131,858 research outputs found
Catalytic mechanism of a C-C hydrolase enzyme: Evidence for a gem-diol intermediate, not an acyl enzyme
No full text2-Hydroxy-6-keto-nona-2,4-diene 1,9-dioic acid 5,6-hydrolase (MhpC) from Escherichia coli catalyses the hydrolytic cleavage of the extradiol ring fission product on the phenylpropionate catabolic pathway and is a member of the alpha/beta hydrolase family. The catalytic mechanism of this enzyme has previously been shown to proceed via initial ketonization of the dienol substrate (Henderson, I. M. J., and Bugg,T. D. H. (1997) Biochemistry 36, 12252-12258), followed by stereospecific fragmentation. Despite the implication of an active site serine residue in the alpha/beta hydrolase family, attempts to verify a putative acyl enzyme intermediate by radiochemical trapping methods using a C-14-labeled substrate yielded a stoichiometry of <1% covalent intermediate, which could be accounted for by nonenzymatic processes. In contrast, incorporation of 5-6% of two atoms of O-18 from (H2O)-O-18 into succinic acid was observed using the natural substrate, consistent with the reversible formation of a gem-diol intermediate. Furthermore, time-dependent incorporation of O-18 from (H2O)-O-18 into the carbonyl group of a nonhydrolysable analogue 4-keto-nona-1,9-dioic acid was observed in the presence of MhpC, consistent with enzyme-catalyzed attack of water at the ketone carbonyl. These results favor a catalytic mechanism involving base-catalyzed attack of water, rather than nucleophilic attack of an active site serine. The implication of this work is that the putative active site serine in this enzyme may have an alternative function, for example, as a base
Extradiol oxidative cleavage of catechols by ferrous and ferric complexes of 1,4,7-triazacyclononane: Insight into the mechanism of the extradiol catechol dioxygenases
No full textThe major oxygenation product of catechol by dioxygen in the presence of FeCl2 or FeCl3, 1,4,7-triazacyclononane (TACN), and pyridine in methanol is the extradiol cleavage product 2-hydroxymuconic semi-aldehyde methyl ester (Lin, G.; Reid, G.; Bugg, T. D. I-I. J. Chem. Sec. Chem. Commun. 2000, 1119-1120). Under these conditions, extradiol cleavage of a range of 3- and 4-substituted catechols with electron-donating substituents is observed. The reaction shows a preference in selectivity and rate for iron(II) rather than iron(III) for the extradiol cleavage, which parallels the selectivity of the extradiol dioxygenase family. The reaction also shows a high selectivity for the macrocyclic ligand, TACN, over a range of other nitrogen-and oxygen-containing macrocycles. Reaction of anaerobically prepared iron-TACN complexes with dioxygen gave the same product as monitored by UV/vis spectroscopy. KO2 is able to oxidize catechols with both electron-donating and electron-withdrawing substituents, implying a different mechanism for extradiol. cleavage. Saturation kinetics were observed for catechols, which fit the Michaelis-Menten equation to give k(cat)(app) = 4.8 x 10(-3) s(-1) for 3-(2' ,3'-dihydroxyphenyl)propionic acid. The reaction was also found to proceed using monosodium catecholate in the absence of pyridine, but with different product ratios, giving insight into the acid/base chemistry of extradiol cleavage. In particular, extradiol cleavage in the presence of iron(II) shows a requirement for a proton donor, implying a role for an acidic group in the extradiol dioxygenase active site
Thioester analogues of peptidoglycan fragment MurNAc-L-Ala-gamma-D-Glu as substrates for peptidoglycan hydrolase MurNAc-L-Ala amidase
No full textMurNAc-L-amidase is one of a family of peptidoglycan hydrolases which catalyses the breakdown of bacterial peptidoglycan. Analogues of the peptidoglycan fragment MurNAc-L-Ala-gamma-D-Glu containing S-thiolactic acid in place of L-alanine were synthesised as thioester substrates for this enzyme. Triphenylmethanethiol was used to develop a stereoselective synthesis of S-thiolactic acid, which was elaborated synthetically into MurNAc-dipeptide analogues. MurNAc-S-thioacetyl-N-propylamide 13 and MurNAc-S-thiolactyl-2R-alaninamide 16 were found not to be substrates for recombinant MurNAc-L-Ala amidases CwlA from Bacillus subtilis and Ply21 from bacteriophage TP21, however, turnover of tripeptide thioester S-propionylthiolactyl-gamma-D-Glu-L-Lys-OMe 21 was observed using amidase Ply21. Therefore, recognition of the amino acid at position 3 of the pentapeptide sidechain appears to be important for enzymatic turnover
Enzymatic breakdown of poly-?-D-glutamic acid in Bacillus licheniformis: Identification of a polyglutamyl ?-hydrolase enzyme
No full textA polyglutamyl gamma -hydrolase enzyme has been identified which catalyses the hydrolytic breakdown of poly-gamma -D-glutamic acid (PGA) from Bacillus licheniformis 9945a. The enzyme was found to be physically associated with the polymer and was activated by Zn2+ or Ca2+ salts. The enzyme can be solubilized from the polymer by treatment with 0.5% SDS and 1 mM ZnCl2 and can then be renatured onto exogenous PGA upon dilution below the detergent critical micellar concentration. The enzyme was partially purified by affinity chromatography, using immobilized PGA. Peptide thioesters containing one and two gamma -glutamyl units were synthesized as potential chromogenic substrates but showed no activity with the solubilized enzyme. Examination of C-14-labeled reaction products indicated that the enzyme is an endo-type hydrolase
A biomimetic model reaction for the extradiol catechol dioxygenases
No full textA model reaction is described for extradiol catechol cleavage involving FeCl2 or FeCl3, 1,4,9-triazacyclononane (TACN), pyridine and dioxygen which shows similar cofactor and regio-selectivity to the extradiol catechol dioxygenases
MeSH term explosion and author rank improve expert recommendations
No full textInformation overload is an often-cited phenomenon that reduces the productivity, efficiency and efficacy of scientists. One challenge for scientists is to find appropriate collaborators in their research. The literature describes various solutions to the problem of expertise location, but most current approaches do not appear to be very suitable for expert recommendations in biomedical research. In this study, we present the development and initial evaluation of a vector space model-based algorithm to calculate researcher similarity using four inputs: 1) MeSH terms of publications; 2) MeSH terms and author rank; 3) exploded MeSH terms; and 4) exploded MeSH terms and author rank. We developed and evaluated the algorithm using a data set of 17,525 authors and their 22,542 papers. On average, our algorithms correctly predicted 2.5 of the top 5/10 coauthors of individual scientists. Exploded MeSH and author rank outperformed all other algorithms in accuracy, followed closely by MeSH and author rank. Our results show that the accuracy of MeSH term-based matching can be enhanced with other metadata such as author rank
Phage display-derived inhibitor of the essential cell wall biosynthesis enzyme MurF
No full textBackground
To develop antibacterial agents having novel modes of action against bacterial cell wall biosynthesis, we targeted the essential MurF enzyme of the antibiotic resistant pathogen Pseudomonas aeruginosa. MurF catalyzes the formation of a peptide bond between D-Alanyl-D-Alanine (D-Ala-D-Ala) and the cell wall precursor uridine 5'-diphosphoryl N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-diaminopimelic acid (UDP-MurNAc-Ala-Glu-meso-A2pm) with the concomitant hydrolysis of ATP to ADP and inorganic phosphate, yielding UDP-N-acetylmuramyl-pentapeptide. As MurF acts on a dipeptide, we exploited a phage display approach to identify peptide ligands having high binding affinities for the enzyme.
Results
Screening of a phage display 12-mer library using purified P. aeruginosa MurF yielded to the identification of the MurFp1 peptide. The MurF substrate UDP-MurNAc-Ala-Glumeso-A2pm was synthesized and used to develop a sensitive spectrophotometric assay to quantify MurF kinetics and inhibition. MurFp1 acted as a weak, time-dependent inhibitor of MurF activity but was a potent inhibitor when MurF was pre-incubated with UDP-MurNAc-Ala-Glu-meso-A2pm or ATP. In contrast, adding the substrate D-Ala-D-Ala during the pre-incubation nullified the inhibition. The IC50 value of MurFp1 was evaluated at 250 μM, and the Ki was established at 420 μM with respect to the mixed type of inhibition against D-Ala-D-Ala.
Conclusion
MurFp1 exerts its inhibitory action by interfering with the utilization of D-Ala-D-Ala by the MurF amide ligase enzyme. We propose that MurFp1 exploits UDP-MurNAc-Ala-Glu-meso-A2pm-induced structural changes for better interaction with the enzyme. We present the first peptide inhibitor of MurF, an enzyme that should be exploited as a target for antimicrobial drug development
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
"Closing the R&D Gap, Evaluating the Sources of R&D Spending"
No full textBoth spending and tax policies have been implemented in the United States with the goal of stimulating private sector research and development (R&D). Karier questions whether current R&D policy, especially the research and experimentation tax credit, can contribute to closing the gap between nondefense expenditures on R&D in the United States and such expenditures in other countries, such as Japan and Germany. He also explores possible changes to our current R&D policy to make it more effective.
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