Spectrophotometric determination of carboxlic acids by the formation of hydroxamic acids with dicyclohexylcarbodiimide

Enlightening the Path to Protein Engineering: Chemoselective Turn-On Probes for High-Throughput Screening of Enzymatic Activity

Many successful stories in enzyme engineering are based on the creation of randomized diversity in large mutant libraries, containing millions to billions of enzyme variants. Methods that enabled their evaluation with high throughput are dominated by spectroscopic techniques due to their high speed and sensitivity. A large proportion of studies relies on fluorogenic substrates that mimic the chemical properties of the target or coupled enzymatic assays with an optical read-out that assesses the desired catalytic efficiency indirectly. The most reliable hits, however, are achieved by screening for conversions of the starting material to the desired product. For this purpose, functional group assays offer a general approach to achieve a fast, optical read-out. They use the chemoselectivity, differences in electronic and steric properties of various functional groups, to reduce the number of false-positive results and the analytical noise stemming from enzymatic background activities. This review summarizes the developments and use of functional group probes for chemoselective derivatizations, with a clear focus on screening for enzymatic activity in protein engineering.

A high-throughput screening strategy for nitrile-hydrolyzing enzymes based on ferric hydroxamate spectrophotometry

Nitrile-hydrolyzing enzymes (nitrilase or nitrile hydratase/amidase) have been widely used in the pharmaceutical industry for the production of carboxylic acids and their derivatives, and it is important to build a method for screening for nitrile-hydrolyzing enzymes. In this paper, a simple, rapid, and high-throughput screening method based on the ferric hydroxamate spectrophotometry has been proposed. To validate the accuracy of this screening strategy, the nitrilases from Rhodococcus erythropolis CGMCC 1.2362 and Alcaligenes sp. ECU0401 were used for evaluating the method. As a result, the accuracy for assaying aliphatic and aromatic carboxylic acids was as high as the HPLC-based method. Therefore, the method may be potentially used in the selection of microorganisms or engineered proteins with nitrile-hydrolyzing enzymes.

Biochemical and molecular characterization of a periplasmic hydrolase for oxidized polyvinyl alcohol from Sphingomonas sp. strain 113P3

Oxidized polyvinyl alcohol hydrolase (OPH) and polyvinyl alcohol dehydrogenase were found to be constitutively present in the periplasm of Sphingomonas sp. strain 113P3 (formerly Pseudomonas sp. 113P3). The OPH was purified to homogeneity with a yield of 40 % and a 5.9-fold increase in specific activity. The enzyme was a homodimer consisting of 35 kDa subunits. Its activity was inhibited by PMSF, Hg(2+) and Zn(2+). The enzyme hydrolysed oxidized polyvinyl alcohol (oxidized PVA) and p-nitrophenyl acetate (PNPA), but did not hydrolyse any of the mono- or diketones tested. K(m) and V(max) values for oxidized PVA and PNPA were 0.2 and 0.3 mM, and 0.1 and 3.4 micromol min(-1) mg(-1), respectively. The gene for OPH was cloned and sequenced. Sequencing analysis revealed that the open reading frame consisted of 1095 bp, corresponding to a protein of 364 amino acids residues, encoding a signal peptide and a mature protein of 34 and 330 amino acids residues, respectively. The presence of a serine-hydrolase motif (a lipase box; Gly-X-Ser-X-Gly) strongly suggested that the enzyme belongs to the serine-hydrolase family. The protein exhibited homology with OPH of the Pseudomonas sp. strain VM15C (63 % identity) and the polyhydroxybutyrate depolymerases from Mesorhizobium loti, Rhizobium sp. and Sinorhizobium meliloti (29-32 % identity). The oph gene was expressed in Escherichia coli under the control of the lac promoter. The recombinant protein had the same molecular mass and N-terminal amino acid sequence as the purified OPH from strain 113P3.

Macrostatin, a novel macromolecular inhibitor of topoisomerases produced by Streptomyces avermitilis no. C-127

A novel inhibitor of topoisomerases designated as Macrostatin has been isolated from the culture filtrate of Streptomyces avermitilis strain No. C-127 and purified by successive chromatography on Dowex, activated charcoal, gel filtration and cellulose. It is an acidic macromolecule having 45 kD molecular weight as determined by gel filtration. Macrostatin inhibited topoisomerase I and II in a noncompetitive manner with Ki = 3.7 and 1.3 nM respectively. Macrostatin differed from well-known inhibitors of topoisomerase such as camptothecin, etoposide and doxorubicin which induce topoisomerase-mediated DNA cleavage by stabilizing the cleavable complex or intercalation into DNA strands. Macrostatin had neither ability to stabilize the cleavable complex nor ability to intercalate into DNA strands. It was suggested that Macrostatin inhibits topoisomerase by a direct action on the enzyme.

Mechanized assay of serum cholinesterase by specific colorimetric detection of released acid

An automated assay method has been developed for the measurement of serum cholinesterase activity. The samples were prepared by an automated liquid handling unit and incubated for 9.7 min at 30 degrees C, followed by automatic injection into a colorimetric flow injection determination system for acetic acid liberated from acetylcholine by cholinesterase catalytic activity. The coloration reaction employed is based upon the formation of 2-nitrophenylhydrazide utilizing a water-soluble carbodiimide and has a high selectivity for carboxylic acids. The coefficients of variation of the proposed method were 2.4% for within-run analysis (n = 14) and 2.6% for between-run analysis (n = 6). Sera of 55 hospitalized patients were analyzed and the values obtained correlated well with an automated differential pH method (gamma = 0.989).

Automated precolumn fluorescence labelling by carbodiimide activation of N-acetylaspartate and N-acetylaspartylglutamate applied to an HPLC brain tissue analysis

An automated method is described to couple carboxyl-containing metabolites to the fluorophore 2-aminoanthracene in aqueous solution (containing 75% methanol) in the presence of N,N-dicyclohexylcarbodiimide. The reaction was optimized for N-acetylaspartate (N-Ac-Asp) and N-acetylaspartylglutamate (N-Ac-Asp-Glu). The reactions occurred within 5 min at room temperature in the presence of 0.5-2 mM HCl. At concentrations of electrolytes exceeding 10 mM the coupling reaction became suboptimal. Derivatization was performed in a commercial precolumn derivatization unit. Additional tubing was needed to provide the reagents prior to reversed-phase HPLC and fluorescence detection. The assay is linear over at least three orders of magnitude; as little as 1 pmol could reproducibly be assayed in 100 micrograms wet weight brain tissue extracted with a mixture of methanol and 4 mM HCl (9:1, v/v). N-Ac-Asp and N-Ac-Asp-Glu levels in several brain regions and spinal cord were similar to those so far reported. The compounds could not be detected in peripheral tissue. The advantages, prospects and limitations of the present approach over existing methods to estimate water-soluble carboxylic acids is discussed.

Stereospecific HPLC method for the quantitation of the enantiomers of MK-0571, a potent leukotriene D4 receptor antagonist, in biological specimens

A stereospecific HPLC bioanalytical method was developed for quantitation of the enantiomers of MK-0571, a leukotriene D4 receptor antagonist. The procedure involves the addition of an internal standard analog to the biological matrix followed by extraction of the free acids into ethyl acetate. The acids are subsequently reacted with the homochiral reagent, (+)-(R)-alpha-(1-naphthyl)ethylamine (NEA) to form diastereomers. Following removal of excess reagent and side products by a dilute acid wash, the NEA-MK-0571 diastereomers are separated on a phenyl urea chiral column using a mobile phase containing hexane, isopropanol, and acetonitrile and are detected with a fluorescence detector. The sensitivity of the method is such that 50 ng of each enantiomer can be quantitated. In the 0.05 to 10 micrograms range the recoveries of the enantiomers of MK-0571 from plasma were 100.4 +/- 7.9% and 100.0 +/- 7.2%. NMR and mass spectral data confirmed the structure of the derivative. The method has been utilized in drug safety evaluation studies to demonstrate enantioselectivity in disposition of the enantiomers of MK-0571 in rats and monkeys but not in mice.

Use of water-soluble 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide for the fluorescent determination of uronic acids and carboxylic acids

Reaction between glucuronic acid and 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) was monitored by the o-phthalaldehyde (OPA) method, which was developed for the fluorescent assay of compounds containing an amino group. About 1 nmol of glucuronic acid was detected by this method. This EDC-OPA method was effective in detecting not only acidic sugar but also carboxylic acid. Although the sensitivity of the EDC-OPA method was somewhat lower than that of amino acid determination by OPA, a very simple and convenient assay was attained for compounds containing a carboxyl group.

The effect of interaction between human urokinase and its competitive inhibitor, N alpha-benzoyl-L-arginine amide, on reduction of a specific SS bond related to enzymatic activity

The 55- (H-UK) and 36-kDa forms (L-UK) of human urinary urokinase lost most of esterase activity toward acetyl-glycyl-L-lysine methyl ester upon reductive cleavage of 3 SS bonds with dithiothreitol in the presence of the competitive inhibitor, N alpha-benzoyl-L-arginine amide (BAA), bound to polyacrylyl azide with C16N3-arm (PAA) at 0.3 M guanidine, a threshold point of the native state where a protein-denaturating transition began. One of the 3 SS bonds was protected from reduction, with an unaltered activity, under the similar conditions except for replacement of BAA-PAA conjugate by glycine-PAA conjugate. This "specific" SS bond was reduced and, after the other SH groups produced were blocked with iodoacetamide (IAM), selectively reoxidized, which resulted in complete reactivation. The intact B-chain isolated from H-UK was completely inactivated when its specific SS bond was reduced and selectively alkylated with IAM after the other SH groups were reversibly blocked with 5, 5'-dithiobis (2-nitrobenzoic acid), which was finally removed. The results indicate that a single specific SS bond is essential for retaining a conformation necessary to activity exhibition.

Structural studies on HCN oligomers

NMR spectral studies on the HCN oligomers suggest the presence of carboxamide and urea groupings. The release of CO2, H2O, HCN, CH3CN, HCONH2 and pyridine on pyrolysis is consistent with the presence of these groupings as well as carboxylic acid groups. No basic primary amine groupings could be detected with fluorescamine. Hydrazinolysis of the HCN oligomers releases 10% of the amino acids normally released by acid hydrolysis. The oligomers give a positive biuret test but this is not due to the presence of peptide bonds. There is no conclusive evidence for the presence of peptide bonds in the HCN oligomers. No diglycine was detected on partial hydrolysis of the HCN oligomers at pH 8.5 suggesting that HCN oligomers were not a source of prebiotic peptides.

Beta-hydroxy-alpha-ketobutyric acid in Drosophila melanogaster, with reference to biosynthesis of drosopterins

A substance designated as compound D, which reacts spontaneously with 7,8-dihydropterin to give drosopterins, is found in Drosophila melanogaster. The compound was partially purified from the extract of flies by column chromatography and identified as beta-hydroxy-alpha-ketobutyric acid by analysis of its 2,4-dinitrophenylhydrazone, mass spectrometry and reactivity with 7,8-dihydropterin. A highly significant correlation (r=0.969, p less than 0.001) was found between the amounts of the compound and drosopterins in the eye-pigment mutants of Drosophila. Changes of the compound during development of flies were also closely related to those of drosopterins. Based on these observations, a role of the compound in biosynthesis of drosopterins has been discussed.

Colorimetric determination of aliphatic acids

A colorimetric method for the determination of carboxylic acids based on the dicyclohexylcarbodiimide-coupled reaction of 2-nitrophenylhydrazine and carboxylic acids is described. The product of the reaction is extracted into aqueous sodium hydroxide to produce a blue color. This method is suitable for the analysis of aliphatic acids, but aromatic acids do not react under these conditions.

A highly efficient carboxylic acid analyzer and its application

A new highly efficient carboxylic acid analyzer, employed with liquid chromatography and a specific detection method, has been designed for the quantitative analysis of carboxylic acids in foods and biological samples. This apparatus is particularly advanced in terms of its sensitivity and resolution as a result of the extensive modifications to our previous system. The applications of this analyzer to the analyses of juices, beer, human serum and urine are presented.