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Find video protocols related to scientific articles indexed in Pubmed.
Exploring the correlation between the sequence composition of the nucleotide binding G5 loop of the FeoB GTPase domain (NFeoB) and intrinsic GDP release rate.
Biosci. Rep.
PUBLISHED: 09-30-2014
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GDP release from GTPases is usually extremely slow and is in general assisted by external factors, such as association with guanine exchange factors (GEFs) or membrane embedded G protein-coupled receptors (GPCRs), which accelerate the release of GDP by several orders of magnitude. Intrinsic factors can also play a significant role; a single amino acid substitution in one of the guanine nucleotide recognition motifs, G5, results in a drastically altered GDP release rate, indicating that the sequence composition of this motif plays an important role in spontaneous GDP release. In the present study we used the GTPase domain from E. coli FeoB (EcNFeoB) as a model and applied biochemical and structural approaches to evaluate the role of all the individual residues in the G5 loop. Our study confirms that several of the residues in the G5 motif have an important role in the intrinsic affinity and release of GDP. In particular, a T151A mutant (third residue of the G5 loop) leads to a reduced nucleotide affinity and provokes a drastically accelerated dissociation of GDP.
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Dinuclear zinc(II) complexes with hydrogen bond donors as structural and functional phosphatase models.
Inorg Chem
PUBLISHED: 08-14-2014
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It is becoming increasingly apparent that the secondary coordination sphere can have a crucial role in determining the functional properties of biomimetic metal complexes. We have therefore designed and prepared a variety of ligands as metallo-hydrolase mimics, where hydrogen bonding in the second coordination sphere is able to influence the structure of the primary coordination sphere and the substrate binding. The assessment of a structure-function relationship is based on derivates of 2,6-bis{[bis(pyridin-2-ylmethyl)amino]methyl}-4-methylphenol (HBPMP = HL(1)) and 2-{[bis(pyridin-2-ylmethyl)amino]methyl}-6-{[(2-hydroxybenzyl)(pyridin-2-ylmethyl)amino]methyl}-4-methylphenol (H2BPBPMP = H2L(5)), well-known phenolate-based ligands for metallo-hydrolase mimics. The model systems provide similar primary coordination spheres but site-specific modifications in the secondary coordination sphere. Pivaloylamide and amine moieties were chosen to mimic the secondary coordination sphere of the phosphatase models, and the four new ligands H3L(2), H3L(3), HL(4), and H4L(6) vary in the type and geometric position of the H-bond donors and acceptors, responsible for the positioning of the substrate and release of the product molecules. Five dinuclear Zn(II) complexes were prepared and structurally characterized in the solid, and four also in solution. The investigation of the phosphatase activity of four model complexes illustrates the impact of the H-bonding network: the Michaelis-Menten constants (catalyst-substrate binding) for all complexes that support hydrogen bonding are smaller than for the reference complex, and this generally leads to higher catalytic efficiency and higher turnover numbers.
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Comparative investigation of the reaction mechanisms of the organophosphate-degrading phosphotriesterases from Agrobacterium radiobacter (OpdA) and Pseudomonas diminuta (OPH).
J. Biol. Inorg. Chem.
PUBLISHED: 08-08-2014
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Metal ion-dependent, organophosphate-degrading enzymes have acquired increasing attention due to their ability to degrade and thus detoxify commonly used pesticides and nerve agents such as sarin. The best characterized of these enzymes are from Pseudomonas diminuta (OPH) and Agrobacterium radiobacter (OpdA). Despite high sequence homology (>90 % identity) and conserved metal ion coordination these enzymes display considerable variations in substrate specificity, metal ion affinity/preference and reaction mechanism. In this study, we highlight the significance of the presence (OpdA) or absence (OPH) of an extended hydrogen bond network in the active site of these enzymes for the modulation of their catalytic properties. In particular, the second coordination sphere residue in position 254 (Arg in OpdA, His in OPH) is identified as a crucial factor in modulating the substrate preference and binding of these enzymes. Inhibition studies with fluoride also support a mechanism for OpdA whereby the identity of the hydrolysis-initiating nucleophile changes as the pH is altered. The same is not observed for OPH.
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X-ray absorption spectroscopy of dinuclear metallohydrolases.
Biophys. J.
PUBLISHED: 04-22-2014
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In this mini-review, we briefly discuss the physical origin of x-ray absorption spectroscopy (XAS) before illustrating its application using dinuclear metallohydrolases as exemplary systems. The systems we have selected for illustrative purposes present a challenging problem for XAS, one that is ideal to demonstrate the potential of this methodology for structure/function studies of metalloenzymes in general. When the metal ion is redox active, XAS provides a sensitive measure of oxidation-state-dependent differences. When the metal ion is zinc, XAS is the only spectroscopic method that will provide easily accessible structural information in solution. In the case of heterodimetallic sites, XAS has the unique ability to interrogate each metal site independently in the same sample. One of the strongest advantages of XAS is its ability to examine metal ion site structures with crystallographic precision, without the need for a crystal. This is key for studying flexible metal ion sites, such as those described in the selected examples, because it allows one to monitor structural changes that occur during substrate turnover.
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Structural and functional analysis of a FeoB A143S G5 loop mutant explains the accelerated GDP release rate.
FEBS J.
PUBLISHED: 02-04-2014
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GTPases (G proteins) hydrolyze the conversion of GTP to GDP and free phosphate, comprising an integral part of prokaryotic and eukaryotic signaling, protein biosynthesis and cell division, as well as membrane transport processes. The G protein cycle is brought to a halt after GTP hydrolysis, and requires the release of GDP before a new cycle can be initiated. For eukaryotic heterotrimeric G??? proteins, the interaction with a membrane-bound G protein-coupled receptor catalyzes the release of GDP from the G? subunit. Structural and functional studies have implicated one of the nucleotide binding sequence motifs, the G5 motif, as playing an integral part in this release mechanism. Indeed, a G?s G5 mutant (A366S) was shown to have an accelerated GDP release rate, mimicking a G protein-coupled receptor catalyzed release state. In the present study, we investigate the role of the equivalent residue in the G5 motif (residue A143) in the prokaryotic membrane protein FeoB from Streptococcus thermophilus, which includes an N-terminal soluble G protein domain. The structure of this domain has previously been determined in the apo and GDP-bound states and in the presence of a transition state analogue, revealing conformational changes in the G5 motif. The A143 residue was mutated to a serine and analyzed with respect to changes in GTPase activity, nucleotide release rate, GDP affinity and structural alterations. We conclude that the identity of the residue at this position in the G5 loop plays a key role in the nucleotide release rate by allowing the correct positioning and hydrogen bonding of the nucleotide base.
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Determination of the catalytic activity of binuclear metallohydrolases using isothermal titration calorimetry.
J. Biol. Inorg. Chem.
PUBLISHED: 01-12-2014
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Binuclear metallohydrolases are a large and diverse family of enzymes that are involved in numerous metabolic functions. An increasing number of members find applications as drug targets or in processes such as bioremediation. It is thus essential to have an assay available that allows the rapid and reliable determination of relevant catalytic parameters (k cat, K m, and k cat/K m). Continuous spectroscopic assays are frequently only possible by using synthetic (i.e., nonbiological) substrates that possess a suitable chromophoric marker (e.g., nitrophenol). Isothermal titration calorimetry, in contrast, affords a rapid assay independent of the chromophoric properties of the substrate-the heat associated with the hydrolytic reaction can be directly related to catalytic properties. Here, we demonstrate the efficiency of the method on several selected examples of this family of enzymes and show that, in general, the catalytic parameters obtained by isothermal titration calorimetry are in good agreement with those obtained from spectroscopic assays.
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The applications of binuclear metallohydrolases in medicine: recent advances in the design and development of novel drug leads for purple acid phosphatases, metallo-?-lactamases and arginases.
Eur J Med Chem
PUBLISHED: 01-06-2014
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Binuclear metallohydrolases are a family of proteins that can be targeted for drug discovery. The common feature of these enzymes is the presence of two closely spaced metal ions (i.e. less than 4 ? apart) that capture a water molecule that is used as a nucleophile in highly specific hydrolytic reactions. In this mini-review we describe what is known about the biological and catalytic activity, three-dimensional structure and inhibition for three prominent drug targets in this family of enzymes, (i) purple acid phosphatases, (ii) metallo-?-lactamases and (iii) arginases. These enzymes are targets for the development of chemotherapeutics to treat a range of disorders including osteoporosis, cardiovascular disease and erectile dysfunctions, but also to stem the spread of antibiotic resistance, a major threat to global health care.
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Spectroscopic and mechanistic studies of dinuclear metallohydrolases and their biomimetic complexes.
Dalton Trans
PUBLISHED: 10-18-2013
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An enhanced understanding of the metal ion binding and active site structural features of phosphoesterases such as the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ), and the organophosphate degrading agent from Agrobacterium radiobacter (OpdA) have important consequences for potential applications. Coupled with investigations of the metalloenzymes, programs of study to synthesise and characterise model complexes based on these metalloenzymes can add to our understanding of structure and function of the enzymes themselves. This review summarises some of our work and illustrates the significance and contributions of model studies to knowledge in the area.
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Immobilization of the enzyme GpdQ on magnetite nanoparticles for organophosphate pesticide bioremediation.
J. Inorg. Biochem.
PUBLISHED: 06-14-2013
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Annually thousands of people die or suffer from organophosphate (pesticide) poisoning. In order to remove these toxic compounds from the environment, the use of enzymes as bioremediators has been proposed. We report here a Ser127Ala mutant based on the enzyme glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes. The mutant, with improved metal binding abilities, has been immobilized using glutaraldehyde on PAMAM dendrimer-modified magnetite nanoparticles. The immobilized system was characterized using elemental analysis as well as infrared, transmission electron and X-ray photoelectron spectroscopies. The amount of GpdQ that was immobilized with the optimized procedure was 1.488nmol per g MNP. A kinetic assay has been designed to evaluate the activity of the system towards organophosphoester substrates. The specific activity towards BPNPP directly after immobilization was 3.55?molmg(-1)min(-1), after one week 3.39?molmg(-1)min(-1) and after 120days 3.36?molmg(-1)min(-1), demonstrating that the immobilized enzyme was active for multiple cycles and could be stored on the nanoparticles for a prolonged period.
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Identification and characterization of an unusual metallo-?-lactamase from Serratia proteamaculans.
J. Biol. Inorg. Chem.
PUBLISHED: 05-20-2013
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Metallo-?-lactamases (MBLs) are a family of metalloenzymes that are capable of hydrolyzing ?-lactam antibiotics and are an important means by which bacterial pathogens use to inactivate antibiotics. A database search of the available amino acid sequences from Serratia proteamaculans indicates the presence of an unusual MBL. A full length amino acid sequence alignment indicates overall homology to B3-type MBLs, but also suggests considerable variations in the active site, notably among residues that are relevant to metal ion binding. Steady-state kinetic measurements further indicate functional differences and identify two relevant pK a values for catalysis (3.8 for the enzyme-substrate complex and 7.8 for the free enzyme) and a preference for penams with modest reactivity towards some cephalosporins. An analysis of the metal ion content indicates the presence of only one zinc ion per active site in the resting enzyme. In contrast, kinetic data suggest that the enzyme may operate as a binuclear enzyme, and it is thus proposed that a catalytically active di-Zn(2+) center is formed only once the substrate is present.
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Asymmetric zinc(II) complexes as functional and structural models for phosphoesterases.
Dalton Trans
PUBLISHED: 05-15-2013
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We report two asymmetric ligands for the generation of structural and functional dinuclear metal complexes as phosphoesterase mimics. Two zinc(II) complexes, [Zn2(CH3L4)(CH3CO2)2](+) (CH3HL4 = 2-(((2-methoxyethyl)(pyridin-2-ylmethyl)amino)methyl)-4-methyl-6-(((pyridin-2-ylmethyl)amino)methyl)phenol) and [Zn2(CH3L5)(CH3CO2)2](+) (CH3HL5 = 2-(((2-methoxyethyl)(pyridine-2-ylmethyl)amino)methyl)-4-methyl-6-(((pyridin-2-ylmethyl)(4-vinylbenzyl)amino)methyl)phenol) were synthesized and characterized by X-ray crystallography. The structures showed that the ligands enforce a mixed 6,5-coordinate environment in the solid state. (1)H-, (13)C- and (31)P-NMR, mass spectrometry and infrared spectroscopy were used to further characterize the compounds in the solid state and in solution. The zinc(II) complexes hydrolyzed the organophosphate substrate bis-(2,4-dinitrophenol)phosphate (BDNPP), the nucleophile proposed to be a terminal water molecule (pK(a) 7.2). The ligand CH3HL4 was immobilised on Merrifield resin and its zinc(II) complex generated. Infrared spectroscopy, microanalysis and XPS measurements confirmed successful immobilisation, with a catalyst loading of ~1.45 mmol g(-1) resin. The resin bound complex was active towards BDNPP and displayed similar pH dependence to the complex in solution.
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Highly efficient synthetic iron-dependent nucleases activate both intrinsic and extrinsic apoptotic death pathways in leukemia cancer cells.
J. Inorg. Biochem.
PUBLISHED: 03-09-2013
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The nuclease activity and the cytotoxicity toward human leukemia cancer cells of iron complexes, [Fe(HPClNOL)Cl2]NO3 (1), [Cl(HPClNOL)Fe(?-O)Fe(HPClNOL)Cl]Cl2·2H2O (2), and [(SO4)(HPClNOL)Fe(?-O)Fe(HPClNOL)(SO4)]·6H2O (3) (HPClNOL=1-(bis-pyridin-2-ylmethyl-amino)-3-chloropropan-2-ol), were investigated. Each complex was able to promote plasmid DNA cleavage and change the supercoiled form of the plasmid to circular and linear ones. Kinetic data revealed that (1), (2) and (3) increase the rate of DNA hydrolysis about 278, 192 and 339 million-fold, respectively. The activity of the complexes was inhibited by distamycin, indicating that they interact with the minor groove of the DNA. The cytotoxic activity of the complexes toward U937, HL-60, Jukart and THP-1 leukemia cancer cells was studied employing 3-(4,5-dimethythiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT), fluorescence and electronic transmission microscopies, flow cytometry and a cytochrome C release assay. Compound (2) has the highest activity toward cancer cells and is the least toxic for normal ones (i.e. peripheral blood mononuclear cells (PBMCs)). In contrast, compound (1) is the least active toward cancer cells but displays the highest toxicity toward normal cells. Transmission electronic microscopy indicates that cell death shows features typical of apoptotic cells, which was confirmed using the annexin V-FITC/PI (fluorescein isothiocyanate/propidium iodide) assay. Furthermore, our data demonstrate that at an early stage during the treatment with complex (2) mitochondria lose their transmembrane potential, resulting in cytochrome C release. A quantification of caspases 3, 9 (intrinsic apoptosis pathway) and caspase 8 (extrinsic apoptosis pathway) indicated that both the intrinsic (via mitochondria) and extrinsic (via death receptors) pathways are involved in the apoptotic stimuli.
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Synthesis, magnetic properties, and phosphoesterase activity of dinuclear cobalt(II) complexes.
Inorg Chem
PUBLISHED: 02-01-2013
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A series of dinuclear cobalt(II) complexes has been prepared and characterized to generate functional and spectroscopic models for cobalt(II) substituted phosphoesterase enzymes such as the potential bioremediator GpdQ. Reaction of ligands based on 2,2-(((2-hydroxy-5-methyl-1,3-phenylene)bis(methylene))bis((pyridin-2-ylmethyl)azanediyl)))diethanol (L1) and 2,6-bis(((2-methoxyethyl)(pyridin-2-ylmethyl)amino)methyl)-4-methylphenol (L2) with cobalt(II) salts afforded [Co(2)(CO(2)EtH(2)L1)(CH(3)COO)(2)](PF(6)), [Co(2)(CO(2)EtL2)(CH(3)COO)(2)](PF(6)), [Co(2)(CH(3)L2)(CH(3)COO)(2)](PF(6)), [Co(2)(BrL2)(CH(3)COO)(2)](PF(6)), and [Co(2)(NO(2)L2)(CH(3)COO)(2)](PF(6)). Complexes of the L2 ligands contain a coordinated methyl-ether, whereas the L1 ligand contains a coordinated alcohol. The complexes were characterized using mass spectrometry, microanalysis, X-ray crystallography, UV-vis-NIR diffuse reflectance spectroscopy, IR absorption spectroscopy, solid state magnetic susceptibility measurements, and variable-temperature variable-field magnetic circular dichroism (VTVH MCD) spectroscopy. Susceptibility studies show that [Co(2)(CO(2)EtH(2)L1)(CH(3)COO)(2)](PF(6)), [Co(2)(CO(2)EtL2)(CH(3)COO)(2)](PF(6)), and [Co(2)(CH(3)L2)(CH(3)COO)(2)](PF(6)) are weakly antiferromagnetically coupled, whereas [Co(2)(BrL2)(CH(3)COO)(2)](PF(6)) and [Co(2)(NO(2)L2)(CH(3)COO)(2)](PF(6)) are weakly ferromagnetically coupled. The susceptibility results are confirmed by the VTVH MCD studies. Density functional theory calculations revealed that magnetic exchange coupling occurs mainly through the phenolic oxygen bridge. Implications of geometry and ligand design on the magnetic exchange coupling will be discussed. Functional studies of the complexes with the substrate bis(2,4-dinitrophenyl) phosphate showed them to be active towards hydrolysis of phosphoester substrates.
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The role of Zn-OR and Zn-OH nucleophiles and the influence of para-substituents in the reactions of binuclear phosphatase mimetics.
Dalton Trans
PUBLISHED: 12-15-2011
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Analogues of the ligand 2,2-(2-hydroxy-5-methyl-1,3-phenylene)bis(methylene)bis((pyridin-2-ylmethyl)azanediyl)diethanol (CH(3)H(3)L1) are described. Complexation of these analogues, 2,6-bis(((2-methoxyethyl)(pyridin-2-ylmethyl)amino)methyl)-4-methylphenol (CH(3)HL2), 4-bromo-2,6-bis(((2-methoxyethyl)(pyridin-2-ylmethyl)amino)methyl)phenol (BrHL2), 2,6-bis(((2-methoxyethyl)(pyridin-2-ylmethyl)amino)methyl)-4-nitrophenol (NO(2)HL2) and 4-methyl-2,6-bis(((2-phenoxyethyl)(pyridin-2-ylmethyl)amino)methyl)phenol (CH(3)HL3) with zinc(II) acetate afforded [Zn(2)(CH(3)L2)(CH(3)COO)(2)](PF(6)), [Zn(2)(NO(2)L2)(CH(3)COO)(2)](PF(6)), [Zn(2)(BrL2)(CH(3)COO)(2)](PF(6)) and [Zn(2)(CH(3)L3)(CH(3)COO)(2)](PF(6)), in addition to [Zn(4)(CH(3)L2)(2)(NO(2)C(6)H(5)OPO(3))(2)(H(2)O)(2)](PF(6))(2) and [Zn(4)(BrL2)(2)(PO(3)F)(2)(H(2)O)(2)](PF(6))(2). The complexes were characterized using (1)H and (13)C NMR spectroscopy, mass spectrometry, microanalysis, and X-ray crystallography. The complexes contain either a coordinated methyl- (L2 ligands) or phenyl- (L3 ligand) ether, replacing the potentially nucleophilic coordinated alcohol in the previously reported complex [Zn(2)(CH(3)HL1)(CH(3)COO)(H(2)O)](PF(6)). Functional studies of the zinc complexes with the substrate bis(2,4-dinitrophenyl) phosphate (BDNPP) showed them to be competent catalysts with, for example, [Zn(2)(CH(3)L2)](+), k(cat) = 5.70 ± 0.04 × 10(-3) s(-1) (K(m) = 20.8 ± 5.0 mM) and [Zn(2)(CH(3)L3)](+), k(cat) = 3.60 ± 0.04 × 10(-3) s(-1) (K(m) = 18.9 ± 3.5 mM). Catalytically relevant pK(a)s of 6.7 and 7.7 were observed for the zinc(II) complexes of CH(3)L2(-) and CH(3)L3(-), respectively. Electron donating para-substituents enhance the rate of hydrolysis of BDNPP such that k(cat)p-CH(3) > p-Br > p-NO(2). Use of a solvent mixture containing H(2)O(18)/H(2)O(16) in the reaction with BDNPP showed that for [Zn(2)(CH(3)L2)(CH(3)COO)(2)](PF(6)) and [Zn(2)(NO(2)L2)(CH(3)COO)(2)](PF(6)), as well as [Zn(2)(CH(3)HL1)(CH(3)COO)(H(2)O)](PF(6)), the (18)O label was incorporated in the product of the hydrolysis suggesting that the nucleophile involved in the hydrolysis reaction was a Zn-OH moiety. The results are discussed with respect to the potential nucleophilic species (coordinated deprotonated alcohol versus coordinated hydroxide).
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Directed evolution combined with rational design increases activity of GpdQ toward a non-physiological substrate and alters the oligomeric structure of the enzyme.
Protein Eng. Des. Sel.
PUBLISHED: 10-06-2011
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Directed evolution was used to enhance the activity of the glycerophosphodiesterase enzyme from Enterobacter aerogenes, GpdQ, toward bis(para-nitrophenol) phosphate (BpNPP), a substrate that is frequently used to assay phosphodiesterases. Native GpdQ has a low level of activity toward BpNPP while the evolved enzymes exhibited k(cat) values that were well over 100 times better while improvements in k(cat)/K(m) of around 500 times were observed along with improved activity we observed a change in the oligomeric structure in the evolved enzymes. The native enzyme is a hexamer with tightly associated dimers related by a 3-fold axis. The stability of the dimer was attributed in part to the cap domain that forms a disulfide bond with its 2-fold-related subunit and in part due to the fact that dimerization results in burying 23.6% of the monomers accessible surface area. The cap domain also forms the top of the active site and contributes an essential part of the interface between 3-fold-related molecules. The evolved proteins quickly lost one of the cysteine residues that formed the disulfide bond and other mutations that might stabilize the cap domain. The likely effect of these mutations was to open up the active site for the new substrate and to favor the formation of dimeric molecules. The breakdown of the oligomeric structure was accompanied by a reduction in the thermal stability of the protein-as monitored by the residual activity of the native and mutant proteins following pre-incubation at elevated temperatures. A discussion on the evolutionary implications of these studies is presented.
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3-mercapto-1,2,4-triazoles and N-acylated thiosemicarbazides as metallo-?-lactamase inhibitors.
Bioorg. Med. Chem. Lett.
PUBLISHED: 09-27-2011
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The production of ?-lactamases is an effective strategy by which pathogenic bacteria can develop resistance against ?-lactam antibiotics. While inhibitors of serine-?-lactamases are widely used in combination therapy with ?-lactam antibiotics, there are no clinically available inhibitors of metallo-?-lactamases (MBLs), and so there is a need for the development of such inhibitors. This work describes the optimisation of a lead inhibitor previously identified by fragment screening of a compound library. We also report that thiosemicarbazide intermediates in the syntheses of these compounds are also moderately potent inhibitors of the IMP-1 MBL from Pseudomonas aeruginosa. The interactions of these inhibitors with the active site of IMP-1 were examined using in silico methods.
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Synthesis and kinetic testing of new inhibitors for a metallo-?-lactamase from Klebsiella pneumonia and Pseudomonas aeruginosa.
Eur J Med Chem
PUBLISHED: 07-21-2011
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There are currently no clinically useful inhibitors against metallo-?-lactamases (MBLs), enzymes that confer resistance against a broad spectrum of commonly used antibiotics and that are produced by an increasing number of bacterial pathogens. New pyrrole derivatives were synthesized and assayed for their inhibitory effect on the catalytic activity of the IMP-1 MBL from Pseudomonas aeruginosa and Klebsiella pneumoniae. Six compounds tested (3a-3c, 5, 7 and 8) show micromolar inhibition constants (K(i) values range from ?10 to 30 ?M). In silico docking was employed to investigate the binding mode of the strongest inhibitor, 3b, in the active site of IMP-1. Implications for further improvements of binding efficiency and specificity are discussed.
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Electronic and geometric structures of the organophosphate-degrading enzyme from Agrobacterium radiobacter (OpdA).
J. Biol. Inorg. Chem.
PUBLISHED: 03-28-2011
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The organophosphate-degrading enzyme from Agrobacterium radiobacter (OpdA) is a highly efficient catalyst for the degradation of pesticides and some nerve agents such as sarin. OpdA requires two metal ions for catalytic activity, and hydrolysis is initiated by a nucleophilic hydroxide that is bound to one of these metal ions. The precise location of this nucleophile has been contentious, with both a terminal and a metal-ion-bridging hydroxide as likely candidates. Here, we employed magnetic circular dichroism to probe the electronic and geometric structures of the Co(II)-reconstituted dinuclear metal center in OpdA. In the resting state the metal ion in the more secluded ? site is five-coordinate, whereas the Co(II) in the solvent-exposed ? site is predominantly six-coordinate with two terminal water ligands. Addition of the slow substrate diethyl 4-methoxyphenyl phosphate does not affect the ? site greatly but lowers the coordination number of the ? site to five. A reduction in the exchange coupling constant indicates that substrate binding also triggers a shift of the ?-hydroxide into a pseudoterminal position in the coordination sphere of either the ? or the ? metal ion. Mechanistic implications of these observations are discussed.
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Phosphate-bound structure of an organophosphate-degrading enzyme from Agrobacterium radiobacter.
J. Inorg. Biochem.
PUBLISHED: 03-23-2011
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OpdA is a binuclear metalloenzyme that can hydrolyze organophosphate pesticides and nerve agents. In this study the crystal structure of the complex between OpdA and phosphate has been determined to 2.20 Å resolution. The structure shows the phosphate bound in a tripodal mode to the metal ions whereby two of the oxygen atoms of PO(4) are terminally bound to each metal ion and a third oxygen bridges the two metal ions, thus displacing the ?OH in the active site. In silico modelling demonstrates that the phosphate moiety of a reaction product, e.g. diethyl phosphate, may bind in the same orientation, positioning the diethyl groups neatly into the substrate binding pocket close to the metal center. Thus, similar to the binuclear metallohydrolases urease and purple acid phosphatase the tripodal arrangement of PO(4) is interpreted in terms of a role of the ?OH as a reaction nucleophile.
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The identification of new metallo-?-lactamase inhibitor leads from fragment-based screening.
Bioorg. Med. Chem. Lett.
PUBLISHED: 02-22-2011
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The emergence of metallo-?-lactamases (MBLs) capable of hydrolysing a broad spectrum of ?-lactam antibiotics is particularly concerning for the future treatment of bacterial infections. This work describes the discovery of lead compounds for the development of new inhibitors using a competitive colorimetric assay based on the chromogenic cephalosporin CENTA, and a 500 compound Maybridge™ library suitable for fragment-based screening. The interactions between identified inhibitory fragments and the active site of the MBL from Klebsiella pneumoniae and Pseudomonas aeruginosa were probed by in silico docking studies.
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Synthesis, modelling and kinetic assays of potent inhibitors of purple acid phosphatase.
Bioorg. Med. Chem. Lett.
PUBLISHED: 01-29-2011
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Purple acid phosphatases (PAPs) are binuclear metallohydrolases that have been isolated from various mammals, plants, fungi and bacteria. In mammals PAP activity is associated with bone resorption and can lead to bone metabolic disorders such as osteoporosis; thus human PAP is an attractive target to develop anti-osteoporotic drugs. Based on a previous lead compound and rational drug design, acyl derivatives of ?-aminonaphthylmethylphosphonic acid were synthesised and tested as PAP inhibitors. Kinetic analysis showed that they are good PAP inhibitors whose potencies improve with increasing acyl chain length. Maximum potency is reached when the number of carbons in the acyl chain is between 12 and 14. The most potent inhibitor of red kidney bean PAP is the dodecyl-derivative with K(ic)=5 ?M, while the most potent pig PAP inhibitor is the tetradecyl-derivative with K(ic)=8 ?M, the most potent inhibitor of a mammalian PAP yet reported.
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Improving a natural enzyme activity through incorporation of unnatural amino acids.
J. Am. Chem. Soc.
PUBLISHED: 12-16-2010
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The bacterial phosphotriesterases catalyze hydrolysis of the pesticide paraoxon with very fast turnover rates and are thought to be near to their evolutionary limit for this activity. To test whether the naturally evolved turnover rate could be improved through the incorporation of unnatural amino acids and to probe the role of peripheral active site residues in nonchemical steps of the catalytic cycle (substrate binding and product release), we replaced the naturally occurring tyrosine amino acid at position 309 with unnatural L-(7-hydroxycoumarin-4-yl)ethylglycine (Hco) and L-(7-methylcoumarin-4-yl)ethylglycine amino acids, as well as leucine, phenylalanine, and tryptophan. Kinetic analysis suggests that the 7-hydroxyl group of Hco, particularly in its deprotonated state, contributes to an increase in the rate-limiting product release step of substrate turnover as a result of its electrostatic repulsion of the negatively charged 4-nitrophenolate product of paraoxon hydrolysis. The 8-11-fold improvement of this already highly efficient catalyst through a single rationally designed mutation using an unnatural amino acid stands in contrast to the difficulty in improving this native activity through screening hundreds of thousands of mutants with natural amino acids. These results demonstrate that designer amino acids provide easy access to new and valuable sequence and functional space for the engineering and evolution of existing enzyme functions.
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Electronic structure and spectro-structural correlations of Fe(III)Zn(II) biomimetics for purple acid phosphatases: relevance to DNA cleavage and cytotoxic activity.
Inorg Chem
PUBLISHED: 11-16-2010
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Purple acid phosphatases (PAPs) are a group of metallohydrolases that contain a dinuclear Fe(III)M(II) center (M(II) = Fe, Mn, Zn) in the active site and are able to catalyze the hydrolysis of a variety of phosphoric acid esters. The dinuclear complex [(H(2)O)Fe(III)(?-OH)Zn(II)(L-H)](ClO(4))(2) (2) with the ligand 2-[N-bis(2-pyridylmethyl)aminomethyl]-4-methyl-6-[N-(2-pyridylmethyl)(2-hydroxybenzyl) aminomethyl]phenol (H(2)L-H) has recently been prepared and is found to closely mimic the coordination environment of the Fe(III)Zn(II) active site found in red kidney bean PAP (Neves et al. J. Am. Chem. Soc. 2007, 129, 7486). The biomimetic shows significant catalytic activity in hydrolytic reactions. By using a variety of structural, spectroscopic, and computational techniques the electronic structure of the Fe(III) center of this biomimetic complex was determined. In the solid state the electronic ground state reflects the rhombically distorted Fe(III)N(2)O(4) octahedron with a dominant tetragonal compression aligned along the ?-OH-Fe-O(phenolate) direction. To probe the role of the Fe-O(phenolate) bond, the phenolate moiety was modified to contain electron-donating or -withdrawing groups (-CH(3), -H, -Br, -NO(2)) in the 5-position. The effects of the substituents on the electronic properties of the biomimetic complexes were studied with a range of experimental and computational techniques. This study establishes benchmarks against accurate crystallographic structural information using spectroscopic techniques that are not restricted to single crystals. Kinetic studies on the hydrolysis reaction revealed that the phosphodiesterase activity increases in the order -NO(2) ?Br ?H ?CH(3) when 2,4-bis(dinitrophenyl)phosphate (2,4-bdnpp) was used as substrate, and a linear free energy relationship is found when log(k(cat)/k(0)) is plotted against the Hammett parameter ?. However, nuclease activity measurements in the cleavage of double stranded DNA showed that the complexes containing the electron-withdrawing -NO(2) and electron-donating -CH(3) groups are the most active while the cytotoxic activity of the biomimetics on leukemia and lung tumoral cells is highest for complexes with electron-donating groups.
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Using a genetically encoded fluorescent amino acid as a site-specific probe to detect binding of low-molecular-weight compounds.
Assay Drug Dev Technol
PUBLISHED: 11-04-2010
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Development of enzyme inhibitors requires an activity assay for the identification of hits and lead compounds. To determine dissociation constants in a straightforward manner, we explored the use of a genetically encoded fluorescent amino acid for site-specific tagging of the target protein. The unnatural amino acid 7-(hydroxy-coumarin-4-yl) ethylglycine (Hco) was site-specifically incorporated in the target protein by cell-free protein synthesis using an orthogonal amber suppressor tRNA/aminoacyl-tRNA synthetase pair. Using the West Nile virus nonstructural protein 2B-nonstructural protein 3 protease as the target protein, the fluorescence of Hco-tagged samples proved to be exquisitely sensitive to the presence of inhibitors and small ligand molecules if they bind in the vicinity of the Hco residue. No significant change in fluorescence was observed when the ligand-binding site was far from the Hco residue. Hco-tagged proteins thus combine outstanding sensitivity with accurate information on the site of binding, making Hco labeling an attractive tool in drug discovery.
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The organophosphate-degrading enzyme from Agrobacterium radiobacter displays mechanistic flexibility for catalysis.
Biochem. J.
PUBLISHED: 09-28-2010
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The OP (organophosphate)-degrading enzyme from Agrobacterium radiobacter (OpdA) is a binuclear metallohydrolase able to degrade highly toxic OP pesticides and nerve agents into less or non-toxic compounds. In the present study, the effect of metal ion substitutions and site-directed mutations on the catalytic properties of OpdA are investigated. The study shows the importance of both the metal ion composition and a hydrogen-bond network that connects the metal ion centre with the substrate-binding pocket using residues Arg254 and Tyr257 in the mechanism and substrate specificity of this enzyme. For the Co(II) derivative of OpdA two protonation equilibria (pKa1 ~5; pKa2 ~10) have been identified as relevant for catalysis, and a terminal hydroxide acts as the likely hydrolysis-initiating nucleophile. In contrast, the Zn(II) and Cd(II) derivatives only have one relevant protonation equilibrium (pKa ~4-5), and the ?OH is the proposed nucleophile. The observed mechanistic flexibility may reconcile contrasting reaction models that have been published previously and may be beneficial for the rapid adaptation of OP-degrading enzymes to changing environmental pressures.
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Phosphate ester cleavage promoted by a tetrameric iron(III) complex.
J. Biol. Inorg. Chem.
PUBLISHED: 05-17-2010
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The purple acid phosphatases (PAPs) are the only binuclear metallohydrolases where the necessity for a heterovalent active site [Fe(III)-M(II) (M is Fe, Zn or Mn)] for catalysis has been established. The paradigm for the construction of PAP biomimetics, both structural and functional, is that the ligands possess characteristics which mimic those of the donor sites of the metalloenzyme and permit discrimination between trivalent and divalent metal ions. The donor atom set of the ligand 2-((2-hydroxy-5-methyl-3-((pyridin-2-ylmethylamino)methyl)benzyl)(2-hydroxybenzyl)amino)acetic acid (H(3)HPBA) mimics that of the active site of PAP although the iron(III) complex of this ligand has been characterized as the tetramer [Fe(4)(HPBA)(2)(?-CH(3)COO)(2)(?-O)(?-OH)(OH(2))(2)]ClO(4)·5H(2)O. The phosphoesterase-like activity of the complex in 1:1 acetonitrile/water has now been investigated using the substrate 2,4-bis(dinitrophenyl)phosphate. The pH dependence of the catalytic rate revealed a non-symmetric bell-shaped profile, with a finite but non-zero rate at high pH. Unlike the traditional approach usually employed to analyse these bell-shaped profiles, the approach used here involved incorporating additional species which contribute to the overall activity. Employing this approach, we show that the complex has a k (cat) of 1.6 (±0.2) × 10(-3) s(-1), three kinetically relevant pK (a) values of 5.3, 6.2 and 8.4, with K (M) of 7.4 ± 0.6 mM. The kinetic parameters are similar to those reported for heterovalent PAP biomimetics. Additionally, it is observed that, unlike the enzyme, the oxidation state is not the determining factor for catalytic activity.
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Mutation of outer-shell residues modulates metal ion co-ordination strength in a metalloenzyme.
Biochem. J.
PUBLISHED: 05-13-2010
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The metal ion co-ordination sites of many metalloproteins have been characterized by a variety of spectroscopic techniques and small-molecule model systems, revealing many important insights into the structural determinants of metal ion co-ordination. However, our understanding of this fundamentally and practically important phenomenon remains frustratingly simplistic; in many proteins it is essentially impossible to predict metal ion specificity and the effects of remote outer-shell residues on metal ion co-ordination strength are also poorly defined. This is exemplified by our inability to explain why metalloenzymes with identical metal ion co-ordination spheres, such as the closely related orthologues of bacterial PTE (phosphotriesterase) from Agrobacterium radiobacter and Pseudomonas diminuta, display different metal ion specificity and co-ordination strength. In the present study, we present a series of PTE variants that all possess identical metal ion co-ordination spheres, yet display large differences in their metal ion co-ordination strength. Using measurement of the rates of metal ion dissociation from the active site alongside analysis of structural data obtained through X-ray crystallography, we show that outer-shell residues provide essential support for the metal ion ligands, in effect buttressing them in their optimal orientation. Remote mutations appear to modulate metal ion interactions by increasing or decreasing the stabilizing effects of these networks. The present study therefore provides a description of how the greater protein fold can be modified to tune the strength of metal ion co-ordination and metal ion specificity, as well as reinforcing the concept of proteins as ensembles of conformational states with unique structures and biochemical properties.
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The divalent metal ion in the active site of uteroferrin modulates substrate binding and catalysis.
J. Am. Chem. Soc.
PUBLISHED: 05-04-2010
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The purple acid phosphatases (PAP) are binuclear metallohydrolases that catalyze the hydrolysis of a broad range of phosphomonoester substrates. The mode of substrate binding during catalysis and the identity of the nucleophile is subject to debate. Here, we used native Fe(3+)-Fe(2+) pig PAP (uteroferrin; Uf) and its Fe(3+)-Mn(2+) derivative to investigate the effect of metal ion substitution on the mechanism of catalysis. Replacement of the Fe(2+) by Mn(2+) lowers the reactivity of Uf. However, using stopped-flow measurements it could be shown that this replacement facilitates approximately a ten-fold faster reaction between both substrate and inorganic phosphate with the chromophoric Fe(3+) site. These data also indicate that in both metal forms of Uf, phenyl phosphate hydrolysis occurs faster than formation of a mu-1,3 phosphate complex. The slower rate of interaction between substrate and the Fe(3+) site relative to catalysis suggests that the substrate is hydrolyzed while coordinated only to the divalent metal ion. The likely nucleophile is a water molecule in the second coordination sphere, activated by a hydroxide terminally coordinated to Fe(3+). The faster rates of interaction with the Fe(3+) site in the Fe(3+)-Mn(2+) derivative than the native Fe(3+)-Fe(2+) form are likely mediated via a hydrogen bond network connecting the first and second coordination spheres, and illustrate how the selection of metal ions may be important in fine-tuning the function of this enzyme.
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Electronic structure analysis of the dinuclear metal center in the bioremediator glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes.
Inorg Chem
PUBLISHED: 02-19-2010
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The glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes is a promiscuous, dinuclear metallohydrolase that has potential application in the remediation of organophosphate nerve agents and pesticides. GpdQ employs an unusual reaction mechanism in which the enzyme is predominantly mononuclear in the resting state, and substrate binding induces the formation of the catalytically competent dinuclear center (Hadler et al. J. Am. Chem. Soc. 2008, 130, 14129). Reactivity is further modulated by the coordination flexibility of Asn80, a ligand that binds to the second, loosely bound metal ion (Hadler et al. J. Am. Chem. Soc. 2009, 131, 11900). It is proposed that hydrolysis is initiated by a terminal, metal-bound hydroxide molecule which is activated at unusually low pH by electrostatic/hydrogen bonding interactions with a bridging hydroxide species. In this study, electronic structure analysis of the dinuclear center is employed to study the coordination environment of the dinuclear center at the resting and product-bound stage of catalysis. This is achieved through the use of variable temperature, variable field magnetic circular dichroism experiments involving the Co(II)-substituted wild type enzyme and its Asn80Asp variant. The data support the above model for the catalytic mechanism whereby the metal ion-bridging hydroxide molecule activates a terminally bound hydroxide nucleophile. Replacement of Asn80 by an aspartate residue does prevent coordination flexibility but also leads to cleavage of the mu-hydroxide bridge and reduced reactivity. This is the first study to investigate the electronic structure of an enzyme with a mu-1,1-carboxylate bridged dicobalt(II) center.
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Structural and catalytic characterization of a heterovalent Mn(II)Mn(III) complex that mimics purple acid phosphatases.
Inorg Chem
PUBLISHED: 10-27-2009
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The binuclear heterovalent manganese model complex [Mn(II)Mn(III)(L1)(OAc)(2)] ClO(4) x H(2)O (H(2)L1 = 2-(((3-((bis(pyridin-2-ylmethyl)amino)methyl)-2-hydroxy-5-methylbenzyl)(pyridin-2-ylmethyl)amino)-methyl)phenol) has been prepared and studied structurally, spectroscopically, and computationally. The magnetic and electronic properties of the complex have been related to its structure. The complex is weakly antiferromagnetically coupled (J approximately -5 cm(-1), H = -2J S(1) x S(2)) and the electron paramagnetic resonance (EPR) and magnetic circular dichroism (MCD) spectra identify the Jahn-Teller distortion of the Mn(III) center as predominantly a tetragonal compression, with a significant rhombic component. Electronic structure calculations using density functional theory have confirmed the conclusions derived from the experimental investigations. In contrast to isostructural M(II)Fe(III) complexes (M = Fe, Mn, Zn, Ni), the Mn(II)Mn(III) system is bifunctional possessing both catalase and hydrolase activities, and only one catalytically relevant pK(a) (= 8.2) is detected. Mechanistic implications are discussed.
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The bioremediator glycerophosphodiesterase employs a non-processive mechanism for hydrolysis.
J. Inorg. Biochem.
PUBLISHED: 08-20-2009
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Glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes is a binuclear metallohydrolase that catalyzes the breakdown of a broad range of phosphate ester substrates, and it is of interest for its potential application in the destruction of organophosphate nerve agents and pesticides. The reaction mechanism of GpdQ has been proposed to involve a nucleophilic attack by a terminally bound hydroxide molecule. The hydroxide species bridging the two metal ions is suggested to activate the nucleophile, thus favoring a sequential rather than a processive mechanism of action. Here, the hydrolysis of the two ester bonds in the substrate bis(para-nitrophenyl) phosphate (bpNPP) is probed using (31)P NMR. The kinetic rates measured compare well with those determined spectrophotometrically. Furthermore, the data indicate that the diester bonds are cleaved in two separate (non-processive) reactions, indicating that only a single nucleophile (the terminal hydroxide molecule) is likely to be employed as a nucleophile for GpdQ.
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Structural flexibility enhances the reactivity of the bioremediator glycerophosphodiesterase by fine-tuning its mechanism of hydrolysis.
J. Am. Chem. Soc.
PUBLISHED: 08-06-2009
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The glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) belongs to the family of binuclear metallohydrolases and has attracted recent attention due to its potential in bioremediation. Formation of a catalytically competent binuclear center is promoted by the substrate (Hadler et al. J. Am. Chem. Soc. 2008, 130, 14129). Using the paramagnetic properties of Mn(II), we estimated the K(d) values for the metal ions in the alpha and beta sites to be 29 and 344 microM, respectively, in the absence of a substrate analogue. In its presence, the affinity of the beta site increases substantially (K(d) = 56 microM), while that of the alpha site is not greatly affected (K(d) = 17 microM). Stopped-flow fluorescence measurements identified three distinct phases in the catalytic turnover, associated with the initial binding of substrate to the active site (k(obs1)), the assembly of a catalytically active binuclear center (k(obs2)), and subsequent slower structural rearrangements to optimize catalysis (k(obs3)). These three phases depend on the concentration of substrate ([S]), with k(obs1) and k(obs2) reaching maximum values at high [S] (354 and 38 s(-1), respectively), whereas k(obs3) is reduced as [S] is increased. The k(cat) for the hydrolysis of the substrate bis(para-nitrophenyl) phosphate (approximately 1 s(-1)) gradually increases from the moment of initiating the reaction, reaching a maximum when the structural change associated with k(obs3) is complete. This structural change is mediated via an extensive hydrogen-bond network that connects the coordination sphere with the substrate binding pocket, as demonstrated by mutation of two residues in this network (His81 and His217). The identities of both the substrate and the metal ion also affect interactions within this H-bond network, thus leading to some mechanistic variations. Overall, the mechanism employed by GpdQ is a paradigm of a substrate- and metal-ion-induced fit to optimize catalysis.
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Unsymmetrical Fe(III)Co(II) and Ga(III)Co(II) complexes as chemical hydrolases: biomimetic models for purple acid phosphatases (PAPs).
Inorg Chem
PUBLISHED: 07-17-2009
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The design and development of suitable biomimetic catalytic systems capable of mimicking the functional properties of enzymes continues to be a challenge for bioinorganic chemists. In this study, we report on the synthesis, X-ray structures, and physicochemical characterization of the novel isostructural [Fe(III)Co(II)(BPBPMP)(mu-OAc)(2)]ClO(4) (1) and [Ga(III)Co(II)(BPBPMP)(mu-OAc)(2)]ClO(4) (2) complexes with the unsymmetrical dinucleating ligand H(2)BPBPMP (2-bis[{(2-pyridyl-methyl)-aminomethyl}-6-{(2-hydroxy-benzyl)-(2-pyridyl-methyl)}-aminomethyl]-4-methylphenol). The previously reported complex [Fe(III)Zn(II)(BPBPMP)(mu-OAc)(2)]ClO(4) (3) was investigated here by electron paramagnetic resonance for comparison with such studies on 1 and 2. A magneto-structural correlation between the exchange parameter J (cm(-1)) and the average bond lengh d (A) of the [Fe(III)-O-M(II)] structural unit for 1 and for related isostructural Fe(III)M(II) complexes using the correlation J = -10(7) exp(-6.8d) reveals that this parameter is the major factor that determines the degree of antiferromagnetic coupling in the series [(BPBPMP)Fe(III)(mu-OAc)(2)M(II)](+) (M(II) = Mn, Fe, Co, Ni) of complexes. Potentiometric and spectrophotometric titrations along with electronic absorption studies show that, in aqueous solution, complexes 1 and 2 generate the [(HO)M(III)(mu-OH)Co(II)(H(2)O)] complex as the catalytically active species in diester hydrolysis reactions. Kinetic studies on the hydrolysis of the model substrate bis(2,4-dinitrophenyl)phosphate by 1 and 2 show Michaelis-Menten behavior, with 2 being 35% more active than 1. In combination with k(H)/k(D) isotope effects, the kinetic studies suggest a mechanism in which a terminal M(III)-bound hydroxide is the hydrolysis-initiating nucleophilic catalyst. In addition, the complexes show maximum catalytic activity in DNA hydrolysis near physiological pH. The modest reactivity difference between 1 and 2 is consistent with the slightly increased nucleophilic character of the Ga(III)-OH terminal group in comparison to Fe(III)-OH in the dinuclear M(III)Co(II) species.
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Metal-ion mutagenesis: conversion of a purple acid phosphatase from sweet potato to a neutral phosphatase with the formation of an unprecedented catalytically competent Mn(II)Mn(II) active site.
J. Am. Chem. Soc.
PUBLISHED: 06-11-2009
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The currently accepted paradigm is that the purple acid phosphatases (PAPs) require a heterovalent, dinuclear metal-ion center for catalysis. It is believed that this is an essential feature for these enzymes in order for them to operate under acidic conditions. A PAP from sweet potato is unusual in that it appears to have a specific requirement for manganese, forming a unique Fe(III)-mu-(O)-Mn(II) center under catalytically optimal conditions (Schenk et al. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 273). Herein, we demonstrate, with detailed electron paramagnetic resonance (EPR) spectroscopic and kinetic studies, that in this enzyme the chromophoric Fe(III) can be replaced by Mn(II), forming a catalytically active, unprecedented antiferromagnetically coupled homodivalent Mn(II)-mu-(H)OH-mu-carboxylato-Mn(II) center in a PAP. However, although the enzyme is still active, it no longer functions as an acid phosphatase, having optimal activity at neutral pH. Thus, PAPs may have evolved from distantly related divalent dinuclear metallohydrolases that operate under pH neutral conditions by stabilization of a trivalent-divalent metal-ion core. The present Mn(II)-Mn(II) system models these distant relatives, and the results herein make a significant contribution to our understanding of the role of the chromophoric metal ion as an activator of the nucleophile. In addition, the detailed analysis of strain broadened EPR spectra from exchange-coupled dinuclear Mn(II)-Mn(II) centers described herein provides the basis for the full interpretation of the EPR spectra from other dinuclear Mn metalloenzymes.
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Catalase vs peroxidase activity of a manganese(II) compound: identification of a Mn(III)-(mu-O)(2)-Mn(IV) reaction intermediate by electrospray ionization mass spectrometry and electron paramagnetic resonance spectroscopy.
Inorg Chem
PUBLISHED: 05-12-2009
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Herein, we report reactivity studies of the mononuclear water-soluble complex [Mn(II)(HPClNOL)(eta(1)-NO(3))(eta(2)-NO(3))] 1, where HPClNOL = 1-(bis-pyridin-2-ylmethyl-amino)-3-chloropropan-2-ol, toward peroxides (H(2)O(2) and tert-butylhydroperoxide). Both the catalase (in aqueous solution) and peroxidase (in CH(3)CN) activities of 1 were evaluated using a range of techniques including electronic absorption spectroscopy, volumetry (kinetic studies), pH monitoring during H(2)O(2) disproportionation, electron paramagnetic resonance (EPR), electrospray ionization mass spectrometry in the positive ion mode [ESI(+)-MS], and gas chromatography (GC). Electrochemical studies showed that 1 can be oxidized to Mn(III) and Mn(IV). The catalase-like activity of 1 was evaluated with and without pH control. The results show that the pH decreases when the reaction is performed in unbuffered media. Furthermore, the activity of 1 is greater in buffered than in unbuffered media, demonstrating that pH influences the activity of 1 toward H(2)O(2). For the reaction of 1 with H(2)O(2), EPR and ESI(+)-MS have led to the identification of the intermediate [Mn(III)Mn(IV)(mu-O)(2)(PClNOL)(2)](+). The peroxidase activity of 1 was also evaluated by monitoring cyclohexane oxidation, using H(2)O(2) or tert-butylhydroperoxide as the terminal oxidants. Low yields (<7%) were obtained for H(2)O(2), probably because it competes with 1 for the catalase-like activity. In contrast, using tert-butylhydroperoxide, up to 29% of cyclohexane conversion was obtained. A mechanistic model for the catalase activity of 1 that incorporates the observed lag phase in O(2) production, the pH variation, and the formation of a Mn(III)-(mu-O)(2)-Mn(IV) intermediate is proposed.
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Inhibition of purple acid phosphatase with alpha-alkoxynaphthylmethylphosphonic acids.
Bioorg. Med. Chem. Lett.
PUBLISHED: 01-29-2009
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Purple acid phosphatases (PAPs) are binuclear hydrolases that catalyse the hydrolysis of a range of phosphorylated substrates. Human PAP is a major histochemical marker for the diagnosis of osteoporosis. In patients suffering from this disorder, PAP activity contributes to increased bone resorption and, therefore, human PAP is a key target for the development of anti-osteoporotic drugs. This manuscript describes the design and synthesis of derivatives of 1-naphthylmethylphosphonic acids as inhibitors of PAP. The K(i) values of these compounds are as low as 4 microM, the lowest reported to date for a PAP inhibitor.
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Spectroscopic Characterization of the Active Fe(III)Fe(III) and Fe(III)Fe(II) Forms of a Purple Acid Phosphatase Model System.
Inorg Chem
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Two new dinucleating ligands (H3L(2) and HL(3)), derivatives of a well-known dinucleating ligand (HL(1)) with two bis-picolylamine sites connected to a bridging phenolate, with hydrogen-bonding donor groups at two of the pyridine moieties were designed and synthesized. Design of these ligands suggests that they will lead to dinuclear complexes with potential to stabilize phosphoester substrates as monodentate rather than bridging ligands. We report the diferric complexes [Fe(III)2(H2L(2))(OH)](4+) and [Fe(III)2(L(3))(OH)(OH2)2](4+), which have been characterized by spectrophotometric titrations, UV-vis, IR, NMR, EPR, and Mössbauer spectroscopy. The phosphatase activity of the diferric systems, in addition to the partially reduced heterovalent [Fe(III)Fe(II)(L(3))(OH)(OH2)2](3+) complex, has been investigated, and the complexes are shown to catalytically hydrolyze the activated phosphodiester substrate BDNPP (bis-dinitrophenylphosphate) as well as the corresponding phosphomonoester substrate DNPP (dinitrophenylphosphate). The results indicate that indeed the secondary interactions lead to an increase of the phosphatase activity and to active phosphomonoesterase catalysts. Interestingly, the heterovalent form of the HL(3)-based complex is more efficient than the diferric complex, and this is also discussed.
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Bacterial and plant ketol-acid reductoisomerases have different mechanisms of induced fit during the catalytic cycle.
J. Mol. Biol.
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Ketol-acid reductoisomerase (KARI) is the second enzyme in the branched-chain amino acid biosynthesis pathway, which is found in plants, fungi and bacteria but not in animals. This difference in metabolism between animals and microorganisms makes KARI an attractive target for the development of antimicrobial agents. Herein we report the crystal structure of Escherichia coli KARI in complex with Mg(2+) and NADPH at 2.3Å resolution. Ultracentrifugation studies confirm that the enzyme exists as a tetramer in solution, and isothermal titration calorimetry shows that the binding of Mg(2+) increases structural disorder while the binding of NADPH increases the structural rigidity of the enzyme. Comparison of the structure of the E. coli KARI-Mg(2+)-NADPH complex with that of enzyme in the absence of cofactors shows that the binding of Mg(2+) and NADPH opens the interface between the N- and C-domains, thereby allowing access for the substrates to bind: the existence of only a small opening between the domains in the crystal structure of the unliganded enzyme signifies restricted access to the active site. This observation contrasts with that in the plant enzyme, where the N-domain can rotate freely with respect to the C-domain until the binding of Mg(2+) and/or NADPH stabilizes the relative positions of these domains. Support is thereby provided for the idea that plant and bacterial KARIs have evolved different mechanisms of induced fit to prepare the active site for catalysis.
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Identification of purple acid phosphatase inhibitors by fragment-based screening: promising new leads for osteoporosis therapeutics.
Chem Biol Drug Des
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Purple acid phosphatases are metalloenzymes found in animals, plants and fungi. They possess a binuclear metal centre to catalyse the hydrolysis of phosphate esters and anhydrides under acidic conditions. In humans, elevated purple acid phosphatases levels in sera are correlated with the progression of osteoporosis and metabolic bone malignancies, making this enzyme a target for the development of new chemotherapeutics to treat bone-related illnesses. To date, little progress has been achieved towards the design of specific and potent inhibitors of this enzyme that have drug-like properties. Here, we have undertaken a fragment-based screening approach using a 500-compound library identifying three inhibitors of purple acid phosphatases with K(i) values in the 30-60 ?m range. Ligand efficiency values are 0.39-0.44 kcal/mol per heavy atom. X-ray crystal structures of these compounds in complex with a plant purple acid phosphatases (2.3-2.7 Å resolution) have been determined and show that all bind in the active site within contact of the binuclear centre. For one of these compounds, the phenyl ring is positioned within 3.5 Å of the binuclear centre. Docking simulations indicate that the three compounds fit into the active site of human purple acid phosphatases. These studies open the way to the design of more potent and selective inhibitors of purple acid phosphatases that can be tested as anti-osteoporotic drug leads.
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Cadmium(II) complexes: mimics of organophosphate pesticide degrading enzymes and metallo-?-lactamases.
Inorg Chem
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Cadmium(II) complexes of ethyl 4-hydroxy-3,5-bis(((2-hydroxyethyl)(pyridin-2-ylmethyl)amino)methyl)benzoate (CO(2)EtH(3)L1) and ethyl 4-hydroxy-3,5-bis(((2-methoxyethyl)(pyridin-2-ylmethyl)amino)methyl)benzoate (CO(2)EtHL2) are described. The two ligands possess an ethyl ester (CO(2)Et-) at the position para to the phenolic -OH; CO(2)EtHL2, with methyl ether donors in contrast to potentially nucleophilic alkoxide donors in CO(2)EtH(3)L1, offers a direct comparison of potential ligand-centered nucleophiles. The complex with CO(2)EtH(3)L1 was characterized using (1)H and (13)C NMR spectroscopy, mass spectrometry and microanalysis; X-ray crystallography defined a tetranuclear structure [Cd(4)(CO(2)EtH(2)L1)(2)(CH(3)COO)(3.75)Cl(0.25)(H(2)O)(2)](PF(6))(2). Functional studies of the cadmium(II) complexes were undertaken with the substrates bis(2,4-dinitrophenyl)phosphate (BDNPP), and nitrocefin to assess their phosphatase and ?-lactamase activities, respectively. The complexes with CO(2)EtH(3)L1 and CO(2)EtHL2 are competent phosphoesterase mimics with K(M) = 9.4 ± 2.1 mM and 10.1 ± 3.4 mM, k(cat) = 9.4 ± 0.2 × 10(-3) s(-1) and 9.7 ± 2.7 × 10(-3) s(-1), respectively. Use of a solvent mixture containing H(2)(18)O/H(2)(16)O in the reaction with BDNPP showed that for the complex with CO(2)EtH(3)L1 the (18)O label was incorporated in the reaction product suggesting that the nucleophile involved is a Cd-OH moiety and not a metal bound alkoxide; for CO(2)EtHL2 the presence of the methyl-ether dictates that the active nucleophile must also be a hydroxide. The cadmium(II) complex with CO(2)EtH(3)L1 was furthermore found to be a competent ?-lactamase mimic with k(cat) = 1.39 × 10(-2) ± 3 × 10(-3) s(-1), K(M) = 0.11 ± 0.03 mM, and pK(a) = 7.9 ± 0.1. Mass spectral evidence suggested that the active nucleophile in this reaction is the alkoxide; lack of ?-lactamase activity of the complex with CO(2)EtHL2 supports this assignment. Similar to enzyme-catalyzed reactions, a blue reaction intermediate in the ?-lactamase reaction of the CO(2)EtH(3)L1 complex was also identified. It is proposed that the Cd(II) complexes of CO(2)EtH(3)L1 and CO(2)EtHL2 react identically as phosphatases, with a terminal hydroxide as the nucleophile; the former exhibits ?-lactamase activity with the alkoxide as a nucleophile, while the latter, without a potentially nucleophilic alkoxide, is inactive.
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Synthesis and kinetic testing of tetrahydropyrimidine-2-thione and pyrrole derivatives as inhibitors of the metallo-?-lactamase from Klebsiella pneumonia and Pseudomonas aeruginosa.
Chem Biol Drug Des
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Metallo-?-lactamases (MBLs), produced by an increasing number of bacterial pathogens, facilitate the hydrolysis of many commonly used ?-lactam antibiotics. There are no clinically useful antagonists against MBLs. Two sets of tetrahydropyrimidine-2-thione and pyrrole derivatives were synthesized and assayed for their inhibitory effects on the catalytic activity of the IMP-1 MBL from Pseudomonas aeruginosa and Klebsiella pneumoniae. Nine compounds tested (1a, 3b, 5c, 6b, 7a, 8a, 11c, 13a, and 16a) showed micromolar inhibition constants (K(i) values range from ?20-80 ?M). Compounds 1c, 2b, and 15a showed only weak inhibition. In silico docking was employed to investigate the binding mode of each enantiomer of the strongest inhibitor, 5c (K(i) = 19 ± 9 ?M), as well as 7a (K(i) =21 ± 10 ?M), the strongest inhibitor of the pyrrole series, in the active site of IMP-1.
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Binuclear metallohydrolases: complex mechanistic strategies for a simple chemical reaction.
Acc. Chem. Res.
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Binuclear metallohydrolases are a large family of enzymes that require two closely spaced transition metal ions to carry out a plethora of hydrolytic reactions. Representatives include purple acid phosphatases (PAPs), enzymes that play a role in bone metabolism and are the only member of this family with a heterovalent binuclear center in the active form (Fe(3+)-M(2+), M = Fe, Zn, Mn). Other members of this family are urease, which contains a di-Ni(2+) center and catalyzes the breakdown of urea, arginase, which contains a di-Mn(2+) center and catalyzes the final step in the urea cycle, and the metallo-?-lactamases, which contain a di-Zn(2+) center and are virulence factors contributing to the spread of antibiotic-resistant pathogens. Binuclear metallohydrolases catalyze numerous vital reactions and are potential targets of drugs against a wide variety of human disorders including osteoporosis, various cancers, antibiotic resistance, and erectile dysfunctions. These enzymes also tend to catalyze more than one reaction. An example is an organophosphate (OP)-degrading enzyme from Enterobacter aerogenes (GpdQ). Although GpdQ is part of a pathway that is used by bacteria to degrade glycerolphosphoesters, it hydrolyzes a variety of other phosphodiesters and displays low levels of activity against phosphomono- and triesters. Such a promiscuous nature may have assisted the apparent recent evolution of some binuclear metallohydrolases to deal with situations created by human intervention such as OP pesticides in the environment. OP pesticides were first used approximately 70 years ago, and therefore the enzymes that bacteria use to degrade them must have evolved very quickly on the evolutionary time scale. The promiscuous nature of enzymes such as GpdQ makes them ideal candidates for the application of directed evolution to produce new enzymes that can be used in bioremediation and against chemical warfare. In this Account, we review the mechanisms employed by binuclear metallohydrolases and use PAP, the OP-degrading enzyme from Agrobacterium radiobacter (OPDA), and GpdQ as representative systems because they illustrate both the diversity and similarity of the reactions catalyzed by this family of enzymes. The majority of binuclear metallohydrolases utilize metal ion-activated water molecules as nucleophiles to initiate hydrolysis, while some, such as alkaline phosphatase, employ an intrinsic polar amino acid. Here we only focus on catalytic strategies applied by the former group.
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Penicillin inhibitors of purple acid phosphatase.
Bioorg. Med. Chem. Lett.
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Purple acid phosphatases (PAPs) are binuclear metallohydrolases that have a multitude of biological functions and are found in fungi, bacteria, plants and animals. In mammals, PAP activity is linked with bone resorption and over-expression can lead to bone disorders such as osteoporosis. PAP is therefore an attractive target for the development of drugs to treat this disease. A series of penicillin conjugates, in which 6-aminopenicillanic acid was acylated with aromatic acid chlorides, has been prepared and assayed against pig PAP. The binding mode of most of these conjugates is purely competitive, and some members of this class have potencies comparable to the best PAP inhibitors yet reported. The structurally related penicillin G was shown to be neither an inhibitor nor a substrate for pig PAP. Molecular modelling has been used to examine the binding modes of these compounds in the active site of the enzyme and to rationalise their activities.
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Promiscuity comes at a price: catalytic versatility vs efficiency in different metal ion derivatives of the potential bioremediator GpdQ.
Biochim. Biophys. Acta
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The glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) is a highly promiscuous dinuclear metallohydrolase with respect to both substrate specificity and metal ion composition. While this promiscuity may adversely affect the enzymes catalytic efficiency its ability to hydrolyse some organophosphates (OPs) and by-products of OP degradation have turned GpdQ into a promising candidate for bioremedial applications. Here, we investigated both metal ion binding and the effect of the metal ion composition on catalysis. The prevalent in vivo metal ion composition for GpdQ is proposed to be of the type Fe(II)Zn(II), a reflection of natural abundance rather than catalytic optimisation. The Fe(II) appears to have lower binding affinity than other divalent metal ions, and the catalytic efficiency of this mixed metal center is considerably smaller than that of Mn(II), Co(II) or Cd(II)-containing derivatives of GpdQ. Interestingly, metal ion replacements do not only affect catalytic efficiency but also the optimal pH range for the reaction, suggesting that different metal ion combinations may employ different mechanistic strategies. These metal ion-triggered modulations are likely to be mediated via an extensive hydrogen bond network that links the two metal ion binding sites via residues in the substrate binding pocket. The observed functional diversity may be the cause for the modest catalytic efficiency of wild-type GpdQ but may also be essential to enable the enzyme to evolve rapidly to alter substrate specificity and enhance k(cat) values, as has recently been demonstrated in a directed evolution experiment. This article is part of a Special Issue entitled: Chemistry and mechanism of phosphatases, diesterases and triesterases.
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Spectroscopic and catalytic characterization of a functional Fe(III)Fe(II) biomimetic for the active site of uteroferrin and protein cleavage.
Inorg Chem
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A mixed-valence complex, [Fe(III)Fe(II)L1(?-OAc)(2)]BF(4)·H(2)O, where the ligand H(2)L1 = 2-{[[3-[((bis(pyridin-2-ylmethyl)amino)methyl)-2-hydroxy-5-methylbenzyl](pyridin-2-ylmethyl)amino]methyl]phenol}, has been studied with a range of techniques, and, where possible, its properties have been compared to those of the corresponding enzyme system purple acid phosphatase. The Fe(III)Fe(II) and Fe(III)(2) oxidized species were studied spectroelectrochemically. The temperature-dependent population of the S = 3/2 spin states of the heterovalent system, observed using magnetic circular dichroism, confirmed that the dinuclear center is weakly antiferromagnetically coupled (H = -2JS(1)·S(2), where J = -5.6 cm(-1)) in a frozen solution. The ligand-to-metal charge-transfer transitions are correlated with density functional theory calculations. The Fe(III)Fe(II) complex is electron paramagnetic resonance (EPR)-silent, except at very low temperatures (<2 K), because of the broadening caused by the exchange coupling and zero-field-splitting parameters being of comparable magnitude and rapid spin-lattice relaxation. However, a phosphate-bound Fe(III)(2) complex showed an EPR spectrum due to population of the S(tot) = 3 state (J= -3.5 cm(-1)). The phosphatase activity of the Fe(III)Fe(II) complex in hydrolysis of bis(2,4-dinitrophenyl)phosphate (k(cat.) = 1.88 × 10(-3) s(-1); K(m) = 4.63 × 10(-3) mol L(-1)) is similar to that of other bimetallic heterovalent complexes with the same ligand. Analysis of the kinetic data supports a mechanism where the initiating nucleophile in the phosphatase reaction is a hydroxide, terminally bound to Fe(III). It is interesting to note that aqueous solutions of [Fe(III)Fe(II)L1(?-OAc)(2)](+) are also capable of protein cleavage, at mild temperature and pH conditions, thus further expanding the scope of this complexs catalytic promiscuity.
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Monoesterase activity of a purple acid phosphatase mimic with a cyclam platform.
Chemistry
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The synthesis and characterization of a novel dinucleating ligand L (L=4,11-dimethyl-1,8-bis{2-[N-(di-2-pyridylmethyl)amino]ethyl}cyclam) and its ?-oxo-bridged diferric complex [(H(2)L){Fe(III)(2)(O)}(Cl)(4)](2+) are reported. This diiron(III) complex is the first example of a truly functional purple acid phosphatase (PAP) mimic as it accelerates the hydrolysis of the activated phosphomonoester 2,4-dinitrophenyl phosphate (DNPP). The spectroscopic and kinetic data indicate that only substrates that are monodentately bound to one of the two ferric ions can be attacked by a suitable nucleophile. This is, most probably, a terminal iron(III)-bound hydroxide. DFT calculations support this assumption and also highlight the importance of secondary interactions, exerted by the protonated cyclam platform, for the positioning and activation of the iron(III)-bound substrate. Similar effects are postulated in the native enzyme but addressed in PAP mimics for the first time.
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