Removal of Metal from Carboxypeptidase A Proceeds via a Split Pathway: Implications for the General Mechanisms of Metalloenzyme Inactivation by Chelating Agents.

The chelation of protein-bound metal ions is typically thought to follow either a dissociative (D) or an associative (A) path. While the former mechanism involves the spontaneous dissociation of the metal from the protein prior to chelation, the latter route is characterized by the formation of an intermediate protein-metal-chelator ternary complex. Using the prototypical zinc protease carboxypeptidase A (CPA) and a variety of charged and neutral chelating agents, we demonstrate that inactivation of the enzyme (and likely other metalloproteins) proceeds through a split pathway with contributions from both D- and A-type mechanisms.

An Excel fitting routine for correcting protein absorption spectra for scatter.

Protein concentrations are often determined in a non-destructive manner by measuring the absorbance at 280 nm. However, light scattering in protein samples can complicate such assessment. We here describe a simple Excel Solver-based fitting routine to correct full protein UV absorption spectra for both Rayleigh and Mie scattering.

Effect of pH and denaturants on the fold and metal status of anthrax lethal factor.

Anthrax lethal factor (LF) is a critical component of the anthrax toxin, and functions intracellularly as a zinc-dependent endopeptidase targeting proteins involved in maintaining critical host signaling pathways. To reach the cytoplasm, LF requires to be unfolded and guided through the narrow protective antigen pore in a pH-dependent process. The current study sought to address the question as to whether LF is capable of retaining its metal ion when exposed to a low-pH environment (similar to that found in late endosomes) and an unfolding stress (induced by urea).

Specificity-directed design of a FRET-quenched heptapeptide for assaying thermolysin-like proteases.

Thermolysin (TL) is an industrially important zinc endopeptidase, and the prototype of the M4 family of metallopeptidases. The catalytic function of TL and its relatives is typically assessed using chromogenic or more sensitive fluorescent peptides, with the latter substrates relying on Förster resonance energy transfer (FRET). Here, we demonstrate that a FRET-quenched heptapeptide designed on the basis of the enzyme's substrate specificity (Dabcyl-FKFLGKE-EDANS) is efficiently cleaved by TL and dispase (a TL-like protease) in between the Phe3 and Leu4 residues.

Binding of Cu, Co, and Cs to fluorescent components of natural organic matter (NOM) from three contrasting sites.

Aqueous natural organic matter (NOM) contains different types of functional groups (carboxylic, phenolic, sulfidic, etc.), and hence could change the speciation of metals in environmental systems. This work is a proof-of-concept study on the interaction of three metals (Cu, Co, and Cs) with NOM using fluorescence spectroscopy.

Structural and Kinetic Studies of the Potent Inhibition of Metallo-β-lactamases by 6-Phosphonomethylpyridine-2-carboxylates.

There are currently no clinically available inhibitors of metallo-β-lactamases (MBLs), enzymes that hydrolyze β-lactam antibiotics and confer resistance to Gram-negative bacteria. Here we present 6-phosphonomethylpyridine-2-carboxylates (PMPCs) as potent inhibitors of subclass B1 (IMP-1, VIM-2, and NDM-1) and B3 (L1) MBLs. Inhibition followed a competitive, slow-binding model without an isomerization step (IC values of 0.

An investigation of the pH dependence of copper-substituted anthrax lethal factor and its mechanistic implications.

Anthrax lethal factor (LF) is a zinc-dependent endopeptidase involved in the cleavage of proteins critical to the maintenance of host signaling pathways during anthrax infections. Although zinc is typically regarded as the native metal ion in vivo, LF is highly tolerant to metal substitution, with its replacement by copper yielding an enzyme (CuLF) 4.5-fold more active than the native zinc protein (at pH 7).

Highly dynamic metal exchange in anthrax lethal factor involves the occupation of an inhibitory metal binding site.

Metal exchange is a common strategy to replace the zinc ion of many zinc proteins with other transition metals amenable to spectroscopic investigations. We here demonstrate that in anthrax lethal factor (and likely other zinc proteases), metal exchange is a fast process, and involves the occupation of an inhibitory metal site by the incoming ion prior to the release of zinc.

Arginine-containing peptides as potent inhibitors of VIM-2 metallo-β-lactamase.

Background: Metallo-β-lactamases (MBLs) play an important role in the emergence of microbial resistance to β-lactam antibiotics, and are hence considered targets for the design of novel therapeutics. We here report on the inhibitory effect of peptides containing multiple arginine residues on VIM-2, a clinically important MBL from Pseudomonas aeruginosa.

Methods: Enzyme kinetic assays in combination with fluorescence spectroscopy and stopped-flow UV-Vis spectrophotometry were utilized to explore the structure-activity relationship of peptides as inhibitors of VIM-2.

Assay for drug discovery: Synthesis and testing of nitrocefin analogues for use as β-lactamase substrates.

We report on the synthesis of three nitrocefin analogues and their evaluation as substrates for the detection of β-lactamase activity. These compounds are hydrolyzed by all four Ambler classes of β-lactamases. Kinetic parameters were determined with eight different β-lactamases, including VIM-2, NDM-1, KPC-2, and SPM-1.

Influence of chemical denaturants on the activity, fold and zinc status of anthrax lethal factor.

Anthrax lethal factor (LF) is a zinc-dependent endopeptidase which, through a process facilitated by protective antigen, translocates to the host cell cytosol in a partially unfolded state. In the current report, the influence of urea and guanidine hydrochloride (GdnHCl) on LF׳s catalytic function, fold and metal binding was assessed at neutral pH. Both urea and GdnHCl were found to inhibit LF prior to the onset of unfolding, with the inhibition by the latter denaturant being a consequence of its ionic strength.

Characterization of the Natural Organic Matter (NOM) in groundwater contaminated with (60)Co and (137)Cs using ultrafiltration, Solid Phase Extraction and fluorescence analysis.

Spot samples of shallow groundwaters have been taken between the years 2004 and 2010 near a site formerly used for the dispersal of radioactive liquid wastes. Three sampling points, one clean (upstream), and two downstream of the contamination source, were processed by ultrafiltration (5000 Da cut-off) and Solid Phase Extraction (SPE) to determine the association of selected artificial radionuclides ((60)Co, (137)Cs) with Natural Organic Matter (NOM). The last two sampling episodes (2008 and 2010) also benefited from fluorescence analysis to determine the major character of the NOM.

Effect of pH on the catalytic function and zinc content of native and immobilized anthrax lethal factor.

Translocation of the zinc-dependent metalloendopeptidase anthrax lethal factor (LF) from the endosome to the cytosol requires an acidic endosomal milieu. In the current study, we utilized immobilized (to prevent protein aggregation below pH 5.5) and native LF to assess the effect of pH on the function and metal content of LF.

Preparation and characterization of cobalt-substituted anthrax lethal factor.

Anthrax lethal factor (LF) is a zinc-dependent endopeptidase involved in the cleavage of mitogen-activated protein kinase kinases near their N-termini. The current report concerns the preparation of cobalt-substituted LF (CoLF) and its characterization by electronic spectroscopy. Two strategies to produce CoLF were explored, including (i) a bio-assimilation approach involving the cultivation of LF-expressing Bacillus megaterium cells in the presence of CoCl(2), and (ii) direct exchange by treatment of zinc-LF with CoCl(2).

Alkaline earth metals are not required for the restoration of the apoform of anthrax lethal factor to its holoenzyme state.

Anthrax lethal factor (LF) is a zinc-dependent metalloendopeptidase previously shown to require calcium and magnesium for the restoration of its catalytic function upon exposure of the apoprotein (apoLF) to Zn(2+). Since concrete Ca(2+)/Mg(2+) binding sites have not been identified in LF, the effects of alkaline earth metals on the enzymatic function of holoLF (ZnLF) and on the reconstitution of apoLF were reinvestigated. The current study reveals alkaline earth metals to be inhibitory at concentrations higher than 1mM.

A spectrophotometric method for the determination of zinc, copper, and cobalt ions in metalloproteins using Zincon.

Zincon (2-carboxy-2'-hydroxy-5'-sulfoformazylbenzene) has long been known as an excellent colorimetric reagent for the detection of zinc and copper ions in aqueous solution. To extend the chelator's versatility to the quantification of metal ions in metalloproteins, the spectral properties of Zincon and its complexes with Zn(2+), Cu(2+), and Co(2+) were investigated in the presence of guanidine hydrochloride and urea, two common denaturants used to labilize metal ions in proteins. These studies revealed the detection of metals to be generally more sensitive with urea.

A direct spectrophotometric method for the simultaneous determination of zinc and cobalt in metalloproteins using 4-(2-pyridylazo)resorcinol.

An assay involving the direct and simultaneous determination of low micromolar concentrations (1-10 microM) of both zinc and cobalt ions suitable for metal content analyses of metalloproteins is described. The procedure exploits differences in the visible absorption spectra of the chromophoric chelator 4-(2-pyridylazo)resorcinol (PAR) resulting from its complexation to Zn2+ and/or Co2+ ions and is based on the fit of experimental spectra to a linear addition of Beer-Lambert law. The method eliminates the need for separating or masking one of the metal ions prior to their quantification and could prove to be particularly useful in studies on Co2+-substituted zinc proteins.

Chelator-facilitated chemical modification of IMP-1 metallo-beta-lactamase and its consequences on metal binding.

A method involving the reversible chemical modification of an active site, zinc-binding cysteine residue (Cys221) for the specific removal of one of the two zinc ions in the metallo-beta-lactamase IMP-1 was explored. Covalent modification of Cys221 by 5,5'-dithio-bis(2-nitrobenzoic acid) was greatly enhanced by the presence of dipicolinic acid, and subsequent removal of the modifying group was easily achieved by reduction of the disulfide bond. However, mass spectrometric analyses and an assessment of IMP-1's catalytic competence are consistent with the maintenance of the enzyme's binuclear status.

68Zn isotope exchange experiments reveal an unusual kinetic lability of the metal ions in the di-zinc form of IMP-1 metallo-beta-lactamase.

The apparently paradoxical behaviour of facile exchange (kinetic lability) of tightly bound (thermodynamic stability) zinc ions in the enzyme IMP-1 metallo-beta-lactamase with Zn-68 and cadmium ions, as indicated by in-torch vaporization inductively-coupled plasma mass spectrometry (ITV-ICP-MS) and electrospray-ionization mass spectrometry (ESI-MS), is consistent with the involvement of a third metal ion in promoting Lewis acid/base type exchange processes.

Molecular cloning, expression, purification, and characterization of fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis--a novel Class II A tetramer.

The Class II fructose 1,6-bisphosphate aldolase (fda, Rv0363c) from the pathogen Mycobacterium tuberculosis H37RV was subcloned in the Escherichia coli vector pT7-7 and purified to near homogeneity. The specific activity (35 U/mg) is approximately 9 times higher than previously reported for the enzyme partially purified from the pathogen. Attempts to express the enzyme with an N-terminal fusion tag yielded inactive, mostly insoluble protein.

Characterization of a tungsten-substituted nitrogenase isolated from Rhodobacter capsulatus.

In the phototrophic non-sulfur bacterium Rhodobacter capsulatus, the biosynthesis of the conventional Mo-nitrogenase is strictly Mo-regulated. Significant amounts of both dinitrogenase and dinitrogenase reductase were only formed when the growth medium was supplemented with molybdate (1 microM). During cell growth under Mo-deficient conditions, tungstate, at high concentrations (1 mM), was capable of partially (approximately 25%) substituting for molybdate in the induction of nitrogenase synthesis.

Thiols as classical and slow-binding inhibitors of IMP-1 and other binuclear metallo-beta-lactamases.

The inhibitory effect of a variety of thiol compounds on the function of binuclear metallo-beta-lactamases, with a particular focus on IMP-1 from Pseudomonas aeruginosa, has been investigated. Thiol inhibitors, depending on their structural features, fall into two categories, one in which inhibition at neutral pH was instantaneous and the other in which inhibition was time-dependent. While mercaptans with anionic substituents in the vicinity of their SH groups exhibited the former type of inhibition, neutral thiols appear to induce a slow, time-dependent isomerization of the initially formed EI complex to a tighter EI complex.

N-arylsulfonyl hydrazones as inhibitors of IMP-1 metallo-beta-lactamase.

Members of a family of N-arylsulfonyl hydrazones have been identified as novel inhibitors of IMP-1, a metallo-beta-lactamase of increasing prevalence. Structure-activity relationship studies have indicated a requirement for bulky aromatic substituents on each side of the sulfonyl hydrazone backbone for these compounds to serve as efficient inhibitors of IMP-1. Molecular modeling has provided insight into the structural basis for the anti-metallo-beta-lactamase activity exhibited by this class of compounds.

IMP-1 metallo-beta-lactamase: effect of chelators and assessment of metal requirement by electrospray mass spectrometry.

Metallo-beta-lactamases have attracted considerable attention due to their role in microbial resistance to beta-lactam antibiotics. IMP-1, the binuclear Zn-dependent beta-lactamase produced by Pseudomonas aeruginosa and other microorganisms, is of particular interest in view of its increasing prevalence. An examination of the susceptibility of IMP-1 to inactivation by six different divalent metal ion chelators has revealed that all except Zincon cause inhibition by forming a complex with the holoenzyme.