Cobalt-substituted zinc finger 3 of transcription factor IIIA: interactions with cognate DNA detected by (31)P ENDOR spectroscopy

Electronic Structure of Three-Coordinate FeII and CoII β-Diketiminate Complexes

The β-diketiminate supporting group, [ArNCRCHCRNAr]-, stabilizes low coordination number complexes. Four such complexes, where R = tert-butyl, Ar = 2,6-diisopropylphenyl, are studied: (nacnactBu)ML, where M = FeII, CoII and L = Cl, CH3. These are denoted FeCl, FeCH3, CoCl, and CoCH3 and have been previously reported and structurally characterized. The two FeII complexes (S = 2) have also been previously characterized by Mössbauer spectroscopy, but only indirect assessment of the ligand-field splitting and zero-field splitting (zfs) parameters was available. Here, EPR spectroscopy is used, both conventional field-domain for the CoII complexes (with S = 3/2) and frequency-domain, far-infrared magnetic resonance spectroscopy (FIRMS) for all four complexes. The CoII complexes were also studied by magnetometry. These studies allow accurate determination of the zfs parameters. The two FeII complexes are similar with nearly axial zfs and large magnitude zfs given by D = -37 ± 1 cm-1 for both. The two CoII complexes likewise exhibit large and nearly axial zfs, but surprisingly, CoCl has positive D = +55 cm-1 while CoCH3 has negative D = -49 cm-1. Theoretical methods were used to probe the electronic structures of the four complexes, which explain the experimental spectra and the zfs parameters.

Synthesis, structure, and characterisation of a ferromagnetically coupled dinuclear complex containing Co(II) ions in a high spin configuration and thiodiacetate and phenanthroline as ligands and of a series of isomorphous heterodinuclear complexes containing different Co : Zn ratios

We report the synthesis, crystal structure, and characterisation of a dinuclear Co(II) compound with thiodiacetate (tda) and phenanthroline (phen) as ligands (1), and of a series of metal complexes isomorphous to 1 with different Co : Zn ratios (2, 4 : 1; 3, 1 : 1; 4, 1 : 4; 5, 1 : 10). General characterisation methodologies and X-ray data showed that all the synthesised complexes are isomorphous to Zn(II) and Cu(II) analogues (CSD codes: DUHXEL and BEBQII). 1 consists of centrosymmetric Co(II) ion dimers in which the ions are 3.214 Å apart, linked by two μ-O bridges. Each cobalt atom is in a distorted octahedral environment of the N2O3S type. UV-vis spectra of 1 and 5 are in line with high spin (S = 3/2) Co(II) ions in octahedral coordination and indicate that the electronic structure of both Co(II) ions in the dinuclear unit does not significantly change relative to that of the magnetically isolated Co(II) ion. EPR spectra of powder samples of 5 (Co : Zn ratio of 1 : 10) together with spectral simulation indicated high spin Co(II) ions with high rhombic distortion of the zfs [E/D = 0.31(1), D > 0]. DC magnetic susceptibility experiments on 1 and analysis of the data constraining the E/D value obtained by EPR yielded g = 2.595(7), |D| = 61(1) cm-1, and an intradimer ferromagnetic exchange coupling of J = 1.39(4) cm-1. EPR spectra as a function of Co : Zn ratio for both powder and single crystal samples confirmed that they result from two effective S' = 1/2 spins that interact through dipolar and isotropic exchange interactions to yield magnetically isolated S' = 1 centres and that interdimeric exchange interactions, putatively mediated by hydrophobic interactions between phen moieties, are negligible. The latter observation contrasts with that observed in the Cu(II) analogue, where a transition from S = 1 to S' = 1/2 was observed. Computational calculations indicated that the absence of the interdimeric exchange interaction in 1 is due to a lower Co(II) ion spin density delocalisation towards the metal ligands.

Cobalt(II) "Scorpionate" complexes as electronic ground state models for cobalt-substituted zinc enzymes: Structure investigation by magnetic circular dichroism

Zinc centers in pseudo-tetrahedral geometry are widely found in biology, often with three histidine ligands from protein. The trispyrazolylborate "scorpionate" ligand is used as a model for this tris(histidine) motif, and spectroscopically active Co^II is often used as a substitute for spectroscopically silent Zn^II. In this work, four pseudo-tetrahedral scorpionate complexes with the formula (Tp^t-Bu,Tn)CoL, where Tp^t-Bu,Tn = hydrotris(3-tert-butyl, 5-2'-thienyl-pyrazol-1-yl)borate anion and L = Cl^-, N₃^-, NCO^-, or NCS^-, were studied using variable-temperature, variable-field magnetic circular dichroism (VTVH MCD) spectroscopy. The major goal was to determine the axial and rhombic zero field splitting (ZFS) parameters (D and E, respectively) of these S = 3/2 systems and compare these ZFS parameters to those determined previously by high-frequency and -field electron paramagnetic resonance (HFEPR) spectroscopy on the same (L = Cl^- and NCS^-) or closely related complexes. Additionally, HFEPR studies were undertaken here on the complexes with L = N₃^-, NCO^-. Crystal structures for these two complexes are also first reported here. The values of D determined by VTVH MCD were + 12.8 and + 3.6 cm^-1 for the L = Cl^- and NCS^- complexes, respectively. These values are in close agreement with those for the same complexes as previously determined by HFEPR. The values of D determined by VTVH MCD were + 3.0 and + 6.6 cm^-1 for the L = N₃^- and NCO^- complexes, respectively. These values were not as close to those determined by HFEPR in the present study, which are 4.2 cm^-1 ≤ |D| ≤ 5.6 cm^-1 in Tp^t-Bu,TnCoN₃, and 8.3 cm^-1 ≤ |D| ≤ 11.0 cm^-1 in Tp^t-Bu,TnCoNCO. The bands in MCD spectra of these complexes were assigned in C_3v symmetry and a complete ligand-field analysis of the MCD data was made using the Angular Overlap Model (AOM), which is compared to previous results.

Solvent water interactions within the active site of the membrane type I matrix metalloproteinase

Matrix metalloproteinases (MMP) are an important family of proteases which catalyze the degradation of extracellular matrix components. While the mechanism of peptide cleavage is well established, the process of enzyme regeneration, which represents the rate limiting step of the catalytic cycle, remains unresolved. This step involves the loss of the newly formed N-terminus (amine) and C-terminus (carboxylate) protein fragments from the site of catalysis coupled with the inclusion of one or more solvent waters. Here we report a novel crystal structure of membrane type I MMP (MT1-MMP or MMP-14), which includes a small peptide bound at the catalytic Zn site via its C-terminus. This structure models the initial product state formed immediately after peptide cleavage but before the final proton transfer to the bound amine; the amine is not present in our system and as such proton transfer cannot occur. Modeling of the protein, including earlier structural data of Bertini and coworkers [I. Bertini, et al., Angew. Chem., Int. Ed., 2006, 45, 7952-7955], suggests that the C-terminus of the peptide is positioned to form an H-bond network to the amine site, which is mediated by a single oxygen of the functionally important Glu240 residue, facilitating efficient proton transfer. Additional quantum chemical calculations complemented with magneto-optical and magnetic resonance spectroscopies clarify the role of two additional, non-catalytic first coordination sphere waters identified in the crystal structure. One of these auxiliary waters acts to stabilize key intermediates of the reaction, while the second is proposed to facilitate C-fragment release, triggered by protonation of the amine. Together these results complete the enzymatic cycle of MMPs and provide new design criteria for inhibitors with improved efficacy.

Co(II) Coordination in Prokaryotic Zinc Finger Domains as Revealed by UV-Vis Spectroscopy

Co(II) electronic configuration allows its use as a spectroscopic probe in UV-Vis experiments to characterize the metal coordination sphere that is an essential component of the functional structure of zinc-binding proteins and to evaluate the metal ion affinities of these proteins. Here, exploiting the capability of the prokaryotic zinc finger to use different combinations of residues to properly coordinate the structural metal ion, we provide the UV-Vis characterization of Co(II) addition to Ros87 and its mutant Ros87_C27D which bears an unusual CysAspHis₂ coordination sphere. Zinc finger sites containing only one cysteine have been infrequently characterized. We show for the CysAspHis₂ coordination an intense d-d transition band, blue-shifted with respect to the Cys₂His₂ sphere. These data complemented by NMR and CD data demonstrate that the tetrahedral geometry of the metal site is retained also in the case of a single-cysteine coordination sphere.

Paramagnetic Resonance of Cobalt(II) Trispyrazolylmethanes and Counterion Association

Paramagnetic resonance studies (EPR, ESEEM, ENDOR, and NMR) of a series of cobalt(II) bis-trispyrazolylmethane tetrafluoroborates are presented. The complexes studied include the parent, unsubstituted ligand (Tpm), two pyrazole-substituted derivatives (4Me and 3,5-diMe), and tris(1-pyrazolyl)ethane (Tpe), which includes a methyl group on the apical carbon atom. NMR and ENDOR establish the magnitude of ¹H hyperfine couplings, while ESEEM provides information on the coordinated ¹⁴N. The data show that the pyrazole 3-position is more electron rich in the Tpm analogues, that the geometry about the apical atom influences the magnetic resonance, and that apical atom geometry appears more fixed in Tpm than in Tp. NMR and ENDOR establish that the BF₄^- counterion remains associated in fluid solution. In the case of the Tpm^3,5Me complex, it appears to associate in solution, in the same position it occupies in the X-ray structure.

A role for hydrogen bonding in DNA recognition by the non-classical CCHHC type zinc finger, NZF-1

The non-classical zinc finger protein, Neural Zinc Finger Factor-1, contains six Cys2His2Cys domains. All three cysteines and the second histidine directly bind Zn(II). Using a combination of mutagenesis, metal coordination and DNA binding studies, we report that the first histidine is involved in a functionally important hydrogen bonding interaction.

Magnetic properties of weakly exchange-coupled high spin Co(II) ions in pseudooctahedral coordination evaluated by single crystal X-band EPR spectroscopy and magnetic measurements

We report single-crystal X-band EPR and magnetic measurements of the coordination polymer catena-(trans-(μ2-fumarato)tetraaquacobalt(II)), 1, and the Co(II)-doped Zn(II) analogue, 2, in different Zn:Co ratios. 1 presents two magnetically inequivalent high spin S = 3/2 Co(II) ions per unit cell, named A and B, in a distorted octahedral environment coordinated to four water oxygen atoms and trans coordinated to two carboxylic oxygen atoms from the fumarate anions, in which the Co(II) ions are linked by hydrogen bonds and fumarate molecules. Magnetic susceptibility and magnetization measurements of 1 indicate weak antiferromagnetic exchange interactions between the S = 3/2 spins of the Co(II) ions in the crystal lattice. Oriented single crystal EPR experiments of 1 and 2 were used to evaluate the molecular g-tensor and the different exchange coupling constants between the Co(II) ions, assuming an effective spin S′= 1/2. Unexpectedly, the eigenvectors of the molecular g-tensor were not lying along any preferential bond direction, indicating that, in high spin Co(II) ions in roughly octahedral geometry with approximately axial EPR signals, the presence of molecular pseudo axes in the metal site does not determine preferential directions for the molecular g-tensor. The EPR experiment and magnetic measurements, together with a theoretical analysis relating the coupling constants obtained from both techniques, allowed us to evaluate selectively the exchange coupling constant associated with hydrogen bonds that connect magnetically inequivalent Co(II) ions (|JAB(1/2)| = 0.055(2) cm(–1)) and the exchange coupling constant associated with a fumarate bridge connecting equivalent Co(II) ions (|JAA(1/2)| ≈ 0.25 (1) cm(–1)), in good agreement with the average J(3/2) value determined from magnetic measurements.

Characterization of a cobalt-specific P(1B)-ATPase

The P(1B)-type ATPases are a ubiquitous family of P-type ATPases involved in the transport of transition metal ions. Divided into subclasses based on sequence characteristics and substrate specificity, these integral membrane transporters play key roles in metal homeostasis, metal tolerance, and the biosynthesis of metalloproteins. The P(1B-4)-ATPases have the simplest architecture of the five P(1B)-ATPase families and have been suggested to play a role in Co(2+) transport. A P(1B-4)-ATPase from Sulfitobacter sp. NAS-14.1, designated sCoaT, has been cloned, expressed, and purified. Activity assays indicate that sCoaT is specific for Co(2+). A single Co(2+) binding site is present, and optical, electron paramagnetic resonance, and X-ray absorption spectroscopic data are consistent with tetrahedral coordination by oxygen and nitrogen ligands, including a histidine and likely a water. Surprisingly, there is no evidence for coordination by sulfur. Mutation of a conserved cysteine residue, Cys 327, in the signature transmembrane Ser-Pro-Cys metal binding motif does not abolish the ATP hydrolysis activity or affect the spectroscopic analysis, establishing that this residue is not involved in the initial Co(2+) binding by sCoaT. In contrast, replacements of conserved transmembrane residues Ser 325, His 657, Glu 658, and Thr 661 with alanine abolish ATP hydrolysis activity and Co(2+) binding, indicating that these residues are necessary for Co(2+) transport. These data represent the first in vitro characterization of a P(1B-4)-ATPase and its Co(2+) binding site.

Multifrequency EPR study of Fe3+ and Co2+ in the active site of desulforedoxin

The understanding of the electronic structure of S > 1/2 transition-metal sites that show a large zero-field splitting (ZFS) of the magnetic sublevels benefits greatly from study by electron-paramagnetic-resonance (EPR) spectroscopy at frequencies above the standard 9.5 GHz. However, high-frequency EPR spectroscopy is technically challenging and still developing. Particularly the sensitivity of high-frequency EPR spectrometers is often too low to apply the technique in the study of transition-metal sites in proteins and enzymes. Here we report a multifrequency EPR study (at 9.5, 94.9, and 275.7 GHz) of the active site of the protein desulforedoxin, both in its natural Fe(3+) form and substituted with Co(2+). The 275.7 GHz EPR spectra made it possible to determine the ZFS parameters of the Fe(3+) site with high precision. No 275.7 GHz spectrum could be observed of the Co(2+) site, but based on 9.5 GHz spectra, its ZFS parameters could be estimated. We find that the typical variation in the geometry of the active site of a protein or enzyme, referred to as conformational strain, does not only make the detection of EPR spectra challenging, but also their analysis. Comparison of the EPR results on the active site of desulforedoxin to those of the closely related active site of rubredoxin illustrates the necessity of explicit quantum-chemical calculations in order to interrelate the electronic and geometric structure of biological transition-metal sites.

Cysteine and histidine shuffling: mixing and matching cysteine and histidine residues in zinc finger proteins to afford different folds and function

Zinc finger proteins utilize zinc for structural purposes: zinc binds to a combination of cysteine and histidine ligands in a tetrahedral coordination geometry facilitating protein folding and function. While much is known about the classical zinc finger proteins, which utilize a Cys(2)His(2) ligand set to coordinate zinc and fold into an anti-parallel beta sheet/alpha helical fold, there are thirteen other families of 'non-classical' zinc finger proteins for which relationships between metal coordination and protein structure/function are less defined. This 'Perspective' article focuses on two classes of these non-classical zinc finger proteins: Cys(3)His type zinc finger proteins and Cys(2)His(2)Cys type zinc finger proteins. These proteins bind zinc in a tetrahedral geometry, like the classical zinc finger proteins, yet they adopt completely different folds and target different oligonucleotides. Our current understanding of the relationships between ligand set, metal ion, fold and function for these non-classical zinc fingers is discussed.

Zinc finger proteins as templates for metal ion exchange and ligand reactivity. Chemical and biological consequences

Zinc finger reactions with inorganic ions and coordination compounds are as diverse as the zinc fingers themselves. Use of metal ions such as Co(2+) and Cd(2+) has given structural, thermodynamic and kinetic information on zinc fingers and zinc-finger-DNA/RNA interactions. It is a general truism that alteration of the coordination sphere in the finger environment will disrupt the recognition with DNA/RNA and this has implications for mechanism of toxicity and carcinogenesis of metal ions. Structural zinc fingers are susceptible to electrophilic attack and the recognition that the coordination sphere of inorganic compounds may be modulated for control of electrophilic attack on zinc fingers raises the possibility of systematic studies of zinc fingers as drug targets using inorganic chemistry. Some inorganic compounds such as those of As(III) and Au(I) may exert their biological effects through inactivation of zinc fingers and novel approaches to specifically attack the zinc-bound ligands using Co(III)-Schiff bases and Platinum(II)-Nucleobase compounds have been proposed. The genomic importance of zinc fingers suggests that the "coordination chemistry" of zinc fingers themselves is ripe for exploration to design new targets for medicinal inorganic chemistry.

Anisotropic Fermi couplings due to large unquenched orbital angular momentum: Q-band (1)H, (14)N, and (11)B ENDOR of bis(trispyrazolylborate) cobalt(II)

We report Q-band ENDOR of (1)H, (14)N, and (11)B at the g( parallel) extreme of the EPR spectrum of bis(trispyrazolylborate) cobalt(II) [Co(Tp)(2)] and two structural analogs. This trigonally symmetric, high-spin (hs) S = 3/2 Co(II) complex shows large unquenched ground-state orbital angular momentum, which leads to highly anisotropic electronic g-values (g( parallel) = 8.48, g( perpendicular) = 1.02). The large g-anisotropy is shown to result in large dipolar couplings near g( parallel) and uniquely anisotropic (14)N Fermi couplings, which arise from spin transferred to the nitrogen 2s orbital (2.2%) via antibonding interactions with singly occupied metal d(x(2)-y(2)) and d(z(2)) orbitals. Large, well-resolved (1)H and (11)B dipolar couplings were also observed. Taken in concert with our previous X-band ENDOR measurements at g( perpendicular) ( Myers, W. K.; et al. Inorg. Chem. 2008, 47, 6701-6710 ), the present data allow a detailed analysis of the dipolar hyperfine tensors of two of the four symmetry distinct protons in the parent molecule. In the substituted analogs, changes in hyperfine coupling due to altered metal-proton distances give further evidence of an anisotropic Fermi contact interaction. For the pyrazolyl 3H proton, the data indicate a 0.2 MHz anisotropic contact interaction and approximately 4% transfer of spin away from Co(II). Dipolar coupling also dominates for the axial boron atoms, consistent with their distance from the Co(II) ion, and resolved (11)B quadrupolar coupling showed approximately 30% electronic inequivalence between the B-H and B-C sp(3) bonds. This is the first comprehensive ENDOR study of any hs Co(II) species and lays the foundation for future development.

Integrated paramagnetic resonance of high-spin Co(II) in axial symmetry: chemical separation of dipolar and contact electron-nuclear couplings

Integrated paramagnetic resonance, utilizing electron paramagnetic resonance (EPR), NMR, and electron-nuclear double resonance (ENDOR), of a series of cobalt bis-trispyrazolylborates, Co(Tp ( x )) 2, are reported. Systematic substitutions at the ring carbons and on the apical boron provide a unique opportunity to separate through-bond and through-space contributions to the NMR hyperfine shifts for the parent, unsubstituted Tp complex. A simple relationship between the chemical shift difference (delta H - delta Me) and the contact shift of the proton in that position is developed. This approach allows independent extraction of the isotropic hyperfine coupling, A iso, for each proton in the molecule. The Co..H contact coupling energies derived from the NMR, together with the known metrics of the compounds, were used to predict the ENDOR couplings at g perpendicular. Proton ENDOR data is presented that shows good agreement with the NMR-derived model. ENDOR signals from all other magnetic nuclei in the complex ( (14)N, coordinating and noncoordinating, (11)B and (13)C) are also reported.

Enzyme Control of Small-Molecule Coordination in FosA as Revealed by 31P Pulsed ENDOR and ESE-EPR

FosA is a manganese metalloglutathione transferase that confers resistance to the broad-spectrum antibiotic fosfomycin, which contains a phosphonate group. The active site of this enzyme consists of a high-spin Mn(2+) ion coordinated by endogenous ligands (a glutamate and two histidine residues) and by exogenous ligands, such as substrate fosfomycin. To study the Mn(2+) coordination environment of FosA in the presence of substrate and the inhibitors phosphonoformate and phosphate, we have used (31)P pulsed electron-nuclear double resonance (ENDOR) at 35 GHz to obtain metrical information from (31)P-Mn(2+) interactions. We have found that continuous wave (CW) (31)P ENDOR is not successful in the study of phosphates and phosphonates coordinated to Mn(2+). Parallel studies of phosph(on)ate binding to the Mn(2+) of FosA and to aqueous Mn(2+) ion disclose how the enzyme modifies the coordination of these molecules to the active site Mn(2+). Through analysis of (31)P hyperfine parameters derived from simulations of the ENDOR spectra we have determined the binding modes of the phosph(on)ates in each sample and discerned details of the geometric and electronic structure of the metal center. The (31)P ENDOR studies of the protein samples agree with, or improve on, the Mn-P distances determined from crystal structures and provide Mn-phosph(on)ate bonding information not available from these studies. Electron spin echo electron paramagnetic resonance (ESE-EPR) spectra have also been recorded. Simulation of these spectra yield the axial and rhombic components of the Mn(2+) (S = (5)/(2)) zero-field splitting (zfs) tensor. Comparison of structural inferences based on these zfs parameters both with the known enzyme structures and the (31)P ENDOR results establishes that the time-honored procedure of analyzing Mn(2+) zfs parameters to describe the coordination environment of the metal ion is not valid or productive.

Definitive spectroscopic determination of zero-field splitting in high-spin cobalt(II)

A high-spin Co(II) complex (3d(7), S = 3/2), Co(PPh(3))(2)Cl(2) (Ph = phenyl), has been investigated in the solid state by both high-frequency and -field electron paramagnetic resonance (HFEPR) and by variable-temperature, variable-field magnetic circular dichroism (VTVH-MCD). In HFEPR spectroscopy, the combination of variable sub-THz frequencies generated by backward wave oscillators (150-700 GHz, corresponding to energy 5-23 cm(-1)) and high magnetic fields (0-25 T) constitutes a novel experimental technique allowing accurate determination of a complete set of spin Hamiltonian parameters for this complex: D = -14.76(2) cm(-1), E = 1.141(8) cm(-1), g(x) = 2.166(4), g(y) = 2.170(4), g(z) = 2.240(5). Independent VTVH-MCD studies on multiple absorption bands of the complex yield D = -14(3) cm(-1), E = 0.96(20) cm(-1) (absolute value of E/D = 0.08(2)), g(x) = 2.15(5), g(y) = 2.16(4), and g(z) = 2.17(3). This very good agreement between HFEPR and MCD indicates that there is no inherent discrepancy between these two quite different experimental techniques. Thus, depending on the nature of the sample, either can be reliably used to determine zero-field splitting parameters in high-spin Co(II), with the HFEPR being more accurate but VTVH-MCD being more sensitive.