and metal coordination need to take radiation effects explicitly into account.
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Affiliation(s)
- Eugenio De la Mora
- Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Janet E. Lovett
- Centre for Advanced Electron Spin Resonance, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, England
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, England
- EaStCHEM School of Chemistry, Joseph Black Building, The King’s Buildings, Edinburgh EH9 3JJ, Scotland
| | - Christopher F. Blanford
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QR, England
- School of Materials, University of Manchester, Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, England
| | - Elspeth F. Garman
- Laboratory of Molecular Biophysics, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, England
| | - Brenda Valderrama
- Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
| | - Enrique Rudino-Pinera
- Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca, Morelos 62210, Mexico
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23
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New SY, Marshall NM, Hor TSA, Xue F, Lu Y. Redox tuning of two biological copper centers through non-covalent interactions: same trend but different magnitude. Chem Commun (Camb) 2012; 48:4217-9. [DOI: 10.1039/c2cc30901g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Wilson TD, Savelieff MG, Nilges MJ, Marshall NM, Lu Y. Kinetics of Copper Incorporation into a Biosynthetic Purple CuA Azurin: Characterization of Red, Blue, and a New Intermediate Species. J Am Chem Soc 2011; 133:20778-92. [DOI: 10.1021/ja205281t] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Tiffany D. Wilson
- Department of Chemistry, University of Illinois at Urbana—Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Masha G. Savelieff
- Department of Chemistry, University of Illinois at Urbana—Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Mark J. Nilges
- Department of Chemistry, University of Illinois at Urbana—Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Nicholas M. Marshall
- Department of Chemistry, University of Illinois at Urbana—Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana—Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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25
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Savelieff MG, Lu Y. CuA centers and their biosynthetic models in azurin. J Biol Inorg Chem 2010; 15:461-83. [DOI: 10.1007/s00775-010-0625-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2009] [Accepted: 01/20/2010] [Indexed: 11/28/2022]
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26
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Abstract
Metal coordination is a key structural and functional component of a large fraction of proteins. Given this dual role we considered the possibility that metal coordination may have played a templating role in the early evolution of protein folds and complexes. We describe here a rational design approach, Metal Templated Interface Redesign (MeTIR), that mimics the time course of a hypothetical evolutionary pathway for the formation of stable protein assemblies through an initial metal coordination event. Using a folded monomeric protein, cytochrome cb(562), as a building block we show that its non-self-associating surface can be made self-associating through a minimal number of mutations that enable Zn coordination. The protein interfaces in the resulting Zn-directed, D(2)-symmetrical tetramer are subsequently redesigned, yielding unique protein architectures that self-assemble in the presence or absence of metals. Aside from its evolutionary implications, MeTIR provides a route to engineer de novo protein interfaces and metal coordination environments that can be tuned through the extensive noncovalent bonding interactions in these interfaces.
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27
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Zhang JL, Garner DK, Liang L, Barrios DA, Lu Y. Noncovalent modulation of pH-dependent reactivity of a Mn-salen cofactor in myoglobin with hydrogen peroxide. Chemistry 2009; 15:7481-9. [PMID: 19557774 DOI: 10.1002/chem.200802449] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
To demonstrate protein modulation of metal-cofactor reactivity through noncovalent interactions, pH-dependent sulfoxidation and 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS) oxidation reactivity of a designed myoglobin (Mb) containing non-native Mn-salen complex (1) was investigated using H2O2 as the oxidant. Incorporation of 1 inside the Mb resulted in an increase in the turnover numbers through exclusion of water from the metal complex and prevention of Mn-salen dimer formation. Interestingly, the presence of protein in itself is not enough to confer the increase activity as mutation of the distal His64 in Mb to Phe to remove hydrogen-bonding interactions resulted in no increase in the turnover numbers, while mutation His64 to Arg, another residue with ability to hydrogen-bond interactions, resulted in an increase in reactivity. These results strongly suggest that the distal ligand His64, through its hydrogen-bonding interaction, plays important roles in enhancing and fine-tuning reactivity of the Mn-salen complex. Nonlinear least-squares fitting of rate versus pH plots demonstrates that 1.Mb(H64X) (X=H, R and F) and the control Mn-salen 1 exhibit pKa values varying from pH 6.4 to 8.3, and that the lower pKa of the distal ligand in 1.Mb(H64X), the higher the reactivity it achieves. Moreover, in addition to the pKa at high pH, 1.Mb displays another pKa at low pH, with pKa of 5.0+/-0.08. A comparison of the effect of different pH on sulfoxidation and ABTS oxidation indicates that, while the intermediate produced at low pH conditions could only perform sulfoxidation, the intermediate at high pH could oxidize both sulfoxides and ABTS. Such a fine-control of reactivity through hydrogen-bonding interactions by the distal ligand to bind, orient and activate H2O2 is very important for designing artificial enzymes with dramatic different and tunable reactivity from catalysts without protein scaffolds.
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Affiliation(s)
- Jun-Long Zhang
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 S. Mathews Ave., Urbana, IL 61801, USA
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28
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Kimura M, Nakano Y, Adachi N, Tatewaki Y, Shirai H, Kobayashi N. Intramolecular Axial Ligation of Zinc Porphyrin Cores with Triazole Links within Dendrimers. Chemistry 2009; 15:2617-24. [DOI: 10.1002/chem.200801557] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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29
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Experimental evidence for a link among cupredoxins: red, blue, and purple copper transformations in nitrous oxide reductase. Proc Natl Acad Sci U S A 2008; 105:7919-24. [PMID: 18535143 DOI: 10.1073/pnas.0711316105] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The cupredoxin fold is an important motif in numerous proteins that are central to several critical cellular processes ranging from aerobic and anaerobic respiration to catalysis and iron homeostasis. Three types of copper sites have been found to date within cupredoxin folds: blue type 1 (T1) copper, red type 2 (T2) copper, and purple Cu(A). Although as much as 90% sequence difference has been observed among some members of this superfamily of proteins that span several kingdoms, sequence alignment and phylogenic trees strongly suggest an evolutionary link and common ancestry. However, experimental evidence for such a link has been lacking. We report herein the observation of pH-dependent transformation between blue T1 copper, red T2 copper, and the native purple Cu(A) centers of nitrous oxide reductase (N2OR) from Paracoccus denitrificans. The blue and red copper centers form initially before they are transformed into purple Cu(A) center. This transformation process is pH-dependent, with lower pH resulting in fewer trapped T1 and T2 coppers and faster transition to purple Cu(A). These observations suggest that the purple Cu(A) site contains the essential elements of T1 and T2 copper centers and that the Cu(A) center is preferentially formed at low pH. Therefore, this work provides an underlying link between the various cupredoxin copper sites and possible experimental evidence in vitro for the evolutionary relationship between the cupredoxin proteins. The findings also lend physiological relevance to cupredoxin site biosynthesis.
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30
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Xie X, Gorelsky SI, Sarangi R, Garner DK, Hwang HJ, Hodgson KO, Hedman B, Lu Y, Solomon EI. Perturbations to the geometric and electronic structure of the CuA site: factors that influence delocalization and their contributions to electron transfer. J Am Chem Soc 2008; 130:5194-205. [PMID: 18348522 DOI: 10.1021/ja7102668] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Using a combination of electronic spectroscopies and DFT calculations, the effect of pH perturbation on the geometric and electronic structure of the CuA site has been defined. Descriptions are developed for high pH (pH = 7) and low pH (pH = 4) forms of CuA azurin and its H120A mutant which address the discrepancies concerning the extent of delocalization indicated by multifrequency EPR and ENDOR data (J. Am. Chem. Soc. 2005, 127, 7274; Biophys. J. 2002, 82, 2758). Our resonance Raman and MCD spectra demonstrate that the low pH and H120A mutant forms are essentially identical and are the perturbed forms of the completely delocalized high pH CuA site. However, in going from high pH to low pH, a seven-line hyperfine coupling pattern associated with complete delocalization of the electron (S = 1/2) over two Cu coppers (I(Cu) = 3/2) changes into a four-line pattern reflecting apparent localization. DFT calculations show that the unpaired electron is delocalized in the low pH form and reveal that its four-line hyperfine pattern results from the large EPR spectral effects of approximately 1% 4s orbital contribution of one Cu to the ground-state spin wave function upon protonative loss of its His ligand. The contribution of the Cu-Cu interaction to electron delocalization in this low symmetry protein site is evaluated, and the possible functional significance of the pH-dependent transition in regulating proton-coupled electron transfer in cytochrome c oxidase is discussed.
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Affiliation(s)
- Xiangjin Xie
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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31
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LAREO LEONARDOR, GONZÁLEZ JANNETH. INTRAMOLECULAR EXCITED ENERGY TRANSFER PATHWAYS IN PROTEINS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2008. [DOI: 10.1142/s0219633608003629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The transfer of energy perturbations within protein structure is an important phenomenon in many biological processes. In particular, the transfer of energy perturbations within a molecule in the absence of electron transfer is critical to the understanding of such processes as signaling involving receptors, channels, and enzymes among others, and to the design and development of relevant conducting materials. In this work, we have proposed a mechanism to explain this nonradiative, nonelectron energy transfer based on the π-orbital interactions of aromatic amino acids. Additionally, some theoretical background and possible computational approaches are presented as support for the proposal.
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Affiliation(s)
- LEONARDO R. LAREO
- Computational and Structural Biochemistry and Bioinformatics, Department of Nutrition and Biochemistry, School of Sciences, Pontificia Universidad Javeriana, Carrera 7a # 43-82, Carlos Ortiz, S. J. Bldg., Rm. 117, Bogota, DC, USA
| | - JANNETH GONZÁLEZ
- Computational and Structural Biochemistry and Bioinformatics, Department of Nutrition and Biochemistry, School of Sciences, Pontificia Universidad Javeriana, Carrera 7a # 43-82, Carlos Ortiz, S. J. Bldg., Rm. 117, Bogota, DC, USA
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32
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Solomon EI, Xie X, Dey A. Mixed valent sites in biological electron transfer. Chem Soc Rev 2008; 37:623-38. [DOI: 10.1039/b714577m] [Citation(s) in RCA: 102] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Affiliation(s)
- My Hang V Huynh
- DE-1: High Explosive Science and Technology Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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34
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Lu Y. Metalloprotein and metallo-DNA/RNAzyme design: current approaches, success measures, and future challenges. Inorg Chem 2007; 45:9930-40. [PMID: 17140190 PMCID: PMC2533576 DOI: 10.1021/ic052007t] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Specific metal-binding sites have been found in not only proteins but also DNA and RNA molecules. Together these metalloenzymes consist of a major portion of the enzyme family and can catalyze some of the most difficult biological reactions. Designing these metalloenzymes can be both challenging and rewarding because it can provide deeper insights into the structure and function of proteins and cheaper and more stable alternatives for biochemical and biotechnological applications. Toward this goal, both rational and combinatorial approaches have been used. The rational approach is good for designing metalloenzymes that are well characterized, such as heme proteins, while the combinatorial approach is better at designing those whose structures are poorly understood, such as metallo-DNA/RNAzymes. Among the rational approaches, de novo design is at its best when metal-binding sites reside in a scaffold whose structure has been designed de novo (e.g., alpha-helical bundles). Otherwise, design using native scaffolds can be equally effective, allowing more choices of scaffolds whose structural stability is often more resistant to multiple mutations. In addition, computational and empirical designs have both enjoyed successes. Because of the limitation in defining structural parameters for metal-binding sites, a computational approach is restricted to mostly metal-binding sites that are well defined, such as mono- or homonuclear centers. An empirical approach, even though it is less restrictive in the metal-binding sites to be designed, depends heavily on one's knowledge and choice of templates and targets. An emerging approach is a combination of both computational and empirical approaches. The success of these approaches can be measured not only by three-dimensional structural comparison between the designed and target enzymes but also by the total amount of insight obtained from the design process and studies of the designed enzymes. One of the biggest advantages of designed metalloenzymes is the potential of placing two different metal-binding sites in the same protein framework for comparison. A final measure of success is how one can utilize the insight gained from the intellectual exercise to design new metalloenzymes, including those with unprecedented structures and functions. Future challenges include designing more complex metalloenzymes such as heteronuclear metal centers with strong nanomolar or better affinities. A key to meeting this challenge is to focus on the design of not only primary but also secondary coordination spheres using a combination of improved computer programs, experimental design, and high-resolution crystallography.
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Affiliation(s)
- Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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35
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Farver O, Hwang HJ, Lu Y, Pecht I. Reorganization Energy of the CuA Center in Purple Azurin: Impact of the Mixed Valence-to-Trapped Valence State Transition. J Phys Chem B 2007; 111:6690-4. [PMID: 17274649 DOI: 10.1021/jp0672555] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mixed valence (MV) coordination compounds play important roles in redox reactions in chemistry and biology. Details of the contribution of a mixed valence state to protein electron transfer (ET) reactivity such as reorganization energy, however, have not been experimentally defined. Herein we report measurements of reorganization energies of a binuclear CuA center engineered into Pseudomonas aeruginosa azurin that exhibits a reversible transition between a totally delocalized MV state at pH 8.0 and a trapped valence (TV) state at pH 4.0. The reorganization energy of a His120Ala variant of CuA azurin that displays a TV state at both the above pH values has also been determined. We found that the MV-to-TV state transition increases the reorganization energy by 0.18 eV, providing evidence that the MV state of the CuA center has lower reorganization energy than its TV counterpart. We have also shown that lowering the pH from 8.0 to 4.0 results in a similar (approximately 0.4 eV) decrease in reorganization energy for both blue (type 1) and purple (CuA) azurins, even though the reorganization energies of the two different copper centers are different at a given pH. These results suggest that the MV state plays only a secondary role in modulation of the ET reactivity via the reorganization energy, as compared to that of the driving force.
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Affiliation(s)
- Ole Farver
- Institute of Analytical and Pharmaceutical Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark.
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Zumft WG, Kroneck PMH. Respiratory transformation of nitrous oxide (N2O) to dinitrogen by Bacteria and Archaea. Adv Microb Physiol 2006; 52:107-227. [PMID: 17027372 DOI: 10.1016/s0065-2911(06)52003-x] [Citation(s) in RCA: 203] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
N2O is a potent greenhouse gas and stratospheric reactant that has been steadily on the rise since the beginning of industrialization. It is an obligatory inorganic metabolite of denitrifying bacteria, and some production of N2O is also found in nitrifying and methanotrophic bacteria. We focus this review on the respiratory aspect of N2O transformation catalysed by the multicopper enzyme nitrous oxide reductase (N2OR) that provides the bacterial cell with an electron sink for anaerobic growth. Two types of Cu centres discovered in N2OR were both novel structures among the Cu proteins: the mixed-valent dinuclear Cu(A) species at the electron entry site of the enzyme, and the tetranuclear Cu(Z) centre as the first catalytically active Cu-sulfur complex known. Several accessory proteins function as Cu chaperone and ABC transporter systems for the biogenesis of the catalytic centre. We describe here the paradigm of Z-type N2OR, whose characteristics have been studied in most detail in the genera Pseudomonas and Paracoccus. Sequenced bacterial genomes now provide an invaluable additional source of information. New strains harbouring nos genes and capability of N2O utilization are being uncovered. This reveals previously unknown relationships and allows pattern recognition and predictions. The core nos genes, nosZDFYL, share a common phylogeny. Most principal taxonomic lineages follow the same biochemical and genetic pattern and share the Z-type enzyme. A modified N2OR is found in Wolinella succinogenes, and circumstantial evidence also indicates for certain Archaea another type of N2OR. The current picture supports the view of evolution of N2O respiration prior to the separation of the domains Bacteria and Archaea. Lateral nos gene transfer from an epsilon-proteobacterium as donor is suggested for Magnetospirillum magnetotacticum and Dechloromonas aromatica. In a few cases, nos gene clusters are plasmid borne. Inorganic N2O metabolism is associated with a diversity of physiological traits and biochemically challenging metabolic modes or habitats, including halorespiration, diazotrophy, symbiosis, pathogenicity, psychrophily, thermophily, extreme halophily and the marine habitat down to the greatest depth. Components for N2O respiration cover topologically the periplasm and the inner and outer membranes. The Sec and Tat translocons share the task of exporting Nos components to their functional sites. Electron donation to N2OR follows pathways with modifications depending on the host organism. A short chronology of the field is also presented.
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Affiliation(s)
- Walter G Zumft
- Institute of Applied Biosciences, Division of Molecular Microbiology, University of Karlsruhe, D-76128 Karlsruhe, Germany
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Lieberman RL, Kondapalli KC, Shrestha DB, Hakemian AS, Smith SM, Telser J, Kuzelka J, Gupta R, Borovik AS, Lippard SJ, Hoffman BM, Rosenzweig AC, Stemmler TL. Characterization of the particulate methane monooxygenase metal centers in multiple redox states by X-ray absorption spectroscopy. Inorg Chem 2006; 45:8372-81. [PMID: 16999437 PMCID: PMC2864602 DOI: 10.1021/ic060739v] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The integral membrane enzyme particulate methane monooxygenase (pMMO) converts methane, the most inert hydrocarbon, to methanol under ambient conditions. The 2.8-A resolution pMMO crystal structure revealed three metal sites: a mononuclear copper center, a dinuclear copper center, and a nonphysiological mononuclear zinc center. Although not found in the crystal structure, solution samples of pMMO also contain iron. We have used X-ray absorption spectroscopy to analyze the oxidation states and coordination environments of the pMMO metal centers in as-isolated (pMMO(iso)), chemically reduced (pMMO(red)), and chemically oxidized (pMMO(ox)) samples. X-ray absorption near-edge spectra (XANES) indicate that pMMO(iso) contains both Cu(I) and Cu(II) and that the pMMO Cu centers can undergo redox chemistry. Extended X-ray absorption fine structure (EXAFS) analysis reveals a Cu-Cu interaction in all redox forms of the enzyme. The Cu-Cu distance increases from 2.51 to 2.65 A upon reduction, concomitant with an increase in the average Cu-O/N bond lengths. Appropriate Cu2 model complexes were used to refine and validate the EXAFS fitting protocols for pMMO(iso). Analysis of Fe EXAFS data combined with electron paramagnetic resonance (EPR) spectra indicates that Fe, present as Fe(III), is consistent with heme impurities. These findings are complementary to the crystallographic data and provide new insight into the oxidation states and possible electronic structures of the pMMO Cu ions.
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Abstract
Inorganic chemistry and biology can benefit greatly from each other. Although synthetic and physical inorganic chemistry have been greatly successful in clarifying the role of metal ions in biological systems, the time may now be right to utilize biological systems to advance coordination chemistry. One such example is the use of small, stable, easy-to-make, and well-characterized proteins as ligands to synthesize novel inorganic compounds. This biosynthetic inorganic chemistry is possible thanks to a number of developments in biology. This review summarizes the progress in the synthesis of close models of complex metalloproteins, followed by a description of recent advances in using the approach for making novel compounds that are unprecedented in either inorganic chemistry or biology. The focus is mainly on synthetic "tricks" learned from biology, as well as novel structures and insights obtained. The advantages and disadvantages of this biosynthetic approach are discussed.
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Affiliation(s)
- Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Gorelsky SI, Ghosh S, Solomon EI. Mechanism of N2O reduction by the mu4-S tetranuclear CuZ cluster of nitrous oxide reductase. J Am Chem Soc 2006; 128:278-90. [PMID: 16390158 DOI: 10.1021/ja055856o] [Citation(s) in RCA: 272] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reaction thermodynamics and potential energy surfaces are calculated using density functional theory to investigate the mechanism of the reductive cleavage of the N-O bond by the mu(4)-sulfide-bridged tetranuclear Cu(Z) site of nitrous oxide reductase. The Cu(Z) cluster provides an exogenous ligand-binding site, and, in its fully reduced 4Cu(I) state, the cluster turns off binding of stronger donor ligands while enabling the formation of the Cu(Z)-N(2)O complex through enhanced Cu(Z) --> N(2)O back-donation. The two copper atoms (Cu(I) and Cu(IV)) at the ligand-binding site of the cluster play a crucial role in the enzymatic function, as these atoms are directly involved in bridged N(2)O binding, bending the ligand to a configuration that resembles the transition state (TS) and contributing the two electrons for N(2)O reduction. The other atoms of the Cu(Z) cluster are required for extensive back-bonding with minimal sigma ligand-to-metal donation for the N(2)O activation. The low reaction barrier (18 kcal mol(-)(1)) of the direct cleavage of the N-O bond in the Cu(Z)-N(2)O complex is due to the stabilization of the TS by a strong Cu(IV)(2+)-O(-) bond. Due to the charge transfer from the Cu(Z) cluster to the N(2)O ligand, noncovalent interactions with the protein environment stabilize the polar TS and reduce the activation energy to an extent dependent on the strength of proton donor. After the N-O bond cleavage, the catalytic cycle consists of a sequence of alternating protonation/one-electron reduction steps which return the Cu(Z) cluster to the fully reduced (4Cu(I)) state for future turnover.
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Affiliation(s)
- Serge I Gorelsky
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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