A method for rapid protease substrate evaluation and optimization

We have developed a high throughput assay for the measurement of protease activity in solution. This technology will accelerate research in functional proteomics and enable biologists to streamline protease substrate evaluation and optimization. The peptide sequences that serve as protease substrates in this assay are labeled on the carboxy terminus with a biotin moiety and a fluorescent tag is attached to the amino terminus. Protease cleavage causes the biotin containing fragment to be detached from the labeled peptide fragment. Following the protease treatment, all biotin containing species (uncleaved substrates and the cleaved carboxy terminal fragment of the substrate) are removed by incubation with streptavidin beads. The cleaved fluorescently labeled amino terminal part of the substrate remains in solution. The measured fluorescence intensity of the solution is directly proportional to the activity of the protease. This assay was validated using trypsin, chymotrypsin, caspase-3, subtilisin-A, enterokinase and tobacco etch virus protease.     

Detection of trypsin- and chymotrypsin-like proteases using p-nitroanilide substrates after sodium dodecyl sulphate polyacrylamide gel electrophoresis

Specific chromogenic p-nitroanilide substrates have proved useful for localizing proteolytic enzymes, such as trypsin, chymotrypsin and elastase after separation of agarose gel electrophoresis and when immobilized on nitrocellulose. This procedure was further developed for use with sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). After SDS-PAGE, proteins were transferred electrophoretically to a nitrocellulose membrane. The membrane was incubated for 10–60 min with Bz-Ile-Glu-Gly-Arg-p-nitroanilide as a substrate for detection of trypsin-like proteases and with MeO-Suc-Arg-Pro-Tyr-p-nitroanilide for detection of chymotrypsin. The yellow p-nitroanilide released at the site of proteolytic activity was converted into a visible and stable red azo dye. By this method was identified and determined the molecular weight of a trypsin-like protease that occurs at high concentrations in mucinous ovarian tumour cyst fluid together with its specific inhibitor peptide, tumour-associated trypsin inhibitor (TATI). The method was also used to visualize trypsin and chymotrypsin in human pancreatic juice. Using the trypsin substrate, three proteolytic bands, corresponding to M_r of 22 000, 24 000 and 26 000 daltons, were visualized in pancreatic juice, while the proteolytic zones in cyst fluid had M_r of 25 000 and 28 000 daltons. With the chymotrypsin substrate, a band of 29 000 daltons was visualized in pancreatic juice, whereas no activity was detected in cyst fluid. By incubation of the blotted cyst fluid proteins with ¹²⁵I-labelled TATI, a pattern of bands at 25 000 and 28 000 daltons was detected identical to that obtained with the chromogenic substrate.     

Assessing protease activity pattern by means of multiple substrate ESI-MS assays

The development of a simultaneous multiple substrate enzymatic assay based on electrospray ionization mass spectrometry (ESI-MS) detection is described. This multiplexing assay scheme was employed in a parallel proteolytic enzyme activity screening. As model systems, the respective activities of trypsin, thrombin, chymotrypsin, bromelain, ficin and elastase towards seven different substrates were assessed. The resulting activity patterns were evaluated semi-quantitatively ranking the enzymatic activities in five classes of activity (very high, high, medium, low and no activity) with respect to the individual substrates. The validity of the MS-based multiplexing assay scheme was proved by comparison with the results obtained from single substrate assays detected by means of UV/vis absorption at 405 nm, showing good agreement of the resulting activity patterns and classifications.     

Highly efficient proteinase assay with chromogenic substrates and its application in a study of enzyme inhibitors

A simple and rapid method for the determination of enzyme activities with chromogenic substrates is described. Trypsin and papain were used as model proteinases and N-benzoyl-dl-arginine p-nitroanilide (BAPNA) was applied as substrate. The enzyme assay was performed on a multi-scale using 96-well microtitration plates and product release was detected with the aid of an automatic plate reader, widely used in ELISA tests. The procedure was used for electrophoretic studies of trypsin and a crude papain preparation. It was also applied for the investigation of N-peptidyl-O-acylhydroxylamine proteinase inhibitors. In comparison with commonly used procedures with chromogenic substrates, the proposed approach consumes markedly reduced amounts of all reagents. It allows an almost unlimited number of samples to be assayed in a short time and should be applicable to the detection and determination of any enzyme activitiy where chromogenic substrates are applicable.     

Structural Optimization of Photoswitch Ligands for Surface Attachment of α‐Chymotrypsin and Regulation of Its Surface Binding

A modified gold surface that allows photoregulated binding of α‐chymotrypsin has previously been reported. Here the development of this surface is reported, through the synthesis of a series of trifluoromethyl ketones and α‐keto esters containing the azobenzene group and a surface attachment group as photoswitch inhibitors of α‐chymotrypsin. All of the compounds are inhibitors of the enzyme, with activity that can be modulated by photoisomerization. The best photoswitch shows a reversible change in IC₅₀ inhibition constant of >5.3 times on photoisomerization. The trifluoromethyl ketone 1 exhibited excellent photoswitching and was attached to a gold surface in a two‐step procedure involving an azide–alkyne cycloaddition. The resulting modified surface bound α‐chymotrypsin to a degree that could be modulated by UV/Vis irradiation, showing “slow‐tight” enzyme binding as observed for inhibitors in solution.     

Globular Polymer Grafts Require a Critical Size for Efficient Molecular Sieving of Enzyme Substrates

A series of 2,2‐bis(hydroxymethyl)propionic acid dendrons of generation 2 through 8 having a strained cyclooctyne at the core and hydroxy groups at the periphery were prepared by a divergent method and used to functionalize azide‐decorated α‐chymotrypsin. The ability of the appended dendrons to selectively block enzyme activity (through a molecular sieving effect) was investigated using a small molecule substrate (benzoyl‐l ‐tyrosine p‐nitroanilide), as well as two proteins of different size (casein and bovine serum albumin). Additionally, the ability of dendrons to block complexation with a chymotrypsin antagonist, α‐antichymotrypsin, was investigated, and it was found that the dendron coating effectively prevented inhibition by this antagonist. We found that a critical generation is required to achieve efficient sieving with bis‐MPA dendrons, which illustrates the importance of macromolecular architecture and size in the shielding of proteins.     

α‐Chymotrypsin‐Catalyzed Reaction Confined in Block‐Copolymer Vesicles

Herein the reactivity of the enzyme α‐chymotrypsin in the confinement of polystyrene‐block‐poly(acrylic acid) (PS‐b‐PAA) vesicles was investigated. Enzyme and substrate molecules were encapsulated in PS‐b‐PAA vesicles with internal diameters ranging from 26 nm to 165 nm during the formation of the vesicles. While the loading efficiencies of enzyme and substrate molecules were practically identical for vesicles of identical size, they were found to increase with decreasing vesicle size. The kinetics of the α‐chymotrypsin catalyzed hydrolysis of N‐succinyl‐Ala‐Ala‐Phe‐7‐amido‐4‐methylcoumarin (AMC) was evaluated following the increase of the absorption of the product 7‐amino‐4‐methylcoumarin by UV/Vis spectroscopy. The values of the catalytic turnover number obtained for reactions inside vesicles with different sizes showed an increase of up to fourteen times compared to the bulk value with decreasing vesicle volume, while the values of the Michaelis–Menten constant decreased, respectively. This increase in reactivity of α‐chymotrypsin is attributed to the effect of vesicle–wall interactions in the finite encapsulated space, where the reagents could diffuse, leading to enhanced collision frequencies.     

Bifunctional coumarin derivatives in solution and solid phase synthesis of fluorogenic enzyme substrates

The use of the fluorescent bifunctional compounds 7‐amino‐4‐coumarinyl‐acetic acid 1 , 7‐hydroxy‐4‐coumarinyl‐acetic acid 2 and ethyl 7‐amino‐4‐coumarinyl‐acetate 3 in solution and solid phase synthesis of fluorogenic enzyme substrates was examined. The intramolecularly quenched fluorogenic substrate N‐(7‐amino‐4‐coumarinyl‐acetyl)‐L‐phenylalanyl‐p‐nitroanilide 5 , and the fluorogenic one ethyl 7‐(glutaryl‐L‐phenylalanilamido)‐4‐coumarinyl‐acetate 8 , both suitable for chymotrypsin and/or chymotrypsin like enzymes determination, were prepared in solution. The substrates 7‐oleyloxy‐4‐coumarinyl‐acetic acid 13 and 7‐palmitoyloxy‐4‐coumarinyl‐acetic acid 14 , suitable for the enzymatic study of lipases, were prepared by solid phase technique using 2‐chloro‐chlorotrityl‐resin. The study of the fluorescence properties of the fluorophores 1, 2, 3 , and substrates 5, 8,13,14 showed that the examined bifunctional coumarin derivatives are suitable markers for solution and solid phase synthesis of fluorogenic enzyme substrates.     

Proteinase inhibitory assays of serum using high-performance size exclusion chromatography

A size exclusion column (Spherogel TSK-2000 SW) was utilized in a high-performance size exclusion chromatographic assay to determine the proteinase inhibitory capacity of human sera. Values from assays using this technique agreed well with the standard spectrophotometric inhibitory assays. Nanogram to milligram amounts of protein, namely, alpha 1-proteinase inhibitor, elastase, trypsin, chymotrypsin and their corresponding complexes with the inhibitor, were fractionated in less than 15 min. The nitrated or oxidized alpha 1-proteinase inhibitor was shown to retain its ability to form stable complexes with trypsin or chymotrypsin; however, they lost the inhibitory activity against elastase and instead they behaved as common protein substrates for this enzyme. The present chromatographic procedure was unable to detect any peptide released when the native inhibitor and any of the proteinases reacted to form a complex. Moreover, dissociation of the alpha 1-proteinase inhibitor--elastase complex in an alkaline pH did not result in the formation or release of any peptide.     

Biochemical analysis with microfluidic systems

Microfluidic systems are capillary networks of varying complexity fabricated originally in silicon, but nowadays in glass and polymeric substrates. Flow of liquid is mainly controlled by use of electroosmotic effects, i.e. application of electric fields, in addition to pressurized flow, i.e. application of pressure or vacuum. Because electroosmotic flow rates depend on the charge densities on the walls of capillaries, they are influenced by substrate material, fabrication processes, surface pretreatment procedures, and buffer additives. Microfluidic systems combine the properties of capillary electrophoretic systems and flow-through analytical systems, and thus biochemical analytical assays have been developed utilizing and integrating both aspects. Proteins, peptides, and nucleic acids can be separated because of their different electrophoretic mobility; detection is achieved with fluorescence detectors. For protein analysis, in particular, interfaces between microfluidic chips and mass spectrometers were developed. Further levels of integration of required sample-treatment steps were achieved by integration of protein digestion by immobilized trypsin and amplification of nucleic acids by the polymerase chain reaction. Kinetic constants of enzyme reactions were determined by adjusting different degrees of dilution of enzyme substrates or inhibitors within a single chip utilizing mainly the properties of controlled dosing and mixing liquids within a chip. For analysis of kinase reactions, however, a combination of a reaction step (enzyme with substrate and inhibitor) and a separation step (enzyme substrate and reaction product) was required. Microfluidic chips also enable separation of analytes from sample matrix constituents, which can interfere with quantitative determination, if they have different electrophoretic mobilities. In addition to analysis of nucleic acids and enzymes, immunoassays are the third group of analytical assays performed in microfluidic chips. They utilize either affinity capillary electrophoresis as a homogeneous assay format, or immobilized antigens or antibodies in heterogeneous assays with serial supply of reagents and washing solutions.     

Anomalous electrophoretic migration of short oligodeoxynucleotides labelled with 5′‐terminal Cy5 dyes

By using a fluorescent exonuclease assay, we reported unusual electrophoretic mobility of 5′‐indocarbo‐cyanine 5 (5′‐Cy5) labelled DNA fragments in denaturing polyacrylamide gels. Incubation time and enzyme concentration were two parameters involved in the formation of 5′‐Cy5‐labelled degradation products, while the structure of the substrate was slightly interfering. Replacement of positively charged 5′‐Cy5‐labelled DNA oligonucleotides (DNA oligos) by electrically neutral 5′‐carboxyfluorescein (5′‐FAM) labelled DNA oligos abolished the anomalous migration pattern of degradation products. MS analysis demonstrated that anomalously migrating products were in fact 5′‐labelled DNA fragments ranging from 1 to 8 nucleotides. Longer 5′‐Cy5‐labelled DNA fragments migrated at the expected position. Altogether, these data highlighted, for the first time, the influence of the mass/charge ratio of 5′‐Cy5‐labelled DNA oligos on their electrophoretic mobility. Although obtained by performing 3′ to 5′ exonuclease assays with the family B DNA polymerase from Pyrococcus abyssi, these observations represent a major concern in DNA technology involving most DNA degrading enzymes.     

High temporal resolution monitoring of enzyme reaction and inhibition using optically gated vacancy capillary electrophoresis and immobilized enzyme

A novel method for monitoring of enzyme reaction and inhibition with high temporal resolution was developed by using optically gated vacancy capillary electrophoresis (OGVCE) with laser-induced fluorescence (LIF) detection and immobilized enzyme. Trypsin cleavage reaction and inhibition were investigated by the presented OGVCE-LIF assay, using carboxyfluorescein (FAM) end-labeled Angiotensin as the substrate and commercially available immobilized trypsin. The substrate and the product were continuously loaded into the capillary by the electroosmotic flow while the immobilized enzyme remained in the sample vial. Substrate consumption and product formation were monitored simultaneously at 5 s interval during the whole reaction time. The enzymatic reaction rates obtained from the substrate and the product were highly consistent. The enzyme activity and the Michaelis constants of trypsin cleavage reaction, as well as the inhibition constant (for reversible competitive inhibitor) and the inhibition fraction (for irreversible inhibitor), were obtained. It was showed that the reported OGVCE-LIF method can perform fast, accurate, sensitive and reproducible CE enzyme assay with high temporal resolution, thus has great potential in application of the enzyme-substrate systems with fast reaction rate and the fluorescent substrate and products.     

Development of a liquid chromatography-based screening methodology for proteolytic enzyme activity

A new methodology for the detection and isolation of serine proteases in complex mixtures has been developed. It combines the characterization of crude samples by electrospray tandem mass spectrometry (ESI-MS/MS) in a multi-substrate assay and the differentiated sensitive detection of the responsible enzymes by means of liquid chromatography hyphenated online to biochemical detection (BCD). First, active samples are identified in the multi-substrate assay monitoring the conversion of eight substrates in multiple reaction monitoring in parallel within 60 s. Hereby, the product patterns are investigated and the suitable peptide as substrate for BCD analysis is selected. Subsequently, the active proteases are identified online in the continuous-flow reactor serving as BCD after non-denaturing separation by size-exclusion chromatography and ion-exchange chromatography. For BCD, the selected para-nitroaniline (pNA) labeled peptide is added post-column and is cleaved by eluting proteases under release of the coloured pNA in a reaction coil (reaction time 5 min). The method was optimized and the figures of merit were characterized with trypsin and chymotrypsin serving as the model proteases. For trypsin, a limit of detection in LC–BCD of 0.1 U/mL corresponding to an injected amount of 0.4 ng protein (∼18 fmol) was observed. The BCD signal remained linear for an injected enzyme concentration of 0.3–10 U/mL (1.3–42 ng enzyme). The method was applied to the characterization of the crude venom of the pit viper Bothrops moojeni and the extracellular protease of the pathogenic amoeba Acanthamoeba castellanii. In the two samples, fractions with proteolytic activity potentially interfering with the blood coagulation cascade were identified. The described methodology represents a tool for serine protease screening in complex mixtures by a fast ESI-MS/MS identification of active samples followed by the separation and isolation of active sample constituents in LC–BCD.     

A CIEF‐LIF method for simultaneous analysis of multiple protein kinases and screening of inhibitors

Here, a CIEF‐LIF method for multiple protein kinase simultaneous analysis and inhibitors throughput screening with fast rate and low cost is presented. Comparing with CZE, CIEF‐LIF exhibited great focusing ability and high separation efficiency for substrate and phosphorylated peptides, and is applicable for multiple kinases simultaneous analysis regardless of their substrate peptides compositions and charge statuses. Thus, highly sensitive analysis for cyclic adenosine 3’, 5’‐monophosphate‐dependent protein kinase (PKA) and cyclin‐dependent kinase 1 (CDK1) was achieved in CIEF‐LIF analysis with detection sensitivity up to 1.25 mU/μL and 0.4 mU/μL, respectively, two magnitudes higher than that of CZE and comparable with that in nanomaterials or green fluorescent protein‐based kinase assay. Moreover, the inhibition effect of inhibitors on multiple kinases could be simultaneously readout in a single electrophoretic run, with half maximal inhibitory concentration of H‐89 for PKA and Ro‐3306 for CDK1 calculated as 37.0 and 35.9 nM, respectively, consistent with literatures reported. The CIEF‐LIF also exhibited strong anti‐interference ability in human breast cancer cell lysates analysis and simulators such as forskolin and 3‐isobutyl‐1‐methylxantine assessment. Therefore, CIEF‐LIF is desirable for future biological application and clinical diagnostics and drug discovery.     

THE CHEMICAL MODIFICATION OF E.Coli L—ASPARAGINASE WITH O—CARBOXYMETHYLATED CHITOSAN

Escherichia coli L-asparaginase was modified with O-car-boxymethylated chitosan using glutaraldehyde as a coupling agent.The resulting coujugate retained more than 50% of its original enzyme activity under the protection of its normal substrate or product and showed marked resistance to proteolysis by trypsin and chymotrypsin.     

Preparation and characterization of acrylic‐based black particles of poly(methyl methacrylate‐co‐ethylene glycol dimethacrylate) by dispersion polymerization for electrophoretic displays

Ultrafine black particles, ranging in diameter from 1 to 3 μm, were prepared by dispersion polymerization in a methanol/water mixture with vinyl monomers, nonpolymerizable Sudan black B dyes, and fluorescein isothiocyanate labeled charge control additives. Both the ratio of the methanol to the water dispersion medium and the polymeric stabilizer concentration had significant effects on the particle size. The important role of the stabilizer concentration lay in the particle formation step, during which it determined the particle stability and final particle size. These could affect the extent of the aggregation of nuclei by changing the adsorption rate of the stabilizer and the viscosity of the dispersion medium, resulting in smaller particles. The fluorescent‐labeled charge control additives strongly affected the electrophoretic mobility. A small concentration of fluorescent‐labeled charge control additives increased the electrophoretic mobility. However, a further addition reduced the electrophoretic mobility of the polymer particles. The concentration dependence of the fluorescent‐labeled charge control additives on the deposition behavior in the polymer particles was successfully imaged and thereafter quantified by image analysis. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5608–5616, 2004     

A combined tryptic peptide and winged peptide internal standard approach for the determination of α‐lactalbumin in dairy products by ultra high performance liquid chromatography with tandem mass spectrometry

A robust ultra high performance liquid chromatography with tandem mass spectrometry method at peptide level was established for measuring α‐lactalbumin in various dairy products. An isotope‐labeled winged peptide (VKKILDKVG*I NYW*L AHKALCSEKL) with extra amino acids of the sequence of signature peptide concatenated at each end as the internal standard was spiked in samples to participate in the whole tryptic digestion process. The peptide VG*I NYW*L AHK that resulted from the isotope‐labeled winged peptide was used as the final isotopically labeled internal standard of the α‐lactalbumin signature peptide (VGINYWLAHK) during the quantitative analysis. The contents of α‐lactalbumin in samples were calculated based on the equimolar relationship between the α‐lactalbumin protein and signature peptide. The optimized molar ratio of trypsin to protein (1:60) and enzymatic digestion time (5 h) could not only improve the digestion efficiency and reduce the cost, but also minimize the period of sample pretreatment. Considering the robustness of the current method using the isotopically labeled internal standard and acceptable measurement cost, its application may promote the development of nutrient investigation and quality control of α‐lactalbumin in dairy products. This protein analysis method might provide a new reference strategy for food analysis and quantitative protein analysis.     

Capillary electrophoretic analysis of alkaline phosphatase inhibition by theophylline

An analytical method for studying enzyme inhibition has been developed using capillary electrophoresis with laser-induced fluorescence detection. This technique is based on electrophoretic mixing of zones of enzyme and inhibitor in substrate-filled capillaries. Enzyme catalytic activity is measured by detecting the fluorescent reaction product as it migrates past the detector. Reversible enzyme inhibition is indicated by a transient decrease in product formation. The enzyme, alkaline phosphatase, has been studied using the fluorogenic substrate AttoPhos ([2,2'-bibenzothiazol]-6-hydroxy-benzthiazole phosphate). This assay has been used to quantify theophylline, a noncompetitive, reversible inhibitor of alkaline phosphatase. The detection limit for theophylline is estimated at 3 microM, and 8.6 amole of alkaline phosphatase are required for each assay. The calculated K(i) for theophylline is 90 microM for the capillary electrophoretic enzyme-inhibitor assays.     

Solution‐State 17O Quadrupole Central‐Transition NMR Spectroscopy in the Active Site of Tryptophan Synthase

Oxygen is an essential participant in the acid–base chemistry that takes place within many enzyme active sites, yet has remained virtually silent as a probe in NMR spectroscopy. Here, we demonstrate the first use of solution‐state ¹⁷O quadrupole central‐transition NMR spectroscopy to characterize enzymatic intermediates under conditions of active catalysis. In the 143 kDa pyridoxal‐5′‐phosphate‐dependent enzyme tryptophan synthase, reactions of the α‐aminoacrylate intermediate with the nucleophiles indoline and 2‐aminophenol correlate with an upfield shift of the substrate carboxylate oxygen resonances. First principles calculations suggest that the increased shieldings for these quinonoid intermediates result from the net increase in the charge density of the substrate–cofactor π‐bonding network, particularly at the adjacent α‐carbon site.     

Reverse zymography using fluorogenic substrates for protease inhibitor detection

A novel, sensitive method for detecting protease inhibitors by using fluorescent protease substrates in gels is described. The protease inhibitors were separated on sodium dodecyl sulfate (SDS)-polyacrylamide gels containing a copolymerized peptide substrate, namely 4-methyl-coumaryl-7-amide (MCA). As the incorporated substrates in the gel, Boc-Phe Ser-Arg-MCA was used for trypsin, Suc-Ala-Ala-Pro-Phe-MCA for alpha-chymotrypsin, and Z-Phe-Arg-MCA for papain. After electrophoresis, washing and incubating the gel with the target protease solutions allowed the substrate to be cleaved by the protease, and the release of the fluorescent 7 amino-4 methyl-coumarin (AMC), which was detected under a UV transilluminator. The uncleaved peptide-MCA substrate remained where the inhibitors were present, and was visualized as dark blue bands on the light-green fluorescent background gel. This new method offers several advantages over other previous methods including: (i) greatly increased sensitivity can be achieved in a shorter period of time, which may be useful for discovering new protease inhibitors in small amounts of crude material; (ii) the procedure is quite simple and quick since the incubation period is very short and no time is needed for staining and destaining steps; (iii) since these probes using substrate specificity/target proteases, they are excellent tools for detection and discrimination of unknown protease inhibitors for various target proteases.