A study of human furin specificity using synthetic peptides derived from natural substrates, and effects of potassium ions

We explored furin substrate requirements in addition to the motif R-X-K/R-R using synthetic fluorescent resonance energy transfer (FRET) decapeptides. These decapeptides were derived from furin cleavage sites in viral coat glycoproteins and human and bacterial protein precursors. The hydrolysis by furin of most substrate was activated by K⁺ ion, whereas kosmotropic anions of the Hofmeister series were inhibitors. The analysis of furin hydrolytic activity showed that its efficiency is highly dependent on the particular combinations of amino acids at different substrate positions. There is a clear interdependence of furin subsites that must be taken in account in determining its specificity and also for the design of inhibitors. However, clear preferences were detected for substrates with S at P₁′, and V at P₂′, at P₃′ the amino acids D, S, L and A are almost equally frequent. In the non-prime subsites the best substrates presented S and H at P₆; basic amino acids at P₅; and no clear tendency at P₃. Interestingly, two amino acid substitutions on the prime side of the peptide derived from H5N1 influenza hemagglutinin furin processing site highly improved its hydrolysis. These modifications are possible by single point mutations, suggesting a potential yield of a more infectious virus.     

Isolation and properties of a metal-dependent endopeptidase from human uterus hydrolysing synthetic collagenase substrates.

A metal-dependent peptidase was isolated from the homogenate of human uterus by standard chromatographic techniques and purified to apparent homogeneity. The peptidase hydrolysed the synthetic vertebrate collagenase substrate 2,4-dinitrophenyl-Pro-Gln-Gly-Ile-Ala-Gly-Gln-D-Arg (Dnp-peptide), the synthetic bacterial collagenase substrate 4-phenylazobenzyloxycarbonyl-Pro-Leu-Gly-Pro-D-Arg (PZ-peptide) and gelatinolytic peptides of gelatin, but was inactive against collagen type I, gelatin and casein. The cleavage site for the Dnp-peptide was the Gly-Ile bond. The enzyme was not only inhibited by metal chelators, such as EDTA, 1,10-phenantroline and dithiothreitol but also by thiol reagents, such as mersalylic acid and N-ethylmaleimid. However, E-64, an inhibitor for thiolproteinases, and leupeptin, an inhibitor for thiol- and serine proteases, did not exhibit any inhibitory activity. Pepstatin, an inhibitor for aspartate proteinases, and inhibitors for serine proteinases like phenylmethanesulfonyl fluoride and Trasylol were ineffective as well. The purified peptidase displayed a single band in the SDS-PAGE with an apparent molecular mass of 65 kDa. Employing isoelectric focusing an IP of 5.0 could be determined. The enzyme's properties are discussed in relation to the proteinase EC 3.4.24.11 and to proteinases of the collagenase family as well as the possibility to discriminate these three metalloproteinase classes by employing the Dnp-peptide.     

A study of hydrolysis of various synthetic peptides with gastrointestinal enzymes using thin-layer chromatography

Hydrolysis in vitro of alpha- and epsilon-peptide bonds of synthetic amino acids and peptide substrates,--models of protein fragments, with digestive enzymes was studied. The kinetics of hydrolysis was studied by quantitative thin-layer chromatography followed by densitometric analysis of the chromatographic patterns. The rate constants of hydrolysis of Phe-Lys, Gly-Lys dipeptides and their epsilon-acetyl and epsilon-succinyl derivatives with leucine aminopeptidase and pancreatic enzymes were calculated. epsilon-Acyl residues of the substrates failed to split off under these conditions. The digestive enzymes hydrolysed the alpha-peptide bonds adjacent to the acylated lysine. Hydrolysis of epsilon-acetyl substrates proceeded faster as compared to epsilon-succinyl derivatives.     

Study of the specificity of human lysosomal glycolipid hydrolases using synthetic fluorogenic substrates

On the basis of o-acylamino-4-methylumbelliferon, a number of beta-galactosides and beta-glucosides have been synthesized. The fluorogenic compounds obtained differ by the length of acyl residues. 6- and 8-hexadecanoylamino-4-methylumbelliferyl-beta-D-galactopyranosides (6-HMGal and 8-HMGal) are shown to be substrates for human galactocerebroside-beta-D-galactosidase. 6-HMGal analogues with shorter acyl residues, octanoyl (OMGal) and butanoyl (BMGal), were cleaved by another type of beta-galactosidase, GM1-ganglioside-beta-galactosidase. It has been established that 6-hexadecanoylamino-4-methylumbelliferyl-beta-D-glucopyranoside (HMGlc) is cleaved by human and animal glucocerebrosidase much slower than its chromogenic analogue (HMGlc). OMGlc did not exceed HNGlc either, though it is cleaved by glucocerebrosidase faster than HMGlc.     

Single cell protein from various chemically pretreated wood substrates using Chaetomium cellulolyticum

The growth behavior of Chaetomium cellulolyticum, a new cellulolytic fungus, has been examined in slurry fermentation systems using various chemically pretreated sawdusts from hardwoods as substrates. Both acid- and alkali-pretreatment methods were used and the fermentation media included the spent pretreatment liquor in an attempt to concurrently maximize substrate utilization and minimize the biological oxygen demand (BOD) level in the process effluent. Diauxic growth patterns were found in the three cases studied, suggesting an initial utilization of soluble hemicellulose sugars followed by utilization of the insoluble cellulose. This behavior patterns was supported by separate growth experiments using the major sugars of hemicellulose as carbon sources. The organism was found to be a good convertor of both cellulose and hemicelluloses into single cell protein (SCP). In terms of rate and extent of protein production in the insoluble biomass product, acid pretreatment appears to be better than alkali pretreatment if the product is intended as ruminant feed.     

Structural properties of the membrane of intact human spermotozoa: A study with fluorescent probes

The properties of the membrane of intact, metabolically active, human persmatozoa have been studied by the use of 1-anilino-8-napthalene sulfonate (ANS). By fluorescence microscopy it was found that at neutral pH ANS is bound exclusively to the membrane of the entire sperm with some preferential binding to the midpiece, while at low pH some preferential binding to the aerosome was observed. By spectrofluorimetry, fluorescence was found to be enhanced 48-fold on binding of ANS to the spermatozoal membrane, with a 50-nm shift in the emission spectrum of the bound dye. $\text{2.47 ± 0.02}$ nmoles of ANS were bound per 10⁶ spermatozoa ($\text{K=2.3–10}{}^{\mathrm{?5}}\text{M}$). Scatchard plots indicate that all the binding sites on the spermatozoal membrane have similar binding characteristics with aZ value of 84.8. Energy transfer with an efficiency of 7% was found for recently ejaculated spermatozoa. The fluorescence of bound ANS depends on the pH of the medium and possibly on the metabolic state of the cell, since addition of succinate or fructose produces an enhancement of fluorescence, while addition of glucose results in a decrease of this parameter. These changes are inhibited by the presence of cyanide.     

Purification and various properties of uracil-DNA-glycosylase from human placenta

Uracil-DNA-glycosylase was isolated from human placenta and purified 2100-fold. The apparent Km value for non-methylated DNA substrate of the enzyme is 3.10(-7) M. However, Km for uracil-DNA-glycosylase was 3 times as low when methylated DNA was used as a substrate. It was shown that the initial rate of uracil excision was greater for the non-methylated than for the hypermethylated DNA. The experimental results indicate that the postreplicative methylation of DNA can interfere with uracil excision.     

Kinetic comparisons of amniotic fluid inactive renin and renal renin using synthetic and human renin substrates

Inactive renin has been isolated from pooled amniotic fluid and purified approximately 642-fold. Prior to activation the isolates had approximately 4% of the activity found after activation. The observation is similar to that reported for inactive renin from chorionic cell culture and suggests a placental origin of amniotic fluid inactive renin. Using plasma from an estrogen-treated woman, renin substrate was recovered free of renin and inactive renin and a portion was separated into NMW and HMW components. The NMW form constituted approximately 93% and the HMW form approximately 7% of the renin substrate. Amniotic fluid inactive renin was used for determinations of enzyme-substrate kinetics with the pooled, NMW, and HMW plasma substrate and tetradecapeptide synthetic substrate, and the results were compared to similar determinations using standard renal renin. Using synthetic substrate, the kinetics of renal renin and amniotic fluid inactive renin before and after activation were similar. The kinetics of renal renin with pooled, NMW, and HMW plasma substrate were also similar. Amniotic fluid inactive renin had a lower Km with pooled than with NMW substrate, however, which resulted from a significantly smaller Km with HMW component. Although the affinity constants with pooled substrate were not different for renin and inactive renin, the Km of inactive renin was significantly less with the HMW component of plasma renin substrate. The observations are compatible with a role for placental inactive renin in normal pregnancy and suggest the possibility of a further role in hypertensive pregnancy.     

High-throughput kinase assays with protein substrates using fluorescent polymer superquenching

Background  

High-throughput screening is used by the pharmaceutical industry for identifying lead compounds that interact with targets of pharmacological interest. Because of the key role that aberrant regulation of protein phosphorylation plays in diseases such as cancer, diabetes and hypertension, kinases have become one of the main drug targets. With the exception of antibody-based assays, methods to screen for specific kinase activity are generally restricted to the use of small synthetic peptides as substrates. However, the use of natural protein substrates has the advantage that potential inhibitors can be detected that affect enzyme activity by binding to a site other than the catalytic site. We have previously reported a non-radioactive and non-antibody-based fluorescence quench assay for detection of phosphorylation or dephosphorylation using synthetic peptide substrates. The aim of this work is to develop an assay for detection of phosphorylation of chemically unmodified proteins based on this polymer superquenching platform.     

Properties of human chorion neuraminidase

Some properties of human chorion neuraminidase were studied. Using n-butanol, a solubilized preparation of neuraminidase with specific activity considerably exceeding the initial activity of the chorion homogenate was obtained. The pH-dependence and substrate specificity of the enzyme towards low molecular weight (sialylglycolipids and sialylglycoproteins) native substrates were examined. These properties of solubilized neuraminidase from human chorion were found to be similar to those of the lysosomal enzyme from other animal tissues. The results abtained are consistent with the properties of neuraminidase from native chorion and amniotic fluid cell cultures. Based on the substrate specificity of the solubilized enzyme, it was found that chorion biopsy specimens could be used for prenatal diagnosing of sialidoses and mucolipidoses IV. Some properties of solubilized human chorion beta-galacotosidase were studied.     

Cleavage specificity on synthetic peptide substrates of human rhinovirus 2 proteinase 2A.

Proteinase 2A of human rhinovirus serotype 2 (HRV2 2A) was expressed in Escherichia coli and partially purified; the preparation was used to study various enzymatic parameters. Using a 16-amino acid peptide representing the native cleavage region of HRV2 2A, an apparent Km value of 5.4 x 10(-4) mol/liter was determined. A minimum of 9 amino acids (comprising residues P8 to P1') was necessary for cleavage to occur. Proteolysis of substituted peptides was highly tolerant toward changes at P1, P2', and P3' but an absolute requirement for glycine P1' and a high preference for threonine P2 was found. Furthermore, HRV2 2A only cleaved peptide substrates derived from other rhinovirus serotypes and poliovirus that possessed P2 Thr and P1' Gly. Thus, the sequence Thr-X-Gly may form the basis of the cellular cleavage site processed by rhinoviral 2As during viral replication. Studies with various inhibitors support the hypothesis that HRV2 2A belongs to a new class of cysteine proteinases.     

Design and synthesis of fluorescent substrates for human tyrosyl-DNA phosphodiesterase I

Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a DNA repair enzyme that acts upon protein–DNA covalent complexes. Tdp1 hydrolyzes 3′-phosphotyrosyl bonds to generate 3′-phosphate DNA and free tyrosine in vitro. Mutations in Tdp1 have been linked to patients with spinocerebellar ataxia, and over-expression of Tdp1 results in resistance to known anti-cancer compounds. Tdp1 has been shown to be involved in double-strand break repair in yeast, and Tdp1 has also been implicated in single-strand break repair in mammalian cells. Despite the biological importance of this enzyme and the possibility that Tdp1 may be a molecular target for new anti-cancer drugs, there are very few assays available for screening inhibitor libraries or for characterizing Tdp1 function, especially under pre-steady-state conditions. Here, we report the design and synthesis of a fluorescence-based assay using oligonucleotide and nucleotide substrates containing 3′-(4-methylumbelliferone)-phosphate. These substrates are efficiently cleaved by Tdp1, generating the fluorescent 4-methylumbelliferone reporter molecule. The kinetic characteristics determined for Tdp1 using this assay are in agreement with the previously published values, and this fluorescence-based assay is validated using the standard gel-based methods. This sensitive assay is ideal for kinetic analysis of Tdp1 function and for high-throughput screening of Tdp1 inhibitory molecules.     

Synthesis and properties of fluorescent nucleotide substrates for DNA-dependent RNA polymerases.

A new class of fluorescent nucleotide analogs which contain the fluorophore 1-aminonaphthalene-5-sulfonate attached via a gamma-phosphoamidate bond has been synthesized. Both the purine and pyrimidine analogs have fluorescence emission maxima at 460 nm. Cleavage of the alpha-beta-phosphoryl bond produces change in both the absorption and fluorescence emission spectra. The fluorescence of the pyrimidine analogs is quenched; cleavage of the alpha-beta-phosphoryl bond of the UTP analog produces about a 14-fold increase in fluorescence intensity at 500 nm. Under the same conditions the fluorescence of the CTP analog increases about 8-fold, whereas the fluorescence of the purine analogs shows only a slight change. These derivatives are good substrates for Escherichia coli RNA polymerase with only slightly increased Km values and with Vmax values about 50 to 70% that of the normal nucleotides. They are used less efficiently by wheat germ RNA polymerase II. The ATP analog can be used by E. coli RNA polymerase to initiate RNA chains.     

A sensitive colorimetric assay for various proteases using naphthyl ester derivatives as substrates

A convenient and highly sensitive colorimetric assay for various proteases, such as trypsin, chymotrypsin, plasmin, thrombin, and urokinase is described. The substrates used are alpha-naphthyl ester derivatives of N alpha-tosyl-L-lysine, N alpha-acetylglycyl-L-ination of alpha-naphthol released from them. Use of these alpha-naphthyl ester derivatives made the method more sensitive than the use of the corresponding methyl or ethyl ester derivatives. The minimum detectable concentrations of trypsin, chymotrypsin, plasmin, thrombin and urokinase in this method were about 0.002 micrograms, 0.01 microgram, 0.002 CU, 0.01 IU, and 2 IU, respectively. The Km values of trypsin and thrombin for TLNE were 0.11 mM and 0.15 mM while those for TLME were 2.5 mM and 6.7 mM, respectively; the Km values of chymotrypsin for ATNE and ATEE were 0.18 mM and 0.7 mM, respectively; and the Km values of urokinase for AGLNE and AGLME were 0.17 mM and 4 mM, respectively. Zymograms of various proteases were easy to prepare using these alpha-naphthyl ester substrates, and zymograms of trypsin and chymotrypsin were made with TLNE and ATNE, respectively, as substrates.     

Genetic diversity among Geotrichum candidum strains from various substrates studied using RAM and RAPD-PCR

AIMS: Assessment of genetic diversity within the species Geotrichum candidum and development of tools to trace the strains that play an important role in the agro food industry. METHODS AND RESULTS: RAM-PCR and RAPD-PCR techniques were assessed for their ability to discriminate 57 strains of various morphotypes, substrates and geographical origin. The techniques were complementary and, when combined, allowed us to discriminate isolates. Moreover, we established a link between a taxon and its occupation of an ecological niche, which should not be confused with the substrate of isolation. CONCLUSIONS: We observed a high degree of diversity, which could be linked to the variety of the ecological niches chosen and to the high degree of morphological polymorphism encountered within the species. SIGNIFICANCE AND IMPACT OF THE STUDY: Used in combination, RAM-PCR and RAPD-PCR permit traceability and monitoring systems for G. candidum strains during food processing.     

New ribose-modified fluorescent analogs of adenine and guanine nucleotides available as substrates for various enzymes

The synthesis of fluorescent derivatives of nucleosides and nucleotides, by reaction with isatoic anhydride in aqueous solution at mild pH and temperature, yielding their 3'-O-anthraniloyl derivatives, is here described. The N-methylanthraniloyl derivatives were also synthesized by reaction with N-methylisatoic anhydride. Upon excitation at 330-350 nm these derivatives exhibited maximum fluorescence emission at 430-445 nm in aqueous solution with quantum yields of 0.12-0.24. Their fluorescence was sensitive to the polarity of the solvent; in N,N-dimethylformamide the quantum yields were 0.83-0.93. The major differences between the two fluorophores were the longer wavelength of the emission maximum of the N-methylanthraniloyl group and its greater quantum yield in water. All anthraniloyl derivatives, as well as the N-methylanthraniloyl ones, had virtually identical fluorescent properties, regardless of their base structures. The ATP derivatives showed considerable substrate activity as a replacement of ATP with adenylate kinase, guanylate kinase, glutamine synthetase, myosin ATPase and sodium-potassium transport ATPase. The ADP derivatives were good substrates for creatine kinase and glutamine synthetase (gamma-glutamyl transfer activity). The GMP and adenosine derivatives were substrates for guanylate kinase and adenosine deaminase, respectively. All derivatives had only slightly altered Km values for these enzymes. While more fluorescent in water, the N-methylanthraniloyl derivatives were found to show relatively low substrate activities against some of these enzymes. The results indicate that these ribose-modified nucleosides and nucleotides can be versatile fluorescent substrate analogs for various enzymes.