Insight into the Structure and Mechanism of Nickel-Containing Superoxide Dismutase Derived from Peptide-Based Mimics

ConspectusNickel superoxide dismutase (NiSOD) is a nickel-containing metalloenzyme that catalyzes the disproportionation of superoxide through a ping-pong mechanism that relies on accessing reduced Ni­(II) and oxidized Ni­(III) oxidation states. NiSOD is the most recently discovered SOD. Unlike the other known SODs (MnSOD, FeSOD, and (CuZn)­SOD), which utilize “typical” biological nitrogen and oxygen donors, NiSOD utilizes a rather unexpected ligand set. In the reduced Ni­(II) oxidation state, NiSOD utilizes nitrogen ligands derived from the N-terminal amine and an amidate along with two cysteinates sulfur donors. These are unusual biological ligands, especially for an SOD: amine and amidate donors are underrepresented as biological ligands, whereas cysteinates are highly susceptible to oxidative damage. An axial histidine imidazole binds to nickel upon oxidation to Ni­(III). This bond is long (2.3–2.6 Å) owing to a tight hydrogen-bonding network.All of the ligating residues to Ni­(II) and Ni­(III) are found within the first 6 residues from the NiSOD N-terminus. Thus, small nickel-containing metallopeptides derived from the first 6–12 residues of the NiSOD sequence can reproduce many of the properties of NiSOD itself. Using these nickel-containing metallopeptide-based NiSOD mimics, we have shown that the minimal sequence needed for nickel binding and reproduction of the structural, spectroscopic, and functional properties of NiSOD is H₂N-HCXXPC.Insight into how NiSOD avoids oxidative damage has also been gained. Using small NiN₂S₂ complexes and metallopeptide-based mimics, it was shown that the unusual nitrogen donor atoms protect the cysteinates from oxidative damage (both one-electron oxidation and oxygen atom insertion reactions) by fine-tuning the electronic structure of the nickel center. Changing the nitrogen donor set to a bis-amidate or bis-amine nitrogen donor led to catalytically nonviable species owing to nickel–cysteinate bond oxidative damage. Only the amine/amidate nitrogen donor atoms within the NiSOD ligand set produce a catalytically viable species.These metallopeptide-based mimics have also hinted at the detailed mechanism of SOD catalysis by NiSOD. One such aspect is that the axial imidazole likely remains ligated to the Ni center under rapid catalytic conditions (i.e., high superoxide loads). This reduces the degree of structural rearrangement about the nickel center, leading to higher catalytic rates. Metallopeptide-based mimics have also shown that, although an axial ligand to Ni­(III) is required for catalysis, the rates are highest when this is a weak interaction, suggesting a reason for the long axial His–Ni­(III) bond found in NiSOD. These mimics have also suggested a surprising mechanistic insight: O₂^– reduction via a “H^•” tunneling event from a R–S­(H⁺)–Ni­(II) moiety to O₂^– is possible. The importance of this mechanism in NiSOD has not been verified

Subtle Modulation of Cu₄X₄L₂ Phosphine Cluster Cores Leads to Changes in Luminescence

A series of Cu₄X₄(PPh₂py)₂ compounds (X = Cl (<b>1</b>), Br (<b>2</b>), I (<b>3</b>), PPh₂py = 2-(diphenylphosphino)­pyridine) were prepared and characterized using X-ray crystallography, NMR, UV–vis, and luminescence spectroscopy. The copper chloride and bromide clusters have Cu₄X₄ octahedral cores while the copper iodide clusters contain an unprecedented butterfly shaped core. Crystallization of the copper bromide and iodide clusters from the appropriate solvent produced the solvates <b>2</b>·2CH₂Cl₂, <b>2</b>·2CHCl₃, and <b>3</b>·0.5CH₂Cl₂ where the presence of the lattice solvate influences the overall structural properties. Using TD-DFT calculations, the emission was assigned to a mixed metal- and halide-to-ligand charge transfer, (M + X)­LCT. Subtle differences in the copper core geometry and μ-halide bonding perturb the emissions of these copper­(I) halide clusters

Subtle Modulation of Cu₄X₄L₂ Phosphine Cluster Cores Leads to Changes in Luminescence

A series of Cu₄X₄(PPh₂py)₂ compounds (X = Cl (<b>1</b>), Br (<b>2</b>), I (<b>3</b>), PPh₂py = 2-(diphenylphosphino)­pyridine) were prepared and characterized using X-ray crystallography, NMR, UV–vis, and luminescence spectroscopy. The copper chloride and bromide clusters have Cu₄X₄ octahedral cores while the copper iodide clusters contain an unprecedented butterfly shaped core. Crystallization of the copper bromide and iodide clusters from the appropriate solvent produced the solvates <b>2</b>·2CH₂Cl₂, <b>2</b>·2CHCl₃, and <b>3</b>·0.5CH₂Cl₂ where the presence of the lattice solvate influences the overall structural properties. Using TD-DFT calculations, the emission was assigned to a mixed metal- and halide-to-ligand charge transfer, (M + X)­LCT. Subtle differences in the copper core geometry and μ-halide bonding perturb the emissions of these copper­(I) halide clusters

Adiabaticity of the Proton-Coupled Electron-Transfer Step in the Reduction of Superoxide Effected by Nickel-Containing Superoxide Dismutase Metallopeptide-Based Mimics

Nickel-containing superoxide dismutases (NiSODs) are bacterial metalloenzymes that catalyze the disproportionation of O₂^–. These enzymes take advantage of a redox-active nickel cofactor, which cycles between the Ni­(II) and Ni­(III) oxidation states, to catalytically disprotorptionate O₂^–. The Ni­(II) center is ligated in a square planar N₂S₂ coordination environment, which, upon oxidation to Ni­(III), becomes five-coordinate following the ligation of an axial imidazole ligand. Previous studies have suggested that metallopeptide-based mimics of NiSOD reduce O₂^– through a proton-coupled electron transfer (PCET) reaction with the electron derived from a reduced Ni­(II) center and the proton from a protonated, coordinated Ni^II–S­(H⁺)–Cys moiety. The current work focuses on the O₂^– reduction half-reaction of the catalytic cycle. In this study we calculate the vibronic coupling between the reactant and product diabatic surfaces using a semiclassical formalism to determine if the PCET reaction is proceeding through an adiabatic or nonadiabatic proton tunneling process. These results were then used to calculate H/D kinetic isotope effects for the PCET process. We find that as the axial imidazole ligand becomes more strongly associated with the Ni­(II) center during the PCET reaction, the reaction becomes more nonadiabatic. This is reflected in the calculated H/D KIEs, which moderately increase as the reaction becomes more nonadiabatic. Furthermore, the results suggest that as the axial ligand becomes less Lewis basic the observed reaction rate constants for O₂^– reduction should become faster because the reaction becomes more adiabatic. These conclusions are in-line with experimental observations. The results thus indicate that variations in the axial donor’s ability to coordinate to the nickel center of NiSOD metallopeptide-based mimics will strongly influence the fundamental nature of the O₂^– reduction process

Influence of Sequential Thiolate Oxidation on a Nitrile Hydratase Mimic Probed by Multiedge X-ray Absorption Spectroscopy

Nitrile hydratases (NHases) are Fe­(III)- and Co­(III)-containing hydrolytic enzymes that convert nitriles into amides. The metal-center is contained within an N₂S₃ coordination motif with two post-translationally modified cysteinates contained in a <i>cis</i> arrangement, which have been converted into a sulfinate (R-SO₂^–) and a sulfenate (R-SO^–) group. Herein, we utilize Ru L-edge and ligand (N-, S-, and P-) K-edge X-ray absorption spectroscopies to probe the influence that these modifications have on the electronic structure of a series of sequentially oxidized thiolate-coordinated Ru­(II) complexes ((bmmp-TASN)­RuPPh₃, (bmmp-O₂-TASN)­RuPPh₃, and (bmmp-O₃-TASN)­RuPPh₃). Included is the use of N K-edge spectroscopy, which was used for the first time to extract N-metal covalency parameters. We find that upon oxygenation of the bis-thiolate compound (bmmp-TASN)­RuPPh₃ to the sulfenato species (bmmp-O₂-TASN)­RuPPh₃ and then to the mixed sulfenato/sulfinato speices (bmmp-O₃-TASN)­RuPPh₃ the complexes become progressively more ionic, and hence the Ru^II center becomes a harder Lewis acid. These findings are reinforced by hybrid DFT calculations (B­(38HF)­P86) using a large quadruple-ζ basis set. The biological implications of these findings in relation to the NHase catalytic cycle are discussed in terms of the creation of a harder Lewis acid, which aids in nitrile hydrolysis

Model Peptide Studies Reveal a Mixed Histidine-Methionine Cu(I) Binding Site at the N‑Terminus of Human Copper Transporter 1

Copper is a vital metal cofactor in enzymes that are essential to myriad biological processes. Cellular acquisition of copper is primarily accomplished through the Ctr family of plasma membrane copper transport proteins. Model peptide studies indicate that the human Ctr1 N-terminus binds to Cu­(II) with high affinity through an amino terminal Cu­(II), Ni­(II) (ATCUN) binding site. Unlike typical ATCUN-type peptides, the Ctr1 peptide facilitates the ascorbate-dependent reduction of Cu­(II) bound in its ATCUN site by virtue of an adjacent HH (<i>bis</i>-His) sequence in the peptide. It is likely that the Cu­(I) coordination environment influences the redox behavior of Cu bound to this peptide; however, the identity and coordination geometry of the Cu­(I) site has not been elucidated from previous work. Here, we show data from NMR, XAS, and structural modeling that sheds light on the identity of the Cu­(I) binding site of a Ctr1 model peptide. The Cu­(I) site includes the same <i>bis</i>-His site identified in previous work to facilitate ascorbate-dependent Cu­(II) reduction. The data presented here are consistent with a rational mechanism by which Ctr1 provides coordination environments that facilitate Cu­(II) reduction prior to Cu­(I) transport

Model Peptide Studies Reveal a Mixed Histidine-Methionine Cu(I) Binding Site at the N‑Terminus of Human Copper Transporter 1

Copper is a vital metal cofactor in enzymes that are essential to myriad biological processes. Cellular acquisition of copper is primarily accomplished through the Ctr family of plasma membrane copper transport proteins. Model peptide studies indicate that the human Ctr1 N-terminus binds to Cu­(II) with high affinity through an amino terminal Cu­(II), Ni­(II) (ATCUN) binding site. Unlike typical ATCUN-type peptides, the Ctr1 peptide facilitates the ascorbate-dependent reduction of Cu­(II) bound in its ATCUN site by virtue of an adjacent HH (<i>bis</i>-His) sequence in the peptide. It is likely that the Cu­(I) coordination environment influences the redox behavior of Cu bound to this peptide; however, the identity and coordination geometry of the Cu­(I) site has not been elucidated from previous work. Here, we show data from NMR, XAS, and structural modeling that sheds light on the identity of the Cu­(I) binding site of a Ctr1 model peptide. The Cu­(I) site includes the same <i>bis</i>-His site identified in previous work to facilitate ascorbate-dependent Cu­(II) reduction. The data presented here are consistent with a rational mechanism by which Ctr1 provides coordination environments that facilitate Cu­(II) reduction prior to Cu­(I) transport

Modulation of Luminescence by Subtle Anion–Cation and Anion−π Interactions in a Trigonal Au^I···Cu^I Complex

The trigonally coordinated [AuCu­(PPh₂py)₃]­(BF₄)₂ (<b>1</b>) crystallizes in two polymorphs and a pseudopolymorph, each of which contains a trigonally coordinated cation with short Au^I–Cu^I separations of ∼2.7 Å. Under UV illumination, these crystals luminesce different colors ranging from blue to yellow. The structures of these cations are nearly superimposable, and the primary difference resides in the relative placement of the anions and solvate molecules. As confirmed by time-dependent density functional theory calculations, it is these interactions that are responsible for the differential emission properties

Isolation of a (Dinitrogen)Tricopper(I) Complex

Reaction of a tris­(β-diketimine) cyclophane, H₃<b>L</b>, with benzyl potassium followed by [Cu­(OTf)]₂(C₆H₆) affords a tricopper­(I) complex containing a bridging dinitrogen ligand. rRaman (ν_N–N = 1952 cm^–1) and ¹⁵N NMR (δ = 303.8 ppm) spectroscopy confirm the presence of the dinitrogen ligand. DFT calculations and QTAIM analysis indicate minimal metal-dinitrogen back-bonding with only one molecular orbital of significant N2­(2pπ*) and Cu­(3dπ)/Cu­(3dσ) character (13.6% N, 70.9% Cu). ∇²ρ values for the Cu–N₂ bond critical points are analogous to those for polar closed-shell/closed-shell interactions

Isolation of a (Dinitrogen)Tricopper(I) Complex

Reaction of a tris­(β-diketimine) cyclophane, H₃<b>L</b>, with benzyl potassium followed by [Cu­(OTf)]₂(C₆H₆) affords a tricopper­(I) complex containing a bridging dinitrogen ligand. rRaman (ν_N–N = 1952 cm^–1) and ¹⁵N NMR (δ = 303.8 ppm) spectroscopy confirm the presence of the dinitrogen ligand. DFT calculations and QTAIM analysis indicate minimal metal-dinitrogen back-bonding with only one molecular orbital of significant N2­(2pπ*) and Cu­(3dπ)/Cu­(3dσ) character (13.6% N, 70.9% Cu). ∇²ρ values for the Cu–N₂ bond critical points are analogous to those for polar closed-shell/closed-shell interactions