Modeling the resting state of oxalate oxidase and oxalate decarboxylase enzymes

Ultrasonic Clusterization Process to Prepare [(NNCO)6Co4Cl2] as a Novel Double-Open-Co4O6 Cubane Cluster: SXRD Interactions, DFT, Physicochemical, Thermal Behaviors, and Biomimicking of Catecholase Activity

A novel double-open-cubane (NNCO)6Co4Cl2 cluster with a Co4O6 core was made available under aqua-ultrasonic open atmosphere conditions for the first time. The ultrasonic clusterization of the (3,5-dimethyl-1H-pyrazol-1-yl)methanol (NNCOH) ligand with CoCl2·6H2O salts in ethanol yielded a high-purity and high-yield cluster product. Energy-dispersive X-ray (EDX), Fourier transform infrared (FT-IR), and ultraviolet (UV)-visible techniques were used to elucidate the clusterization process. The double-open-Co4O6 cubane structure of the (NNCO)6Co4Cl2 cluster was solved by synchrotron single-crystal X-ray diffraction (SXRD) and supported by density functional theory (DFT) optimization and thermogravimetric/differential TG (TG/DTG) measurements; moreover, the DFT structural parameters correlated with the ones determined by SXRD. Molecular electrostatic potential (MEP), Mulliken atomic charge/natural population analysis (MAC/NPA), highest occupied molecular orbital/lowest unoccupied molecular orbital (HOMO/LUMO), density of states (DOS), and GRD quantum analyses were computed at the DFT/B3LYP/6-311G(d,p) theory level. The thermal behavior of the cluster was characterized to support the formation of the Co4O6 core as a stable final product. The catalytic property of the (NNCO)6Co4Cl2 cluster was predestined for the oxidation process of 3,5-DTBC diol (3,5-di-tert-butylbenzene-1,2-diol) to 3,5-DTBQ dione (3,5-di-tert-butylcyclohexa-3,5-diene-1,2-dione).

Bioinspired mononuclear Mn complexes for O2 activation and biologically relevant reactions

A general interest in harnessing the oxidizing power of dioxygen (O₂) continues to motivate research efforts on bioinspired and biomimetic complexes to better understand how metalloenzymes mediate these reactions. The ubiquity of Fe- and Cu-based enzymes attracts significant attention and has resulted in many noteworthy developments for abiotic systems interested in direct O₂ reduction and small molecule activation. However, despite the existence of Mn-based metalloenzymes with important O₂-dependent activity, there has been comparatively less focus on the development of these analogues relative to Fe- and Cu-systems. In this Perspective, we summarize important contributions to the development of bioinspired mononuclear Mn complexes for O₂ activation and studies on their reactivity, emphasizing important design parameters in the primary and secondary coordination spheres and outlining mechanistic trends.

Understanding the Effect of the Electron Spin Relaxation on the Relaxivities of Mn(II) Complexes with Triazacyclononane Derivatives

Investigating the relaxation of water ¹H nuclei induced by paramagnetic Mn(II) complexes is important to understand the mechanisms that control the efficiency of contrast agents used in diagnostic magnetic resonance imaging (MRI). Herein, a series of potentially hexadentate triazacyclononane (TACN) derivatives containing different pendant arms were designed to explore the relaxation of the electron spin in the corresponding Mn(II) complexes by using a combination of ¹H NMR relaxometry and theoretical calculations. These ligands include 1,4,7-triazacyclononane-1,4,7-triacetic acid (H₃NOTA) and three derivatives in which an acetate group is replaced by sulfonamide (H₃NO2ASAm), amide (H₂NO2AM), or pyridyl (H₂NO2APy) pendants. The analogue of H₃NOTA containing three propionate pendant arms (H₃NOTPrA) was also investigated. The X-ray structure of the derivative containing two acetate groups and a sulfonamide pendant arm [Mn(NO2ASAm)]^- evidenced six-coordination of the ligand to the metal ion, with the coordination polyhedron being close to a trigonal prism. The relaxivities of all complexes at 20 MHz and 25 °C (1.1-1.3 mM^-1 s^-1) are typical of systems that lack water molecules coordinated to the metal ion. The nuclear magnetic relaxation profiles evidence significant differences in the relaxivities of the complexes at low fields (<1 MHz), which are associated with different spin relaxation rates. The zero field splitting (ZFS) parameters calculated by using DFT and CASSCF methods show that electronic relaxation is relatively insensitive to the nature of the donor atoms. However, the twist angle of the two tripodal faces that delineate the coordination polyhedron, defined by the N atoms of the TACN unit (lower face) and the donor atoms of the pendant arms (upper face), has an important effect in the ZFS parameters. A twist angle close to the ideal value for an octahedral coordination (60°), such as that in [Mn(NOTPrA)]^-, leads to a small ZFS energy, whereas this value increases as the coordination polyhedron approaches to a trigonal prism.

Binding and Energetics of Electron Transfer between an Artificial Four-Helix Mn-Protein and Reaction Centers from Rhodobacter sphaeroides

The ability of an artificial four-helix bundle Mn-protein, P1, to bind and transfer an electron to photosynthetic reaction centers from the purple bacterium Rhodobacter sphaeroides was characterized using optical spectroscopy. Upon illumination of reaction centers, an electron is transferred from P, the bacteriochlorophyll dimer, to Q_A, the primary electron acceptor. The P1 Mn-protein can bind to the reaction center and reduce the oxidized bacteriochlorophyll dimer, P⁺, with a dissociation constant of 1.2 μM at pH 9.4, comparable to the binding constant of c-type cytochromes. Amino acid substitutions of surface residues on the Mn-protein resulted in increases in the dissociation constant to 8.3 μM. The extent of reduction of P⁺ by the P1 Mn-protein was dependent on the P/P⁺ midpoint potential and the pH. Analysis of the free energy difference yielded a midpoint potential of approximately 635 mV at pH 9.4 for the Mn cofactor of the P1 Mn-protein, a value similar to those found for other Mn cofactors in proteins. The linear dependence of -56 mV/pH is consistent with one proton being released upon Mn oxidation, allowing the complex to maintain overall charge neutrality. These outcomes demonstrate the feasibility of designing four-helix bundles and other artificial metalloproteins to bind and transfer electrons to bacterial reaction centers and establish the usefulness of this system as a platform for designing sites to bind novel metal cofactors capable of performing complex oxidation-reduction reactions.

Biological functions controlled by manganese redox changes in mononuclear Mn-dependent enzymes

Remarkably few enzymes are known to employ a mononuclear manganese ion that undergoes changes in redox state during catalysis. Many questions remain to be answered about the role of substrate binding and/or protein environment in modulating the redox properties of enzyme-bound Mn(II), the nature of the dioxygen species involved in the catalytic mechanism, and how these enzymes acquire Mn(II) given that many other metal ions in the cell form more stable protein complexes. Here, we summarize current knowledge concerning the structure and mechanism of five mononuclear manganese-dependent enzymes: superoxide dismutase, oxalate oxidase (OxOx), oxalate decarboxylase (OxDC), homoprotocatechuate 3,4-dioxygenase, and lipoxygenase (LOX). Spectroscopic measurements and/or computational studies suggest that Mn(III)/Mn(II) are the catalytically active oxidation states of the metal, and the importance of 'second-shell' hydrogen bonding interactions with metal ligands has been demonstrated for a number of examples. The ability of these enzymes to modulate the redox properties of the Mn(III)/Mn(II) couple, thereby allowing them to generate substrate-based radicals, appears essential for accessing diverse chemistries of fundamental importance to organisms in all branches of life.

Oxygen activation by mononuclear Mn, Co, and Ni centers in biology and synthetic complexes

The active sites of metalloenzymes that catalyze O₂-dependent reactions generally contain iron or copper ions. However, several enzymes are capable of activating O₂ at manganese or nickel centers instead, and a handful of dioxygenases exhibit activity when substituted with cobalt. This minireview summarizes the catalytic properties of oxygenases and oxidases with mononuclear Mn, Co, or Ni active sites, including oxalate-degrading oxidases, catechol dioxygenases, and quercetin dioxygenase. In addition, recent developments in the O₂ reactivity of synthetic Mn, Co, or Ni complexes are described, with an emphasis on the nature of reactive intermediates featuring superoxo-, peroxo-, or oxo-ligands. Collectively, the biochemical and synthetic studies discussed herein reveal the possibilities and limitations of O₂ activation at these three "overlooked" metals.

A family of complexes with N-scorpionate-type and other N-donor ligands obtained in situ from pyrazole derivative and zerovalent cobalt. Physicochemical and cytotoxicity studies

In this paper we described one pot synthetic pathways which generated in situ three complexes which contain three different ligands: N,N,N-tris(3,5-dimethylpyrazolylmethyl)amine (L¹), urotropine (L²) and 3,5-dimethylpyrazole (L³).

High-affinity manganese coordination by human calprotectin is calcium-dependent and requires the histidine-rich site formed at the dimer interface

Calprotectin (CP) is a transition metal-chelating antimicrobial protein of the calcium-binding S100 family that is produced and released by neutrophils. It inhibits the growth of various pathogenic microorganisms by sequestering the transition metal ions manganese and zinc. In this work, we investigate the manganese-binding properties of CP. We demonstrate that the unusual His(4) motif (site 2) formed at the S100A8/S100A9 dimer interface is the site of high-affinity Mn(II) coordination. We identify a low-temperature Mn(II) spectroscopic signal for this site consistent with an octahedral Mn(II) coordination sphere with simulated zero-field splitting parameters D = 270 MHz and E/D = 0.30 (E = 81 MHz). This analysis, combined with studies of mutant proteins, suggests that four histidine residues (H17 and H27 of S100A8; H91 and H95 of S100A9) coordinate Mn(II) in addition to two as-yet unidentified ligands. The His(3)Asp motif (site 1), which is also formed at the S100A8/S100A9 dimer interface, does not provide a high-affinity Mn(II) binding site. Calcium binding to the EF-hand domains of CP increases the Mn(II) affinity of the His(4) site from the low-micromolar to the mid-nanomolar range. Metal-ion selectivity studies demonstrate that CP prefers to coordinate Zn(II) over Mn(II). Nevertheless, the specificity of Mn(II) for the His(4) site provides CP with the propensity to form mixed Zn:Mn:CP complexes where one Zn(II) ion occupies site 1 and one Mn(II) ion occupies site 2. These studies support the notion that CP responds to physiological calcium ion gradients to become a high-affinity transition metal ion chelator in the extracellular space where it inhibits microbial growth.

Theoretical and experimental investigation of the semiquinone forms of protocatechuic acid. The effect of manganese

Ten oxidized, oxygenated and dimeric forms of protocatechuic acid (PCA, 3,4-dihydroxybenzoic acid, 3,4-DHBA) have been studied using DFT calculations (at the B3LYP/TZVP level of theory) and their structural and spectroscopic parameters (electronic transitions, NMR resonances) have been calculated. Combination with experimental results (under anaerobic or aerobic environment) determines the conditions for the existence of protonated, fully deprotonate and/or oxygenated semiquinones of PCA. Several energy optimized conformers containing manganese-(PCA-semiquinones) and water or/and peroxo-groups have been drawn (species 11-16) and their structural and spectroscopic properties have been calculated at the same level of theory. Experimental parallel to the theoretical results provide evidence for the existence of Mn(II)- and Mn(III)-[PCA-semiquinone] as well the conditions of dioxygen activation. Two of the blue solids (17 and 18) isolated from these solutions, have been characterized. Elemental analyzes, TGA, IR and ESR spectra support the formulation Mn(2)(PCA)(2)(O(2))(OH)(2)(AcO)(ClO(4))(2)(H(2)O)(3) (17), and Mn(2)(PCA)(2)(O(2))(2)(OH)(2)(AcO)H(2)O (18). Their ESR spectra, in solution (blue solutions), are almost identical and indicative of Mn(IV) existence. From the whole investigation, the activation of dioxygen by the PCA, its relocation on manganese and the oxidation of the metal ion have been provided.

Understanding the influence of the protein environment on the Mn(II) centers in Superoxide Dismutases using High-Field Electron Paramagnetic Resonance

One of the most puzzling questions of manganese and iron superoxide dismutases (SODs) is what is the basis for their metal-specificity. This review summarizes our findings on the Mn(II) electronic structure of SODs and related synthetic models using high-field high-frequency electron paramagnetic resonance (HFEPR), a technique that is able to achieve a very detailed and quantitative information about the electronic structure of the Mn(II) ions. We have used HFEPR to compare eight different SODs, including iron, manganese and cambialistic proteins. This comparative approach has shown that in spite of their high structural homology each of these groups have specific spectroscopic and biochemical characteristics. This has allowed us to develop a model about how protein and metal interactions influence protein pK, inhibitor binding and the electronic structure of the manganese center. To better appreciate the thermodynamic prerequisites required for metal discriminatory SOD activity and their relationship to HFEPR spectroscopy, we review the work on synthetic model systems that functionally mimic Mn-and FeSOD. Using a single ligand framework, it was possible to obtain metal-discriminatory "activity" as well as variations in the HFEPR spectra that parallel those found in the proteins. Our results give new insights into protein-metal interactions from the perspective of the Mn(II) and new steps towards solving the puzzle of metal-specificity in SODs.

Corroborative cobalt and zinc model compounds of alpha-amino-beta-carboxymuconic-epsilon-semialdehyde decarboxylase (ACMSD)

We have synthesised and characterised a series of new Co(II) complexes (1-4, 6, 7) and one new Zn(II) complex (5) employing N(3)- and N(3)O-donor ligands [biap: N,N-bis(2-ethyl-5-methyl-imidazol-4-ylmethyl)amino-propane, KBPZG: potassium N,N-bis(3,5-dimethylpyrazolylmethyl) glycinate, KBPZA: potassium N,N-bis(3,5-dimethylpyrazolylmethyl) alaninate, KB(i)PrPZG: potassium N,N-bis(3,5-di-iso-propylpyrazolylmethyl) glycinate, and KB((t)BuM)PZG: potassium N,N-bis(3-methyl-5-tert-butyl-pyrazolylmethyl)glycinate] as structural models of the metalloenzyme alpha-amino-beta-carboxymuconic-epsilon-semialdehyde decarboxylase (ACMSD). These complexes were characterised by several techniques including X-ray crystallographic analysis, X-band EPR, and mass spectrometry (ESI-MS). The crystal structures of 1, 2, 6,7 revealed that they exist as mononuclear Co(II) complexes with trigonal-bipyramidal geometry in the solid state. Compounds 3 and 5 form infinite polymeric chains of Co(II) or Zn(II) complexes, respectively, linked by the pendant carboxylate arms of the BPZG(-) ligand. By comparing the degree of distortion in the penta-coordinate complexes, defined by the Addison-parameter tau, with the value determined for the five-coordinate centres found in the active site of ACMSD, it could be seen that complexes 5 and 7 are very good matches for the geometry of the zinc(II) centre in monomer A of the native enzyme. All complexes could be seen as model compounds for the active site of the enzyme ACMSD, where the Co(II) complexes reflected the structural flexibility found in case of two histidine (His177 and His228) residues found in the active site of the enzyme.