Characterization of an inhibitory metal binding site in carboxypeptidase A

Phosphorus-solubilizing bacteria improve the growth of Nicotiana benthamiana on lunar regolith simulant by dissociating insoluble inorganic phosphorus

In-situ utilization of lunar soil resources will effectively improve the self-sufficiency of bioregenerative life support systems for future lunar bases. Therefore, we have explored the microbiological method to transform lunar soil into a substrate for plant cultivation. In this study, five species of phosphorus-solubilizing bacteria are used as test strains, and a 21-day bio-improving experiment with another 24-day Nicotiana benthamiana cultivation experiment are carried out on lunar regolith simulant. We have observed that the phosphorus-solublizing bacteria Bacillus mucilaginosus, Bacillus megaterium, and Pseudomonas fluorescens can tolerate the lunar regolith simulant conditions and dissociate the insoluble phosphorus from the regolith simulant. The phosphorus-solubilizing bacteria treatment improves the available phosphorus content of the regolith simulant, promoting the growth of Nicotiana benthamiana. Here we demonstrate that the phosphorus-solubilizing bacteria can effectively improve the fertility of lunar regolith simulant, making it a good cultivation substrate for higher plants. The results can lay a technical foundation for plant cultivation based on lunar regolith resources in future lunar bases.

Regulation of zinc-dependent enzymes by metal carrier proteins

Zn²⁺ ions are essential in many physiological processes, including enzyme catalysis, protein structural stabilization, and the regulation of many proteins. The affinities of proteins for Zn²⁺ ions span several orders of magnitude, with catalytic Zn²⁺ ions generally held more tightly than structural or regulatory ones. Metal carrier proteins, most of which are not specific for Zn²⁺, bind these ions with a broad range of affinities that overlap those of catalytic, structural, and regulatory Zn²⁺ ions and are thought to be responsible for distributing the metal through most cells, tissues, and fluid compartments. While little is known about how many proteins obtain or release these ions, there is now considerable experimental evidence suggesting that metal carrier proteins may be responsible for transferring metals to and from some Zn²⁺-dependent proteins, thus serving as a major regulatory factor for them. In this review, the biological roles of Zn²⁺ and structures of Zn²⁺ binding sites are examined, and experimental evidence demonstrating the direct participation of metal carrier proteins in enzyme regulation is discussed. Mechanisms of metal ion transfer are also offered, and the potential physiological significance of this phenomenon is explored.

Zn-containing Adhesives Facilitate Collagen Protection and Remineralization at the Resin-Dentin Interface: A Narrative Review

This is a narrative review of the literature assessing the potential effectiveness of doping dentin polymeric adhesives with zinc compounds in order to improve bonding efficacy, remineralization and protection against degradation. A literature search was conducted using electronic databases, such as PubMed, MEDLINE, DIMDI and Web of Science. Through our search, we found literature demonstrating that Zn-doped dentin adhesives promote protection and remineralization of the resin-dentin interfaces. The increased bioactivity has also facilitated dentinal tubules' occlusion by crystals' precipitation contributing to improved sealing efficacy of restorations. Loading dentin adhesives with zinc gives rise to an increase of both crystallinity of mineral and crosslinking of collagen. The main role of zinc, in dentin adhesives, is to inhibit collagen proteolysis. We concluded that zinc exerts a protective effect through binding at the collagen-sensitive cleavage sites of matrix-metalloproteinases (MMPs), contributing to dentin matrix stabilization. Zinc may not only act as a MMPs inhibitor, but also influence signaling pathways and stimulate metabolic effects in dentin mineralization and remineralization processes. Zn-doped adhesives increase the longevity of dentin bonding through MMPs inhibition. Zn poses a remineralization strategy in demineralized dentin.

Structural and biochemical analyses of the tetrameric carboxypeptidase S9Cfn from Fusobacterium nucleatum

As one of the most abundant bacteria in the human oral cavity, Fusobacterium nucleatum is closely involved in various oral diseases and is also a risk factor for other diseases. The peptidases of F. nucleatum can digest exogenous peptides into amino acids to satisfy its nutrient requirements. Here, a putative F. nucleatum peptidase, termed S9Cfn, which belongs to the S9C peptidase family was identified. Enzymatic activity assays combined with mass-spectrometric analysis revealed that S9Cfn is a carboxypeptidase, but not an aminopeptidase as previously annotated. The crystal structure of the S9Cfn tetramer was solved at 2.6 Å resolution and was found to contain a pair of oligomeric pores in the center. Structural analysis, together with site-directed mutagenesis and enzymatic activity assays, revealed a substrate-entrance tunnel that extends from each oligomeric pore to the catalytic triad, adjacent to which three conserved arginine residues are responsible for substrate binding. Moreover, comparison with other S9 peptidase structures indicated drastic conformational changes of the oligomeric pores during the catalytic cycle. Together, these findings increase the knowledge of this unique type of tetrameric carboxypeptidase and provide insight into the homeostatic control of microbiota in the human oral cavity.

Novel Antibacterial Resin-Based Filling Material Containing Nanoparticles for the Potential One-Step Treatment of Caries

The aim of this work was to study the application of resin filling containing nanomaterials for the potential treatment of caries. Zinc nanoparticles (ZnO@NP, 50 nm) were chosen for their antimicrobial capacity against aerobic bacteria, and here, they have proved to be bactericidal against anaerobic bacterial strains (Streptococcus mutans, Streptococcus mitis, and Lactobacillus spp.). Potential mechanism of action is proposed based on microbiological assays and seems to be independent of oxidative stress because the nanoparticles are effective in microaerophilic conditions. The loading of nanoparticles on the demineralized dental surface and their infiltration power were significantly improved when ZnO@NP were carried by the resin. Overall, this material seems to have a high potential to become a one-step treatment for caries lesions.

Expression, purification and identification of a thermolysin-like protease, neutral protease I, from Aspergillus oryzae with the Pichia pastoris expression system

Neutral proteases are widely used in the textile, food and medical industries. This study was designed to obtain high expression levels of neutral protease I from Aspergillus oryzae 3.042 by using Pichia pastoris GS115 as the host strain for industrial purposes. The coding sequence of the target gene was modified, synthesized, and then cloned into the expression vector pHBM905BDM, which harbored the d1+2 × 201 AOX1 promoter and the MF4I leader sequence. The recombinant plasmid was transformed into Pichia pastoris GS115. The recombinant strain was used for high-density fermentation in a 4-L fermenter. The yield of the target protein reached 12.87 mg/mL, and the enzyme activity was approximately 49370 U/mL, which indicated that this enzyme was expressed in Pichia pastoris at a high level. The target protein was purified and characterized. Its optimum temperature and pH were 55 °C and 8.0, respectively. This enzyme was extremely sensitive to EDTA, which is consistent with the previous reports that it is a zinc-dependent metalloprotease. Our results indicated that low concentrations of zinc, calcium and magnesium ions stimulated the enzyme activity, whereas high concentrations inhibited its activity. In addition, calcium and magnesium ions increased the thermostability of the enzyme. All of the evidence indicated that this protease is a thermolysin-like peptidase.

[Coordination chemical studies on the zinc enzymes]

The metal dissociation constants of bovine carbonic anhydrase II, bovine carboxypeptidase A, rat aminopeptidase B, and rat dipeptidyl peptidase III were measured using metal buffer solutions. The zinc dissociation constants of bovine carbonic anhydrase II, bovine carboxypeptidase A, rat aminopeptidase B, and rat dipeptidyl peptidase III were 5.8×10(-14), 3.5×10(-12), 3.7×10(-13), and 1.9×10(-13) M, respectively. The ternary complex between metal derivatives of bovine carbonic anhydrase and various chelating agents were characterized using the kinetic method and visible and magnetic circular dichroism spectra. The coordination geometry of the ternary complex was in the equilibrium state between the five and the tetrahedral coordination geometry. The equilibrium state depends on the character of ligands. Dipeptidyl peptidase III which has an abnormal zinc binding motif (HEXXXH) was characterized using the point mutation and computer simulation methods. The abnormal zinc binding motif (HEXXXH) of rat dipeptidyl peptidase III has a large helix part. It is generally known that the cupric derivatives of the zinc peptidase loses enzyme activity, but the cupric derivative of dipeptidyl peptidase III surprisingly has enzyme activity. The measurement of the electron paramagnetic resonance spectra of the cupric rat dipeptidyl peptidase III in the presence of the substrate showed that the coordination geometry is very flexible. The flexibility of the coordination geometry in the cupric rat dipeptidyl peptidase III is important for the expression of enzyme activity. Docking simulation was used to identify the substrate binding site of aminopeptidase B, which is a powerful tool to estimate substrate binding residues in enzymes.

Structure of matrix metalloproteinase-3 with a platinum-based inhibitor

An X-ray investigation has been performed with the aim of characterizing the binding sites of a platinum-based inhibitor (K[PtCl3(DMSO)]) of matrix metalloproteinase-3 (stromelysin-1). The platinum complex targets His224 in the S1' specificity loop, representing the first step in the selective inhibition process (PDB ID code 4JA1).

Alkaline protease from a non-toxigenic mangrove isolate of Vibrio sp. V26 with potential application in animal cell culture

Vibrio sp. V26 isolated from mangrove sediment showed 98 % similarity to 16S rRNA gene of Vibrio cholerae, V. mimicus, V. albensis and uncultured clones of Vibrio. Phenotypically also it resembled both V. cholerae and V. mimicus. Serogrouping, virulence associated gene profiling, hydrophobicity, and adherence pattern clearly pointed towards the non-toxigenic nature of Vibrio sp. V26. Purification and characterization of the enzyme revealed that it was moderately thermoactive, nonhemagglutinating alkaline metalloprotease with a molecular mass of 32 kDa. The application of alkaline protease from Vibrio sp. V26 (APV26) in sub culturing cell lines (HEp-2, HeLa and RTG-2) and dissociation of animal tissue (chick embryo) for primary cell culture were investigated. The time required for dissociation of cells as well as the viable cell yield obtained by while administering APV26 and trypsin were compared. Investigations revealed that the alkaline protease of Vibrio sp. V26 has the potential to be used in animal cell culture for subculturing cell lines and dissociation of animal tissue for the development of primary cell cultures, which has not been reported earlier among metalloproteases of Vibrios.

Zinc and the zinc proteome

Zinc(II) ions are catalytic, structural, and regulatory cofactors in proteins. In contrast to painstakingly collecting the pieces by isolating and characterizing zinc proteins, 'omics' approaches are now allowing us to tease out information about zinc proteins from genomes and to piece together the information to a broader knowledge and appreciation of the role of zinc in biology. Estimates for the number of zinc proteins in the human genome and in genomes of other organisms have been derived from a bioinformatics approach: mining sequence databases for homologies of known zinc-coordination motifs with characteristic ligand signatures for metal binding and combining this information with the knowledge about metal-binding domains of proteins. This approach resulted in an impressive number of almost 3000 human zinc proteins and made major contributions to our understanding of the composition of the zinc proteome and the functions of zinc proteins. However, the impact of zinc on protein science is even greater. Predictions do not include yet undiscovered ligand signatures, coordination environments that employ complex binding patterns with nonsequential binding of ligands and ligand bridges, zinc/protein interactions at protein interfaces, and transient interactions of zinc(II) ions with proteins that are not known to be zinc proteins. All this information and recent discoveries of how cellular zinc is controlled and how zinc(II) ions function as signaling ions add an hitherto unrecognized dimension to the zinc proteome of multicellular eukaryotic organisms. Zinc proteomics employs a combination of approaches from different disciplines, such as bioinformatics, biology, inorganic biochemistry, and significantly, analytical and structural chemistry. It provides crucial large-scale datasets for interpreting the roles of zinc in health and disease at both a molecular and a global, systems biology, level.

Enzymatic characteristics of a recombinant neutral protease I (rNpI) from Aspergillus oryzae expressed in Pichia pastoris

A truncated neutral protease I (NpI) from Aspergillus oryzae 3.042 was expressed in Pichia pastoris with a high enzyme yield of 43101 U/mL. Its optimum pH was about 8.0, and it was stable in the pH range of 5.0-9.0. Its optimum temperature was about 55 °C and retained >90% activity at 50 °C for 120 min. Recombinant NpI (rNpI) was inhibited by Cu(2+) and EDTA. Eight cleavage sites of rNpI in oxidized insulin B-chain were determined by mass spectrometry, and five of them had high hydrophobic amino acid affinity, which makes it efficient in producing antihypertensive peptide IPP from β-casein and a potential debittering agent. The high degree of hydrolysis (DH) of rNpI to soybean protein (8.8%) and peanut protein (11.1%) compared to papain and alcalase makes it a good candidate in the processing of oil industry byproducts. The mutagenesis of H(429), H(433), and E(453) in the deduced zinc-binding motif confirmed rNpI as a gluzincin. All of these results show the great potential of rNpI to be used in the protein hydrolysis industry.

Enzymatic characterization of a serralysin-like metalloprotease from the entomopathogen bacterium, Xenorhabdus

We investigated the enzymatic properties of a serralysin-type metalloenzyme, provisionally named as protease B, which is secreted by Xenorhabdus bacterium, and probably is the ortholog of PrA peptidase of Photorhabdus bacterium. Testing the activity on twenty-two oligopeptide substrates we found that protease B requires at least three amino acids N-terminal to the scissile bond for detectable hydrolysis. On such substrate protease B was clearly specific for positively charged residues (Arg and Lys) at the P1 substrate position and was rather permissive in the others. Interestingly however, it preferred Ser at P1 in the oligopeptide substrate which contained amino acids also C-terminal to the scissile bond, and was cleaved with the highest k(cat)/K(M) value. The pH profile of activity, similarly to other serralysins, has a wide peak with high values between pH 6.5 and 8.0. The activity was slightly increased by Cu(2+) and Co(2+) ions, it was not sensitive for serine protease inhibitors, but it was inhibited by 1,10-phenanthroline, features shared by many Zn-metalloproteases. At the same time, EDTA inhibited the activity only partially even either after long incubation or in excess amount, and Zn(2+) was inhibitory (both are unusual among serralysins). The 1,10-phenanthroline inhibited activity could be restored with the addition of Mn(2+), Cu(2+) and Co(2+) up to 90-200% of its original value, while Zn(2+) was inefficient. We propose that both the Zn inhibition of protease B activity and its resistance to EDTA inhibition might be caused by an Asp in position 191 where most of the serralysins contain Asn.

Addition of zinc methacrylate in dental polymers: MMP-2 inhibition and ultimate tensile strength evaluation

This study evaluated the effect of zinc methacrylate (ZM) on the inhibition of matrix metalloproteinase 2 (MMP-2) and the ultimate tensile strength (UTS) of an experimental polymer. Enzymes secreted from mouse gingival tissues were analyzed by gelatin zymography in buffers containing 5 mM CaCl(2) (Tris-CaCl(2)) in 50 mM Tris-HCl buffer with various concentrations of ZM (0.5, 1, 2, 4, 8, and 16 mM). The matrix metalloproteinases present in the conditioned media were characterized by immunoprecipitation. The polymer UTS evaluation was performed in eight groups with various concentrations of ZM (0, 0.5, 1, 2.5, 5, 10, 20, and 30 wt.%), in a mechanical testing machine. MMP-2 (62 kDa) was detected in the zymographic assays and inhibited by ZM in all tested concentrations. UTS data were submitted to one-way ANOVA and Tukey's test (α = 0.05), and no significant differences were observed among groups, except in the polymer containing 30% ZM, presenting a significantly lower value when compared with the control group (p < 0.05). The results suggest that ZM inhibits MMP-2 expression in all concentrations tested, while small concentrations did not affect the ultimate tensile strength of the polymer. Zinc methacrylate is a metalloproteinase inhibitor that can be copolymerized with other methacrylate monomers. Yet, the addition of ZM did not affect the resin bond strength. Thus, in vivo tests should be performed to evaluate the performance of this material.

Bifunctional role of the Treponema pallidum extracellular matrix binding adhesin Tp0751

Treponema pallidum, the causative agent of syphilis, is a highly invasive pathogenic spirochete capable of attaching to host cells, invading the tissue barrier, and undergoing rapid widespread dissemination via the circulatory system. The T. pallidum adhesin Tp0751 was previously shown to bind laminin, the most abundant component of the basement membrane, suggesting a role for this adhesin in host tissue colonization and bacterial dissemination. We hypothesized that similar to that of other invasive pathogens, the interaction of T. pallidum with host coagulation proteins, such as fibrinogen, may also be crucial for dissemination via the circulatory system. To test this prediction, we used enzyme-linked immunosorbent assay (ELISA) methodology to demonstrate specific binding of soluble recombinant Tp0751 to human fibrinogen. Click-chemistry-based palmitoylation profiling of heterologously expressed Tp0751 confirmed the presence of a lipid attachment site within this adhesin. Analysis of the Tp0751 primary sequence revealed the presence of a C-terminal putative HEXXH metalloprotease motif, and in vitro degradation assays confirmed that recombinant Tp0751 purified from both insect and Escherichia coli expression systems degrades human fibrinogen and laminin. The proteolytic activity of Tp0751 was abolished by the presence of the metalloprotease inhibitor 1,10-phenanthroline. Further, inductively coupled plasma-mass spectrometry showed that Tp0751 binds zinc and calcium. Collectively, these results indicate that Tp0751 is a zinc-dependent, membrane-associated protease that exhibits metalloprotease-like characteristics. However, site-directed mutagenesis of the HEXXH motif to HQXXH did not abolish the proteolytic activity of Tp0751, indicating that further mutagenesis studies are required to elucidate the critical active site residues associated with this protein. This study represents the first published description of a T. pallidum protease capable of degrading host components and thus provides novel insight into the mechanism of T. pallidum dissemination.

Zinc reduces collagen degradation in demineralized human dentin explants

OBJECTIVES

Dentin matrix metalloproteinases are implicated in the pathogenesis of caries and contribute to collagen degradation in resin-dentin interfaces. The objective was to determine if collagen degradation may be modulated by an excess of zinc or zinc chelators.

METHODS

Mineralized and phosphoric acid demineralized human dentin specimens were tested. Chlorhexidine digluconate, doxycycline or ZnCl₂ were added to the media. In half of the groups, active exogenous metalloproteinase-2 was incorporated into the solution. C-terminal telopeptide determinations (radioimmunoassay) were performed after 24 h, 1 and 3 weeks.

RESULTS

Collagen degradation was prominent in demineralized dentin. Doxycycline fully blocked dentin proteolysis. Chlorhexidine digluconate reduced the degradation at the 24-h period. Zinc in excess strongly inhibits hydrolysis of collagen and its effect was maintained for 3 weeks.

CONCLUSIONS

Zinc in excess reduces MMP-mediated collagen degradation. The hypothesis that binding of zinc to collagen results in protection of sensitive cleavage sites of metalloproteinases requires further validation.

Review of matrix metalloproteinases' effect on the hybrid dentin bond layer stability and chlorhexidine clinical use to prevent bond failure

This review describes the relationship between dentin collagen hybrid bond layer degradation and the Matrix Metalloproteinases (MMPs) after their release by acid etch and rinse adhesives and self etching bonding adhesives that can reduce the bond stability over time. MMP-2, MMP-8 and MMP-9 are indicated as the active proteases that breakdown the collagen fibrils in the hybrid bond layer. Phosphoric acid in the acid etch and rinse bonding process and acid primers in the self etch process are implicated in the release of these proteases and their activation by several non-collagen proteins also released from dentin by the etching. MMPs are released in saliva by salivary glands, by cells in the gingival crevices to crevicular fluid and by pulpal odontoblasts cells to the dentinal fluids. These sources may affect the hybrid layer also. Evidence of the bond strength deterioration over time and the ability of Chlorhexidine to prevent bond deterioration by inhibiting MMP action are discussed. Dentin Bonding procedure utilizing Chlorhexidine for different application times and concentrations are being developed. The application of 2% Chlorhexidine to the phosphoric acid etch surface after rinsing off the acid is the only procedure that has been clinically tested for a longer period of time and shown to prevent bond strength degradation so far. The adoption of this procedure is recommended as means of improving bond stability at this time.

Mechanistic insight into the inhibition of matrix metalloproteinases by platinum substrates

Platinum compounds are among the most used DNA-damaging anticancer drugs, however they can also be tailored to target biological substrates different from DNA, for instance enzymes involved in cancer progression. We recently reported that some platinum complexes with three labile ligands inhibit matrix metalloproteinase activity in a selective way. We have now extended the investigation to a series of platinum complexes having three chlorido or one chlorido and a dimethylmalonato leaving ligands. All compounds are strong inhibitors of MMP-3 by a noncompetitive mechanism, while platinum drugs in clinical use are not. Structural investigations reveal that the platinum substrate only loses two labile ligands, which are replaced by an imidazole nitrogen of His224 and a hydroxyl group, while it retains one chlorido ligand. A chlorido and a hydroxyl group are also present in the zinc complex inhibitor of carboxypeptidase A, whose active site has strong analogies with that of MMP-3.

Vibrio zinc-metalloprotease causes photoinactivation of coral endosymbionts and coral tissue lesions

BACKGROUND

Coral diseases are emerging as a serious threat to coral reefs worldwide. Of nine coral infectious diseases, whose pathogens have been characterized, six are caused by agents from the family Vibrionacae, raising questions as to their origin and role in coral disease aetiology.

METHODOLOGY/PRINCIPAL FINDINGS

Here we report on a Vibrio zinc-metalloprotease causing rapid photoinactivation of susceptible Symbiodinium endosymbionts followed by lesions in coral tissue. Symbiodinium photosystem II inactivation was diagnosed by an imaging pulse amplitude modulation fluorometer in two bioassays, performed by exposing Symbiodinium cells and coral juveniles to non-inhibited and EDTA-inhibited supernatants derived from coral white syndrome pathogens.

CONCLUSION/SIGNIFICANCE

These findings demonstrate a common virulence factor from four phylogenetically related coral pathogens, suggesting that zinc-metalloproteases may play an important role in Vibrio pathogenicity in scleractinian corals.

Ni(II), Cu(II), and Zn(II) diethyldithiocarbamate complexes show various activities against the proteasome in breast cancer cells

A series of three complexes with diethyldithiocarbamate ligand and three different metals (Ni, Cu, Zn) was prepared, confirmed by X-ray crystallography, and tested in human breast cancer MDA-MB-231 cells. Zinc and copper complexes, but not nickel complex, were found to be more active against cellular 26S proteasome than against purified 20S proteasome core particle. One of the possible explanations is inhibition of JAMM domain in the 19S proteasome lid.

Purification and characterization of fibrinolytic metalloprotease from Perenniporia fraxinea mycelia

In this study we purified and characterized a fibrinolytic protease from the mycelia of Perenniporia fraxinea. The apparent molecular mass of the purified enzyme was estimated to be 42kDa by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE), fibrin zymography and size exclusion using fast protein liquid chromatography (FPLC). The first 20 amino acid residues of the N-terminal sequence were ASYRVLPITKELLPPEFFVA, which shows a high degree of similarity with a fungalysin metallopeptidase from Coprinopsis cinerea. The optimal reaction pH value and temperature were pH 6.0 and 35-40 degrees C, respectively. Results for the fibrinolysis pattern showed that the protease rapidly hydrolyzed the fibrin alpha-chain followed by the beta-chain. The gamma-gamma chains were also hydrolyzed, but more slowly. The purified protease effectively hydrolyzed fibrinogen, preferentially digesting the Aalpha-chains of fibrinogen, followed by Bbeta- and gamma-chains. We found that protease activity was inhibited by Cu(2+), Fe(3+), and Zn(2+), but enhanced by the additions of Mn(2+), Mg(2+) and Ca(2+) metal ions. Furthermore, the protease activity was inhibited by EDTA, and it was found to exhibit a higher specificity for the chromogenic substrate S-2586 for chymotrypsin, indicating that the enzyme is a chymotrypsin-like metalloprotease. The mycelia of P. fraxinea may thus represent a source of new therapeutic agents to treat thrombosis.

Zinc proteomics and the annotation of the human zinc proteome

Sequence databases can be searched for homologies of zinc coordination motifs with characteristic ligand signatures. Ensuing predictions that 3-10 % of the human genes encodes zinc proteins are most remarkable. But they seem conservative when considering that database mining cannot discover new signatures or coordination environments that employ nonsequential binding of ligands and sulfur-ligand bridges. Predictions also fall short for zinc/protein interactions at protein interfaces and for inhibitory zinc sites. Zinc ions transiently target proteins that are not known to be zinc proteins, adding a hitherto unrecognized dimension to the human zinc proteome. Predicted zinc sites need to be verified experimentally. The metal can be absent or sites may bind metal ions other than zinc because protein coordination environments do not have absolute specificity for zinc. The metaphor of the "galvanization of biology" continues to gain prominence in terms of the sheer number of approximately 3000 human zinc proteins and their annotation with new functions. Clearly, description of zinc proteomes cannot be pursued solely in silico and requires zinc proteomics, an integrated scientific approach. Progress hinges on a combination of bioinformatics, biology, and significantly, analytical and structural chemistry.

Purification and properties of a keratinolytic metalloprotease from Microbacterium sp

AIMS

This study was developed to purify and to characterize a keratinolytic protease from the bacterium Microbacterium sp. strain kr10.

METHODS AND RESULTS

Enzyme purification was carried out by sequential liquid chromatography on Sephadex G-100 and Q-Sepharose columns. The purification was about 255-fold, with a yield of 34%, as determined with azocasein as substrate. The molecular weight of the enzyme was estimated as 42,000 Da by SDS-PAGE. The enzyme had pH and temperature optima of 7.5 and 50 degrees C respectively. This keratinase was inhibited by EDTA and 1,10-phenanthroline, and analysis of metal content indicates that Zn(2+) and Mg(2+) are present. A 2(2) factorial design was developed to investigate the effect of keratinase and mercaptoacetate concentration on feather keratinolysis. Statistical analysis showed that both variables have a significant effect on hydrolysis of keratin.

CONCLUSIONS

A new keratinase produced by Microbacterium sp. was purified and characterized.

SIGNIFICANCE AND IMPACT OF THE STUDY

This keratinolytic enzyme offers an interesting potential for the hydrolysis of keratin wastes to be used as feed supplement or bioconversion to added-value products.

Screening and characterization of a novel fibrinolytic metalloprotease from a metagenomic library

A metagenomic library was constructed using total genomic DNA extracted from the mud in the west coast of Korea and was used together with a fosmid vector, pCC1FOS in order to uncover novel gene sources. One clone from approximately 30,000 recombinant Escherichia coli clones was identified that showed proteolytic activity. The gene for the proteolytic enzyme was subcloned into pUC19 and sequenced, and a database search for homologies revealed it to be a zinc-dependent metalloprotease. The cloned gene included the intact coding gene for a novel metalloproteinase and its own promoter. It comprised an open reading frame of 1,080 base pairs, which encodes a protein of 39,490 Da consisting of 359 amino acid residues. A His-Glu-X-X-His sequence, which is a conserved sequence in the active site of zinc-dependent metalloproteases, was found in the deduced amino acid sequence of the gene, suggesting that the enzyme is a zinc-dependent metalloprotease. The purified enzyme showed optimal activity at 50 degrees C for 1 h and pH 7.0. The enzyme activity was inhibited by metal-chelating reagents, such as EDTA, EGTA and 1,10-phenanthroline. The enzyme hydrolyzed azocasein as well as fibrin. Thus, the enzyme could be useful as a therapeutic agent to treat thrombosis.

Pneumococcal phosphorylcholine esterase, Pce, contains a metal binuclear center that is essential for substrate binding and catalysis

The phosphorylcholine esterase from Streptococcus pneumoniae, Pce, catalyzes the hydrolysis of phosphorylcholine residues from teichoic and lipoteichoic acids attached to the bacterial envelope and comprises a globular N-terminal catalytic module containing a zinc binuclear center and an elongated C-terminal choline-binding module. The dependence of Pce activity on the metal/enzyme stoichiometry shows that the two equivalents of zinc are essential for the catalysis, and stabilize the catalytic module through a complex metal-ligand coordination network. The pH dependence of Pce activity toward the alternative substrate p-nitrophenylphosphorylcholine (NPPC) shows that k(cat) and k(cat)/K(m) depend on the protonation state of two protein residues that can be tentatively assigned to the ionization of the metal-bound water (hydrogen bonded to D89) and to H228. Maximum activity requires deprotonation of both groups, although the catalytic efficiency is optimum for the single deprotonated form. The drastic reduction of activity in the H90A mutant, which still binds two Zn2+ ions at neutral pH, indicates that Pce activity also depends on the geometry of the metallic cluster. The denaturation heat capacity profile of Pce exhibits two peaks with T(m) values of 39.6 degrees C (choline-binding module) and 60.8 degrees C (catalytic module). The H90A mutation reduces the high-temperature peak by about 10 degrees C. Pce is inhibited in the presence of 1 mM zinc, but this inhibition depends on pH, buffer, and substrate species. A reaction mechanism is proposed on the basis of kinetic data, the structural model of the Pce:NPPC complex, and the currently accepted mechanism for other Zn-metallophosphoesterases.

Active site of Zn(2+)-dependent sn-glycerol-1-phosphate dehydrogenase from Aeropyrum pernix K1

The enzyme sn-glycerol-1-phosphate dehydrogenase (Gro1PDH, EC 1.1.1.261) is key to the formation of the enantiomeric configuration of the glycerophosphate backbone (sn-glycerol-1-phosphate) of archaeal ether lipids. This enzyme catalyzes the reversible conversion between dihydroxyacetone phosphate and glycerol-1-phosphate. To date, no information about the active site and catalytic mechanism of this enzyme has been reported. Using the sequence and structural information for glycerol dehydrogenase, we constructed six mutants (D144N, D144A, D191N, H271A, H287A and D191N/H271A) of Gro1PDH from Aeropyrum pernix K1 and examined their characteristics to clarify the active site of this enzyme. The enzyme was found to be a zinc-dependent metalloenzyme, containing one zinc ion for every monomer protein that was essential for activity. Site-directed mutagenesis of D144 increased the activity of the enzyme. Mutants D144N and D144A exhibited low affinity for the substrates and higher activity than the wild type, but their affinity for the zinc ion was the same as that of the wild type. Mutants D191N, H271A and H287A had a low affinity for the zinc ion and a low activity compared with the wild type. The double mutation, D191N/H271A, had no enzyme activity and bound no zinc. From these results, it was clarified that residues D191, H271 and H287 participate in the catalytic activity of the enzyme by binding the zinc ion, and that D144 has an effect on substrate binding. The structure of the active site of Gro1PDH from A. pernix K1 seems to be similar to that of glycerol dehydrogenase, despite the differences in substrate specificity and biological role.

Zinc hydrolases: the mechanisms of zinc-dependent deacetylases

A class of metalloenzymes, known as zinc hydrolases, catalyze a variety of hydrolytic reactions on many different substrates in important metabolic pathways. Deacetylation is an example of one of the types of reactions catalyzed by zinc hydrolases. The biological importance of the reactions catalyzed by many zinc hydrolases, including zinc-dependent deacetylases, has made these enzymes pharmaceutical targets for the development of inhibitors and, therefore, a clear understanding of the mechanisms of these enzymes is warranted. This review focuses on the current understanding of the mechanisms catalyzed by various zinc-dependent deacetylases and, in particular, the reaction mechanism catalyzed by the enzyme UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase, also known as LpxC. In general, the zinc-water functions as the nucleophile with zinc stabilization of the tetrahedral intermediate and general-acid-base catalysis (GABC) provided by enzyme residue(s). Two types of GABC mechanisms have been identified, one that uses a single bifunctional GABC and another that uses a GABC pair.

Disassembly and degradation of photosystem I in an in vitro system are multievent, metal-dependent processes

An in vitro system was created to study the process of membrane protein degradation by using photosystem I (PS1) as a model membrane protein. Purified chloroplast membranes were incubated at 30 degrees C in a defined buffer along with various extracts or reagents to reconstitute the disassembly and degradation of PS1, which was monitored by a variety of techniques that probe the integrity of the PS1 complex: photo-biochemical assays, semi-native gel electrophoresis, low temperature fluorescence spectroscopy, and immunoblots using antibodies against different PS1 subunits. During a typical time course, degradation of PS1 appeared to be a multievent process, with disassembly of the complex preceding proteolysis of the subunits. The first change seen was a rapid (<5 min) decrease in PS1 photochemical activity. This was followed by a diminution of far-red fluorescence emission from the core antenna of PS1 and a slower disassembly of the PS1 chlorophyll-protein core complex, as visualized by semi-native gel electrophoresis. Surprisingly, the latter was not accompanied by a similar rate of proteolysis of the PsaA core subunit. In contrast, addition of soluble proteases caused rapid loss of immuno-detectable PS1 polypeptides and cleavage of the major PS1 polypeptides in interhelical loops. The in vitro degradation process was time- and temperature-dependent but did not require ATP, GTP, or soluble chloroplast proteins. Chelation of divalent cations by EDTA inhibited the later steps of disassembly and proteolysis, and this effect could be reversed by addition of micromolar Zn2+, with Co2+ and Ca2+ providing somewhat lower activity.

Metal and redox modulation of cysteine protein function

In biological systems, the amino acid cysteine combines catalytic activity with an extensive redox chemistry and unique metal binding properties. The interdependency of these three aspects of the thiol group permits the redox regulation of proteins and metal binding, metal control of redox activity, and ligand control of metal-based enzyme catalysis. Cysteine proteins are therefore able to act as "redox switches," to sense concentrations of oxidative stressors and unbound zinc ions in the cytosol, to provide a "storage facility" for excess metal ions, to control the activity of metalloproteins, and to take part in important regulatory and signaling pathways. The diversity of cysteine's multiple roles in vivo is equally as fascinating as it is promising for future biochemical and pharmacological research.

Structure of the LpxC deacetylase with a bound substrate-analog inhibitor

The zinc-dependent UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) catalyzes the first committed step in the biosynthesis of lipid A, the hydrophobic anchor of lipopolysaccharide (LPS) that constitutes the outermost monolayer of Gram-negative bacteria. As LpxC is crucial for the survival of Gram-negative organisms and has no sequence homology to known mammalian deacetylases or amidases, it is an excellent target for the design of new antibiotics. The solution structure of LpxC from Aquifex aeolicus in complex with a substrate-analog inhibitor, TU-514, reveals a novel alpha/beta fold, a unique zinc-binding motif and a hydrophobic passage that captures the acyl chain of the inhibitor. On the basis of biochemical and structural studies, we propose a catalytic mechanism for LpxC, suggest a model for substrate binding and provide evidence that mobility and dynamics in structural motifs close to the active site have key roles in the capture of the substrate.

Cloning and characterization of a metalloprotease from Vibrio harveyi strain AP6

A metalloprotease gene pap6 was cloned from Vibrio harveyi strain AP6. Sequence analysis showed that pap6 was 2034 bp in length and predicted to encode a peptide of 677 amino acids with a molecular mass of 75 kDa. SDS-PAGE analysis of the purified Pap6 revealed that it was 35 kDa in size. N-terminal amino acid sequencing established that the mature protein began at Leu-191, suggesting that the preprotein of Pap6 was processed to generate a mature protease. Purified Pap6 was characterized as a zinc metalloprotease as it was inhibited by zinc- and metal-specific inhibitors such as 1, 10-phenanthroline, EGTA and EDTA. The deduced amino acid sequence revealed the presence of a zinc-binding motif HEXXH approximately 19aa approximately E. Substitution of these active site residues by site-directed mutagenesis caused significant losses in enzyme activity, thus demonstrating their involvement in catalysis. Pap6 was shown to digest a range of host proteins, including gelatin, fibronectin, and type IV collagen, indicating a potential role in pathogenesis.

Zinc-mediated thermal stabilization of carboxypeptidase A

In this study we investigated the contribution of Zn ions to the catalytic and structural thermostability of carboxypeptidase A (CPA). Structural studies on CPA molecule, performed in the presence of a number of ligands, demonstrated the multiple binding models around Zn ions which may affect the enzyme functions. Zinc was reported to bind at various sites in the CPA molecule at room temperature leading to inhibition of its enzymic activity. In this study we found that binding of Zn to CPA molecule followed by exposure to 50 degrees C did not inhibit the enzymic activity but activates and protects it against heat denaturation. The stabilization effect was found to be dependent on the increasing Zn/CPA ratios. The moderate changes of CPA activity as well as the UV and fluorescence spectra analyses indicate that the main function of the newly introduced zinc atoms is structural rather than catalytical.

Effect of zinc ion on the inhibition of carboxypeptidase A by imidazole-bearing substrate analogues

Competitive inhibitors of carboxypeptidase A, 2-(4-imidazoyl)hydrocinnamic acid (1) and its congeners (2-4) that bear an imidazole ring as the zinc-ligating functionality have been evaluated for their CPA inhibitory activity in the presence of zinc ion to find that the zinc ion augments the inhibitory potency by up to 212-fold.

Inhibition of human gelatinases by metals released from dental amalgam

The interaction between metal ions and the oral environment is a major subject matter in dental research. Matrix metalloproteinases (MMPs) have been implicated in pathologic oral processes such as periodontal tissue destruction, root caries, tumor invasion and temporomandibular joint disorders. The aim of this study was to test the effect of metal ions released from dental amalgam on the major gingival gelatinolytic MMPs. Gingival human explants were cultured overnight in DMEM and the activity of secreted enzymes was analyzed by gelatin zymography in buffers conditioned with dispersed phase or concentional phase dental amalgams. The major enzymes present in conditioned media were characterized as MMP-2 and MMP-9 by immunoprecipitation. The proteolytic activities of MMP-2 and MMP-9 were strongly inhibited by dispersed phase amalgams conditioned buffers. Inhibition of MMP-2 and MMP-9 activities was partly prevented by the addition of 1,10 phenanthroline, a divalent metal chelator, to the amalgam conditioned buffers. Dental amalgam conditioned buffer also inhibited the degradation of denatured type I collagen by purified MMP-2 on liquid phase assays. These findings suggest that the activity of oral tissue MMPs may be modulated by metal ions released from dental amalgam.

Novel bifunctional hyperthermostable carboxypeptidase/aminoacylase from Pyrococcus horikoshii OT3

Genome sequencing of the thermophilic archaeon Pyrococcus horikoshii OT3 revealed a gene which had high sequence similarity to the gene encoding the carboxypeptidase of Sulfolobus solfataricus and also to that encoding the aminoacylase from Bacillus stearothermophilus. The gene from P. horikoshii comprises an open reading frame of 1,164 bp with an ATG initiation codon and a TGA termination codon, encoding a 43,058-Da protein of 387 amino acid residues. However, some of the proposed active-site residues for carboxypeptidase were not found in this gene. The gene was overexpressed in Escherichia coli with the pET vector system, and the expressed enzyme had high hydrolytic activity for both carboxypeptidase and aminoacylase at high temperatures. The enzyme was stable at 90 degrees C, with the highest activity above 95 degrees C. The enzyme contained one bound zinc ion per one molecule that was essential for the activity. The results of site-directed mutagenesis of Glu367, which corresponds to the essential Glu270 in bovine carboxypeptidase A and the essential Glu in other known carboxypeptidases, revealed that Glu367 was not essential for this enzyme. The results of chemical modification of the SH group and site-directed mutagenesis of Cys102 indicated that Cys102 was located at the active site and was related to the activity. From these findings, it was proven that this enzyme is a hyperthermostable, bifunctional, new zinc-dependent metalloenzyme which is structurally similar to carboxypeptidase but whose hydrolytic mechanism is similar to that of aminoacylase. Some characteristics of this enzyme suggested that carboxypeptidase and aminoacylase might have evolved from a common origin.

The effect of lead on the eruption rates of incisor teeth in rats

The effects of lead on the continuously erupting rat incisors under normo-, hyper- and hypofunctional conditions were investigated. Left lower incisors of 20 rats were rendered unimpeded (hypofunctional) by cutting them out of occlusion every 2 days; the right lower incisors of these rats were considered hyperfunctional. Measurements on normally growing teeth (normofunctional) were carried out in a group of ten rats whose teeth were not cut but only marked every 2 days. On day 7 of the experiment, half of the rats from these two groups were given a single intraperitoneal injection of lead acetate (40 mg/kg), and the other half received sodium acetate (22 mg/kg). Another group of 15 rats was used to obtain blood samples for lead determination 1 h, and 10, 20, and 30 days after lead administration. Animals were killed on day 32. Hypofunctional incisors from lead-treated rats erupted more slowly than control ones (P<0.05). These results show a previously unreported toxic effect of heavy metals.