Daouda A K Traore

Structural Basis for Delivery of the Intact [Fe2S2] Cluster by Monothiol Glutaredoxin

Glutaredoxins (GRX) are redox proteins which use glutathione as a cofactor and are divided into two classes, monothiol and dithiol. In each class, several GRX have been shown to form [Fe2S2] cluster coordinating homodimers. The dithiol GRX homodimer is proposed to serve as a sequestration form and its iron-sulfur cluster as an oxidative stress sensor. In contrast, the monothiol GRX homodimer has been suggested to act as a scaffold for [Fe2S2] cluster delivery. We present here the structure of a monothiol GRX homodimer (Escherichia coli GRX4) coordinating a [Fe2S2] cluster that reveals the structural basis of intact iron-sulfur cluster delivery.

Structural and functional characterization of 2-oxo-histidine in oxidized PerR protein

In Bacillus subtilis, PerR is a metal-dependent sensor of hydrogen peroxide. PerR is a dimeric zinc protein with a regulatory site that coordinates either Fe(2+) (PerR-Zn-Fe) or Mn(2+) (PerR-Zn-Mn). Though most of the peroxide sensors use cysteines to detect H(2)O(2), it has been shown that reaction of PerR-Zn-Fe with H(2)O(2) leads to the oxidation of one histidine residue. Oxidation of PerR leads to the incorporation of one oxygen atom into His37 or His91. This study presents the crystal structure of the oxidized PerR protein (PerR-Zn-ox), which clearly shows a 2-oxo-histidine residue in position 37. Formation of 2-oxo-histidine is demonstrated and quantified by HPLC-MS/MS. EPR experiments indicate that PerR-Zn-H37ox retains a significant affinity for the regulatory metal, whereas PerR-Zn-H91ox shows a considerably reduced affinity for the metal ion. In spite of these major differences in terms of metal binding affinity, oxidation of His37 and/or His91 in PerR prevents DNA binding.

Crystal structure of the apo‐PerR‐Zn protein from Bacillus subtilis

Bacteria adapt to elevated levels of Reactive Oxygen Species (ROS) by increasing the expression of defence and repair proteins, which is regulated by ROS responsive transcription factors. In Bacillus subtilis the zinc protein PerR, a peroxide sensor that binds DNA in the presence of a regulatory metal Mn2+ or Fe2+, mediates the adaptive response to H2O2. This study presents the first crystal structure of apo‐PerR‐Zn which shows that all four cysteine residues of the protein are involved in zinc co‐ordination. The Zn(Cys)4 site locks the dimerization domain and stabilizes the dimer. Sequence alignment of PerR‐like proteins supports that this structural site may constitute a distinctive feature of this class of peroxide stress regulators.

Structural characterization of the active form of PerR: Insights into the metal-induced activation of PerR and fur proteins for DNA binding

In Bacillus subtilis, the transcription factor PerR is an iron dependant sensor of H2O2. The sensing mechanism relies on a selective metal catalysed oxidation of two histidine residues of the regulatory site. Here we present the first crystal structure of the active PerR protein in complex with a Mn2+ ion. In addition, X‐ray absorption spectroscopy experiments were performed to characterize the corresponding iron form of the protein. Both studies reveal a penta‐coordinate arrangement of the regulatory site that involves three histidines and two aspartates. One of the histidine ligand belongs to the N‐terminal domain. Binding of this residue to the regulatory metal allows the protein to adopt a caliper‐like conformation suited to DNA binding. Since this histidine is conserved in all PerR and a vast majority of Fur proteins, it is likely that the allosteric switch induced by the regulatory metal is general for this family of metalloregulators.

Biochemical and Structural Characterization of the Subclass B1 Metallo-β-Lactamase VIM-4

ABSTRACT The metallo-β-lactamase VIM-4, mainly found in Pseudomonas aeruginosa or Acinetobacter baumannii, was produced in Escherichia coli and characterized by biochemical and X-ray techniques. A detailed kinetic study performed in the presence of Zn2+ at concentrations ranging from 0.4 to 100 μM showed that VIM-4 exhibits a kinetic profile similar to the profiles of VIM-2 and VIM-1. However, VIM-4 is more active than VIM-1 against benzylpenicillin, cephalothin, nitrocefin, and imipenem and is less active than VIM-2 against ampicillin and meropenem. The crystal structure of the dizinc form of VIM-4 was solved at 1.9 Å. The sole difference between VIM-4 and VIM-1 is found at residue 228, which is Ser in VIM-1 and Arg in VIM-4. This substitution has a major impact on the VIM-4 catalytic efficiency compared to that of VIM-1. In contrast, the differences between VIM-2 and VIM-4 seem to be due to a different position of the flapping loop and two substitutions in loop 2. Study of the thermal stability and the activity of the holo- and apo-VIM-4 enzymes revealed that Zn2+ ions have a pronounced stabilizing effect on the enzyme and are necessary for preserving the structure.

Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides

Poly-C-binding proteins are triple KH (hnRNP K homology) domain proteins with specificity for single stranded C-rich RNA and DNA. They play diverse roles in the regulation of protein expression at both transcriptional and translational levels. Here, we analyse the contributions of individual αCP1 KH domains to binding C-rich oligonucleotides using biophysical and structural methods. Using surface plasmon resonance (SPR), we demonstrate that KH1 makes the most stable interactions with both RNA and DNA, KH3 binds with intermediate affinity and KH2 only interacts detectibly with DNA. The crystal structure of KH1 bound to a 5′-CCCTCCCT-3′ DNA sequence shows a 2:1 protein:DNA stoichiometry and demonstrates a molecular arrangement of KH domains bound to immediately adjacent oligonucleotide target sites. SPR experiments, with a series of poly-C-sequences reveals that cytosine is preferred at all four positions in the oligonucleotide binding cleft and that a C-tetrad binds KH1 with 10 times higher affinity than a C-triplet. The basis for this high affinity interaction is finally detailed with the structure determination of a KH1.W.C54S mutant bound to 5′-ACCCCA-3′ DNA sequence. Together, these data establish the lead role of KH1 in oligonucleotide binding by αCP1 and reveal the molecular basis of its specificity for a C-rich tetrad.

TcpM: a novel relaxase that mediates transfer of large conjugative plasmids from Clostridium perfringens.

Conjugative transfer of toxin and antibiotic resistance plasmids in Clostridium perfringens is mediated by the tcp conjugation locus. Surprisingly, neither a relaxase gene nor an origin of transfer (oriT) has been identified on these plasmids, which are typified by the 47 kb tetracycline resistance plasmid pCW3. The tcpM gene (previously called intP) encodes a potential tyrosine recombinase that was postulated to be an atypical relaxase. Mutagenesis and complementation studies showed that TcpM was required for wild‐type transfer of pCW3 and that a tyrosine residue, Y259, was essential for TcpM activity, which was consistent with the need for a relaxase‐mediated hydrophilic attack at the oriT site. Other catalytic residues conserved in tyrosine recombinases were not required for TcpM activity, suggesting that TcpM was not a site‐specific recombinase. Mobilization studies led to the identification of the oriT site, which was located in the 391 bp intergenic region upstream of tcpM. The oriT site was localized to a 150 bp region, and gel mobility shift studies showed that TcpM could bind to this region. Based on these studies we postulate that conjugative transfer of pCW3 involves the atypical relaxase TcpM binding to and processing the oriT site to initiate plasmid transfer.

Synthetic Precursors for TCNQF42– Compounds: Synthesis, Characterization, and Electrochemical Studies of (Pr4N)2TCNQF4 and Li2TCNQF4

Careful control of the reaction stoichiometry and conditions enables the synthesis of both LiTCNQF(4) and Li(2)TCNQF(4) to be achieved. Reaction of LiI with TCNQF(4), in a 4:1 molar ratio, in boiling acetonitrile yields Li(2)TCNQF(4). However, deviation from this ratio or the reaction temperature gives either LiTCNQF(4) or a mixture of Li(2)TCNQF(4) and LiTCNQF(4). This is the first report of the large-scale chemical synthesis of Li(2)TCNQF(4). Attempts to prepare a single crystal of Li(2)TCNQF(4) have been unsuccessful, although air-stable (Pr(4)N)(2)TCNQF(4) was obtained by mixing Pr(4)NBr with Li(2)TCNQF(4) in aqueous solution. Pr(4)NTCNQF(4) was also obtained by reaction of LiTCNQF(4) with Pr(4)NBr in water. Li(2)TCNQF(4), (Pr(4)N)(2)TCNQF(4), and Pr(4)NTCNQF(4) have been characterized by UV-vis, FT-IR, Raman, and NMR spectroscopy, high resolution electrospray ionization mass spectrometry, and electrochemistry. The structures of single crystals of (Pr(4)N)(2)TCNQF(4) and Pr(4)NTCNQF(4) have been determined by X-ray crystallography. These TCNQF(4)(2-) salts will provide useful precursors for the synthesis of derivatives of the dianions.

Spontaneous redox synthesis of the charge transfer material TTF4[SVMo11O40]

The charge-transfer material TTF-SV(IV)Mo(11)O(40) (TTF = tetrathiafulvalene) was prepared by a spontaneous redox reaction between TTF and the vanadium-substituted polyoxometalate (n-Bu(4)N)(3)[SV(V)Mo(11)O(40)] in both solution and solid state phases. Single crystal X-ray diffraction gave the stoichiometry TTF(4)[SVMo(11)O(40)]·2H(2)O·2CH(2)Cl(2), with the single V atom positionally disordered with eight Mo atoms over the whole α-Keggin polyanion [SVMo(11)O(40)](4-). Raman spectra support the 1+ charge assigned to the oxidized TTF deduced from bond lengths, and elemental and voltammetric analysis also are consistent with this formulation. Scanning electron microscopy images showed a rod-type morphology for the new charge-transfer material. The conductivity of the solid at room temperature is in the semiconducting range. The TTF and (n-Bu(4)N)(3)[SV(V)Mo(11)O(40)] solids also undergo a rapid interfacial reaction, as is the case with TTF and TCNQ (TCNQ = tetracyanoquinodimethane) solids. EPR spectra at temperatures down to 2.6 K confirm the presence of two paramagnetic species, V(IV) and the oxidized TTF radical. Spectral evidence shows that the TTF-SV(IV)Mo(11)O(40) materials prepared from either solution or solid state reactions are equivalent. The newly isolated TTF-SV(IV)Mo(11)O(40) material represents a new class of TTF-polyoxometalate compound having dual electrical and magnetic functionality derived from both the cationic and anionic components.

Cyclic Peptides Incorporating Phosphotyrosine Mimetics as Potent and Specific Inhibitors of the Grb7 Breast Cancer Target

The Grb7 adaptor protein is a therapeutic target for both TNBC and HER2+ breast cancer. A nonphosphorylated cyclic peptide 1 (known as G7-18NATE) inhibits Grb7 via targeting the Grb7-SH2 domain, but requires the presence of phosphate ions for both affinity and specificity. Here we report the discovery of malonate bound in the phosphotyrosine binding pocket of the apo-Grb7-SH2 structure. Based on this, we carried out the rational design and synthesis of two analogues of peptide 1 that incorporate carboxymethylphenylalanine (cmF) and carboxyphenylalanine (cF) as mimics of phosphotyrosine (pY). Binding studies using SPR confirmed that affinity for Grb7-SH2 domain is improved up to 9-fold over peptide 1 under physiological phosphate conditions (KD = 2.1-5.7 μM) and that binding is specific for Grb7-SH2 over closely related domains (low or no detectable binding to Grb2-SH2 and Grb10-SH2). X-ray crystallographic structural analysis of the analogue bearing a cmF moiety in complex with Grb7-SH2 has identified the precise contacts conferred by the pY mimic that underpin this improved molecular interaction. Together this study identifies and characterizes the tightest specific inhibitor of Grb7 to date, representing a significant development toward a new Grb7-targeted therapeutic.