Artificial Chromogenic Substrate Research Articles

The use of isothermal titration calorimetry for the assay of enzyme activity: Application in higher education practical classes.

Determination of enzyme activity is crucial for discovery, research, and development in life sciences. The activity of enzymes is routinely determined using spectrophotometric assays that measure rates of substrate consumption or product formation. Though colorimetric-based detection systems are simple, rapid, and economical to perform, the majority of enzymes are unsuitable for this technique as their substrates/products do not absorb in the UV or visible range. This limitation can be addressed by the use of coupled-enzyme assays or artificial chromogenic substrates; however these approaches have their own drawbacks. Here, we describe a method based on the use of an isothermal titration calorimeter (ITC) to measure the heat produced or absorbed during any enzyme-catalyzed reaction. The concept of calorimetric enzyme assays was demonstrated for the determination of enzyme hexokinase activity, which cannot be monitored colorimetrically without first coupling it to another enzymatic reaction. The assay is suitable for incorporation into undergraduate laboratory classes, providing students with an appreciation for; the versatility and ease of use of ITC assays; ITC as a flexible generic method for exploring the functional characteristics of uncharacterized enzymes; an activity detection parameter suitable for enzymes that either have no straightforward colorimetric methods available or require the use of nonartificial chromogenic substrates.

Robust chitinolytic activity of crab-eating monkey (Macaca fascicularis) acidic chitinase under a broad pH and temperature range

Diet of the crab-eating monkey (Macaca fascicularis) consists of both plants and animals, including chitin-containing organisms such as crabs and insects. This omnivorous monkey has a high expression of acidic chitinase (CHIA) in the stomach and here, we report on its enzymatic properties under different conditions. When we compared with Mus musculus CHIA (Mm-CHIA), Macaca fascicularis CHIA (Mf-CHIA) exhibits higher chitinolytic activity at broad pH (1.0–7.0) and temperature (30–70 ℃) range. Interestingly, at its optimum pH (5.0), Mf-CHIA showed the highest activity at 65 °C while maintaining it at robust levels between 50 and 70 °C. The degradation efficiency of Mf-CHIA was superior to Mm-CHIA toward both polymeric chitin as well as an artificial chromogenic substrate. Our results show that unique features of Mf-CHIA including its thermostability warrant the nomination of this enzyme for potential agricultural and biomedical applications.

Active site complementation and hexameric arrangement in the GH family 29; a structure-function study of α-l-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus.

α-l-Fucosidase isoenzyme 1 from bacterium Paenibacillus thiaminolyticus is a member of the glycoside hydrolase family GH29 capable of cleaving l-fucose from nonreducing termini of oligosaccharides and glycoconjugates. Here we present the first crystal structure of this protein revealing a novel quaternary state within this family. The protein is in a unique hexameric assembly revealing the first observed case of active site complementation by a residue from an adjacent monomer in this family. Mutation of the complementing tryptophan residue caused changes in the catalytic properties including a shift of the pH optimum, a change of affinity to an artificial chromogenic substrate and a decreased reaction rate for a natural substrate. The wild-type enzyme was active on most of the tested naturally occurring oligosaccharides and capable of transglycosylation on a variety of acceptor molecules, including saccharides, alcohols or chromogenic substrates. Mutation of the complementing residue changed neither substrate specificity nor the preference for the type of transglycosylation acceptor molecule; however, the yields of the reactions were lower in both cases. Maltose molecules bound to the enzyme in the crystal structure identified surface carbohydrate-binding sites, possibly participating in binding of larger oligosaccharides.

Defining Substrate Specificities for Lipase and Phospholipase Candidates.

Microorganisms produce a wide spectrum of (phospho)lipases that are secreted in order to make external substrates available for the organism. Alternatively, other (phospho)lipases may be physically associated with the producing organism causing a turnover of intrinsic lipids and frequently giving rise to a remodeling of the cellular membranes. Although potential (phospho)lipases can be predicted with a number of algorithms when the gene/protein sequence is available, experimental proof of the enzyme activities, substrate specificities, and potential physiological functions has frequently not been obtained. This manuscript describes the optimization of assay conditions for prospective (phospho)lipases with unknown substrate specificities and how to employ these optimized conditions in the search for the natural substrate of a respective (phospho)lipase. Using artificial chromogenic substrates, such as p-nitrophenyl derivatives, may help to detect a minor enzymatic activity for a predicted (phospho)lipase under standard conditions. Having encountered such a minor enzymatic activity, the distinct parameters of an enzyme assay can be varied in order to obtain a more efficient hydrolysis of the artificial substrate. After having determined the conditions under which an enzyme works well, a variety of potential natural substrates should be assayed for their degradation, a process that can be followed employing distinct chromatographic methods. The definition of substrate specificities for new enzymes, often provides hypotheses for a potential physiological role of these enzymes, which then can be tested experimentally. Following these guidelines, we were able to identify a phospholipase C (SMc00171) that degrades phosphatidylcholine to phosphocholine and diacylglycerol, in a crucial step for the remodeling of membranes in the bacterium Sinorhizobium meliloti upon phosphorus-limiting conditions of growth. For two predicted patatin-like phospholipases (SMc00930 and SMc01003) of the same organism, we could redefine their substrate specificities and clarify that SMc01003 is a diacylglycerol lipase.

Trypsin Immobilized on Magnetic Beads via Click Chemistry: Fast Proteolysis of Proteins in a Microbioreactor for MALDI-ToF-MS Peptide Analysis

In the present work, magnetic poly(2-hydroxyethyl methacrylate–ethyleneglycol dimethacrylate) (mp(HEMA-EGDMA)) beads were prepared by suspension polymerization. The beads were grafted with poly(hydroxylpropyl methacrylate) (pHPMA) and used for immobilization of trypsin via click chemistry. The p(HPMA) units in the brushes made the fibrous polymer hydrophilic. Synthesized beads were characterized by swelling studies, Fourier transform infrared spectroscopy (FTIR), and scanning electron microscopy (SEM). The bromo groups of the grafted polymer were modified into azide groups, and the enzyme was alkyne-functionalized for conjugation with azide-modified magnetic beads via click reaction. The kinetic constants (Km and Vmax) were determined by measuring initial reaction rates using the artificial chromogenic substrate N-benzoyl-dl-arginine 4-nitroanilide hydrochloride (BApNA). The optimal pH value for the immobilized enzyme was slightly higher compared to free enzyme. The immobilized trypsin possessed much high...

Cloning, expression, and biochemical characterization of a novel GH16 β-agarase AgaG1 from Alteromonas sp. GNUM-1

Alteromonas sp. GNUM-1 is known to degrade agar, the main cell wall component of red macroalgae, for their growth. A putative agarase gene (agaG1) was identified from the mini-library of GNUM-1, when extracellular agarase activity was detected in a bacterial transformant. The nucleotide sequence revealed that AgaG1 had significant homology to GH16 agarases. agaG1 encodes a primary translation product (34.7 kDa) of 301 amino acids, including a 19-amino-acid signal peptide. For intracellular expression, a gene fragment encoding only the mature form (282 amino acids) was cloned into pGEX-5X-1 in Escherichia coli, where AgaG1 was expressed as a fusion protein with GST attached to its N-terminal (GST-AgaG1). GST-AgaG1 purified on a glutathione sepharose column had an apparent molecular weight of 59 kDa on SDS-PAGE, and this weight matched with the estimated molecular weight (58.7 kDa). The agarase activity of the purified protein was confirmed by the zymogram assay. GST-AgaG1 could hydrolyze the artificial chromogenic substrate, p-nitrophenyl-β-D-galactopyranoside but not p-nitrophenyl-α-D-galactopyranoside. The optimum pH and temperature for GST-AgaG1 activity were identified as 7.0 and 40 °C, respectively. GST-AgaG1 was stable up to 40 °C (100 %), and it retained more than 70 % of its initial activity at 45 °C after heat treatment for 30 min. The K m and V max for agarose were 3.74 mg/ml and 23.8 U/mg, respectively. GST-AgaG1 did not require metal ions for its activity. Thin layer chromatography analysis, mass spectrometry, and (13)C-nuclear magnetic resonance spectrometry of the GST-AgaG1 hydrolysis products revealed that GST-AgaG1 is an endo-type β-agarase that hydrolyzes agarose and neoagarotetraose into neoagarobiose.

Identification and characterization of a novel β-galactosidase from Victivallis vadensis ATCC BAA-548, an anaerobic fecal bacterium

Victivallis vadensis ATCC BAA-548 is a Gram-negative, anaerobic bacterium that was isolated from a human fecal sample. From the genomic sequence of V. vadensis, one gene was found to encode agarase; however, its enzymatic properties have never been characterized. The gene encoding the putative agarase (NCBI reference number ZP_01923925) was cloned by PCR and expressed in E. coli Rosetta-gami by using the inducible T(7) promoter of pET28a(+). The expressed protein with a 6×His tag at the N-terminus was named His6-VadG925 and purified as a soluble protein by Ni(2+)-NTA agarose affinity column chromatography. The purification of the enzyme was 26.8-fold, with a yield of 73.2% and a specific activity of 1.02 U/mg of protein. The purified His6-VadG925 produced a single band with an approximate MW of 155 kDa, which is consistent with the calculated value (154,660 Da) including the 6×His tag. Although VadG925 and many of its homologs were annotated as agarases, it did not hydrolyze agarose. Instead, purified His(6)-VadG925 hydrolyzed an artificial chromogenic substrate, p-nitrophenyl-β-D-galactopyranoside, but not p-nitrophenyl-α-D-galactopyranoside. The optimum pH and temperature for this β-galactosidase activity were pH 7.0 and 40°C, respectively. The K(m) and V(max) of His6-VadG925 towards p-nitrophenyl-β-D-galactopyranoside were 1.69 mg/ml (0.0056 M) and 30.3 U/mg, respectively. His6-VadG925 efficiently hydrolyzed lactose into glucose and galactose, which was demonstrated by TLC and mass spectroscopy. These results clearly demonstrated that VadG925 is a novel β-galactosidase that can hydrolyze lactose, which is unusual because of its low homology to validated β-galactosidases.

Identification of the acid/base catalyst of a glycoside hydrolase family 3 (GH3) β-glucosidase from Aspergillus niger ASKU28

BackgroundThe commercially important glycoside hydrolase family 3 (GH3) β-glucosidases from Aspergillus niger are anomeric-configuration-retaining enzymes that operate through the canonical double-displacement glycosidase mechanism. Whereas the catalytic nucleophile is readily identified across all GH3 members by sequence alignments, the acid/base catalyst in this family is phylogenetically variable and less readily divined. MethodsIn this report, we employed three-dimensional structure homology modeling and detailed kinetic analysis of site-directed mutants to identify the catalytic acid/base of a GH3 β-glucosidase from A. niger ASKU28. ResultsIn comparison to the wild-type enzyme and other mutants, the E490A variant exhibited greatly reduced kcat and kcat/Km values toward the natural substrate cellobiose (67,000- and 61,000-fold, respectively). Correspondingly smaller kinetic effects were observed for artificial chromogenic substrates p-nitrophenyl β-d-glucoside and 2,4-dinitrophenyl β-d-glucoside, the aglycone leaving groups of which are less dependent on acid catalysis, although changes in the rate-determining catalytic step were revealed for both. pH-rate profile analyses also implicated E490 as the general acid/base catalyst. Addition of azide as an exogenous nucleophile partially rescued the activity of the E490A variant with the aryl β-glucosides and yielded β-glucosyl azide as a product. Conclusions and general significanceThese results strongly support the assignment of E490 as the acid/base catalyst in a β-glucosidase from A. niger ASKU28, and provide crucial experimental support for the bioinformatic identification of the homologous residue in a range of related GH3 subfamily members.

Identification and Biochemical Characterization of Sco3487 from Streptomyces coelicolor A3(2), an Exo- and Endo-Type -Agarase-Producing Neoagarobiose

Streptomyces coelicolor can degrade agar, the main cell wall component of red macroalgae, for growth. To constitute a crucial carbon source for bacterial growth, the alternating α-(1,3) and β-(1,4) linkages between the 3,6-anhydro-L-galactoses and D-galactoses of agar must be hydrolyzed by α/β-agarases. In S. coelicolor, DagA was confirmed to be an endo-type β-agarase that degrades agar into neoagarotetraose and neoagarohexaose. Genomic sequencing data of S. coelicolor revealed that Sco3487, annotated as a putative hydrolase, has high similarity to the glycoside hydrolase (GH) GH50 β-agarases. Sco3487 encodes a primary translation product (88.5 kDa) of 798 amino acids, including a 45-amino-acid signal peptide. The sco3487 gene was cloned and expressed under the control of the ermE promoter in Streptomyces lividans TK24. β-Agarase activity was detected in transformant culture broth using the artificial chromogenic substrate p-nitrophenyl-β-D-galactopyranoside. Mature Sco3487 (83.9 kDa) was purified 52-fold with a yield of 66% from the culture broth. The optimum pH and temperature for Sco3487 activity were 7.0 and 40°C, respectively. The K(m) and V(max) for agarose were 4.87 mg/ml (4 × 10(-5) M) and 10.75 U/mg, respectively. Sco3487 did not require metal ions for its activity, but severe inhibition by Mn(2+) and Cu(2+) was observed. Thin-layer chromatography analysis, matrix-assisted laser desorption ionization-time of flight mass spectrometry, and Fourier transform-nuclear magnetic resonance spectrometry of the Sco3487 hydrolysis products revealed that Sco3487 is both an exo- and endo-type β-agarase that degrades agarose, neoagarotetraose, and neoagarohexaose into neoagarobiose.

Quantitative analysis of Schizophyllum commune metalloprotease ScPrB activity in SDS-gelatin PAGE reveals differential mycelial localization of nitrogen limitation-induced autolysis

The basidiomycete Schizophyllum commune produces a variety of proteolytic enzymes. A number of these, detected in native gelatin-containing polyacrylamide gels, have their activities increased during nitrogen-limited growth of the mycelium. ScPrB, a metallo-endoprotease, appears to have the greatest nitrogen stress-induced increase in activity of all of these enzymes. Quantifying ScPrB has proven difficult because no artificial chromogenic substrate has been found. In addition, it is poorly resolved from another highly active protease, ScPrA, in native gelatin-containing gels. We have developed a method using SDS gelatin-containing polyacrylamide gels for resolving ScPrB from ScPrA and for quantifying its activity by densitometry. This method was used to assess the intramycelial location of ScPrB induction after the transfer of exponentially growing colonies to nitrogen deprivation conditions. By all analyses (proportional, normalized to fresh weight, and normalized to protein), the increase in ScPrB activity was found to occur exclusively in midsections of the growing mycelium, whereas ScPrB activity was found to be decreased or unchanged in the centers of colonies and in colony margins. This implies that proteolysis mediated by ScPrB may supply translocatable amino acids only from the region directly behind the growing hyphal apices.

Identification and characterization of Helicobacter pylori phospholipase C activity

We analyzed 11 H. pylori isolates from humans using the artificial chromogenic substrate paranitrophenylphosphorylcholine to detect phospholipase C (PLC) activity. The range of PLC in sonicates was 8.8-92.3 (Mean 56.9 +/- 6.5) nmol of substrate hydrolysed min-1 mg-1 protein; the amount of activity was not associated with urease or cytotoxin levels. Addition of sorbitol or glycerol enhanced PLC activity of H. pylori sonicate and purified PLC from C. perfringens (PLC1) but not purified PLC from B. cereus (PLC3). H. pylori sonicates had little acid phosphatase and no detectable alkaline phosphatase activity, and H. pylori PLC showed markedly different biochemical characteristics from either phosphatase. In total, these studies indicate that activity measured in H. pylori sonicate by PLC assay is due to PLC and not phosphatase activity. The temperature optimum for PLC activity of H. pylori sonicate was 56 degrees C and for PLC 1 was 65 degrees C. For H. pylori PLC and PLC1, optimal activity occurred at pH 8. Despite multiple similarities between H. pylori PLC and PLC1, known PLC inhibitors show different interactions with each enzyme. Although PLC activity is present in many subcellular constituents of H. pylori, including culture supernatants and water extracts, highest specific activity is associated with a membrane-enriched fraction.

Aminopeptidase activity levels during axonal and dendritic growth in the rat brain.

Brain aminopeptidase activity has been suggested as a candidate for the regulation and biotransformation of several neuropeptides. In this paper, changes in Lys- and Leu-aminopeptidase activities in rat brain hemispheres, cerebellum and medulla were examined in 1-, 3-, 5- and 7-days postnatal subjects. Aminopeptidase activities were studied by measuring the rate of hydrolysis of the artificial chromogenic substrates Lys- and Leu-2-naphthylamides (fluorimetrically detected in triplicate). Both enzyme activities show a decrease on the 3rd day of life followed by increases on the 5th and 7th day postbirth. It is suggested that these activities could play a part in the neurochemical changes that take place during axonal and dendritic growth in the rat brain.

Cloning and characterization of two genes from Bacillus polymyxa expressing beta-glucosidase activity in Escherichia coli

DNA fragments from Bacillus polymyxa which encode beta-glucosidase activity were cloned in Escherichia coli by selection of yellow transformants able to hydrolyze the artificial chromogenic substrate p-nitrophenyl-beta-D-glucopyranoside. Restriction endonuclease maps and Southern analysis of the cloned fragments showed the existence of two different genes. Expression of either one of these genes allowed growth of E. coli in minimal medium with cellobiose as the only carbon source. One of the two enzymes was found in the periplasm of E. coli, hydrolyzed arylglucosides more actively than cellobiose, and rendered glucose as the only product upon cellobiose hydrolysis. The other enzyme was located in the cytoplasm, was more active toward cellobiose, and hydrolyzed this disaccharide, yielding glucose and another, unidentified compound, probably a phosphorylated sugar.

A simple chromogenic assay for arylsulfatase A

Arylsulfatase A hydrolyzes the artificial chromogenic substrate 4-nitrocatecholsulfate at 0°C at a rate of 24% of that at 37°C whereas arylsulfatase B is almost inactive at 0°C. Based on this observation, a simple assay was developed which permits the accurate determination of low residual arylsulfatase A activities in cultured skin fibroblasts of infantile, juvenile and adult MLD patients and pseudodeficient individuals. In cultured skin fibroblasts, the following residual activities were found with this assay system: late-infantile patients, 0.0%, one juvenile patient, 1.0%, adult patients, 4.4–14% of normal average. Healthy pseudodeficient probands ranged between 18% and 32%.

An improved method excluding hemoglobin interferences for lysosomal hydrolase assays using colorimetric synthetic substrates, 2-( N-hexadecanoylamino)-4-nitrophenol derivatives

Artificial chromogenic substrates, derived from 2-( N-hexadecanoylamino)-4-nitrophenol, can be used to assay sphingomyelin phosphodiesterase, glucosylceramidase, or galactosylceramidase. Nevertheless, these enzymatic spectrophotometric assays cannot be realized on tissue preparations containing hemoglobin which interferes in the measurement. We present a selective extraction method of 2-( N-hexadecanoylamino)-4-nitrophenol which allows to avoid hemoglobin interference in this spectrophotometric assay of 2-( N-hexadecanoylamino)-4-nitrophenol. The solvents used have been tested to obtain on the one hand maximal absorbance and organic extraction of 2-( N-hexadecanoylamino)-4-nitrophenol, and on the other hand the minimal hemoglobin interference. None of the pure solvents studied being suitable, two solvent mixtures were selected: ethyl acetate/2-propanol ( 5 1 ) and 2-ethyl-1-hexanol/4-methyl-2-pentanone ( 1 1 ). These methods were tested to determine sphingomyelinase activity in enzymatic preparations and prove that they are available for lysosomal hydrolase assays using these colorimetric substrates.

Purification and properties of cyclic phosphodiesterase: 3′-nucleotidase, a periplasmic enzyme of Haemophilus influenzae

The cyclic phosphodiesterase: 3′-nucleotidase of Haemophilus influenzae catalyzes the cleavage of 2′,3′-cyclic nucleotides to 3′-monoesters, and the hydrolysis of the resulting 3′-nucleotides to nucleosides and inorganic phosphate. It also hydrolyzes the artificial substrate bis( p-nitrophenyl)phosphate, yielding p-nitrophenol and p-nitrophenyl phosphate. The enzyme is located in the periplasmic space of H. influenzae, and can be selectively released by subjecting the cells to osmotic shock, or by converting the cells to spheroplasts. The selective removal of the enzyme from H. influenzae was effected by incubating the cells in a solution of Tris, EDTA, and Nonidet P-40; the enzyme was further purified to apparent electrophoretic homogeneity. The enzyme from H. influenzae hydrolyses 3′-nucleotides in the absence of any added metal ion, although Co 2+ and Ca 2+ stimulate the cleavage of bis( p-nitropheny])phosphate. We have observed a marked competitive inhibition of bis( p-nitrophenyl)phosphate cleavage by 2′-, 3′-, and 5′-adenosine monophosphate. The 2′- and 5′-nucleotides also inhibit the cyclic phosphodiesterase and 3′-nucleotidase activities. These results indicate that nucleotide substrates and the artificial chromogenic substrate interact with the same active site.