Specificity assay of serine proteinases by reverse-phase high-performance liquid chromatography analysis of competing oligopeptide substrate library

Camel whey protein with enhanced antioxidative and antimicrobial properties upon simulated gastro-intestinal digestion

Background: Whey proteins and their peptide derivatives have attracted a great attention of researchers in the pharmaceutical and nutritional fields, due to their numerous bio-functionalities. Aim: In the present research study, enzymatic protein hydrolysates (CWPHs) from camel whey proteins (CWPs) were produced and investigated for their antioxidant and antimicrobial potentials. Methods: Herein, Pepsin (gastric), and Trypsin and Chymotrypsin (pancreatic) enzymes were used to produce CWPHs. The obtained hydrolysates were characterize to ascertain the level of protein degradation and studies on their antimicrobial and antioxidant potential were conducted. Results: Among all CWPHs, a complete degradation of all different protein bands was perceived with Chymotrypsin-derived CWPHs, whereas, light bands of serum albumin and α-lactalbumin were observed with Trypsin and Pepsin-derived CWPHs. After enzymatic degradation, both CWPHs antioxidant and antimicrobial activities were improved. Chymotrypsin-derived CWPHs demonstrated higher DPPH and ABTS radical scavenging activities, anent the increase in proteolysis time. Compared to unhydrolyzed CWPs, higher metal chelating activities were displayed by Trypsin-derived CWPHs. No significant increase in the FRAP activities was noticed after CWPs hydrolysis using Trypsin and Chymotrypsin, while Pepsin-derived CWPHs showed higher reducing power. In terms of antimicrobial activity, significantly higher bacterial growth inhibition rates were exhibited by CWPHs compared to the unhydrolyzed CWP. Conclusion: Overall, CWPHs displayed enhanced antioxidative and antimicrobial properties.

Digestion, absorption, and transport properties of soy-fermented douchi hypoglycemic peptides VY and SFLLR under simulated gastrointestinal digestion and Caco-2 cell monolayers

Two novel hypoglycemic peptides VY and SFLLR were identified from douchi as the major peptides responsible for the glucose uptake activity. The present work aimed to elucidate their digestion, absorption and transport properties using simulated digestion and Caco-2 cell monolayers transport models. Besides, the effects of digestion and absorption on the structure and activity were also studied. The results showed that VY was resistant to gastrointestinal tract digestion and could cross Caco-2 cell monolayers intactly via both TJs-mediated passive paracellular pathway and PepT1-mediated active route. In comparison, SFLLR was partially degraded into small fragments of SFLL, SFL, and SF by the digestive system, leading to increased glucose uptake activity. Notably, SFLLR, SFLL, and SFL were partly hydrolyzed by aminopeptidase N or dipeptidyl peptidase IV during transport, but they were transported intact. SFL was transported via both paracellular diffusion and PepT1-mediated routes, while SFLLR and SFLL were via paracellular route only.

Antioxidant and cytoprotective effect of peptides produced by hydrolysis of whey protein concentrate with trypsin

Whey protein is one of the most relevant co-products manufactured by the dairy industry and it is a powerful environmental pollutant. Therefore, the enzymatic hydrolysis of whey protein concentrate (WPC 35) to produce antioxidant peptides is an innovative approach which can provide added value to whey. The WPC 35 hydrolysis with trypsin was carried out for 4.31 h at 41.1 °C with an enzyme/substrate ratio of 0.017. Under such hydrolysis conditions, the peptides produced have the highest radical scavenging activity and cytoprotector effect. The WPC hydrolysate and a permeate ≤3 kDa were characterized by SDS-page, RP-HPLC and MALDI-TOF-MS. Furthermore, O₂^•- and HO^• scavenging activity and the cytoprotective effect against a stress agent in epithelial cells of the rat ileum (IEC-18) were determined. In this study, strong antioxidant and cytoprotective peptides were obtained from a low-cost dairy industry product, which could improve consumers' health when used as functional ingredients.

Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion

Rapid digestion by proteases limits the application of peptides as therapeutics. One strategy to increase the proteolytic stability of peptides is the modification with fluorinated amino acids. This study presents a systematic investigation of the effects of fluorinated leucine and isoleucine derivatives on the proteolytic stability of a peptide that was designed to comprise substrate specificities of different proteases. Therefore, leucine, isoleucine, and their side-chain fluorinated variants were site-specifically incorporated at different positions of this peptide resulting in a library of 13 distinct peptides. The stability of these peptides towards proteolysis by α-chymotrypsin, pepsin, proteinase K, and elastase was studied, and this process was followed by an FL-RP-HPLC assay in combination with mass spectrometry. In a few cases, we observed an exceptional increase in proteolytic stability upon introduction of the fluorine substituents. The opposite phenomenon was observed in other cases, and this may be explained by specific interactions of fluorinated residues with the respective enzyme binding sites. Noteworthy is that 5,5,5-trifluoroisoleucine is able to significantly protect peptides from proteolysis by all enzymes included in this study when positioned N-terminal to the cleavage site. These results provide valuable information for the application of fluorinated amino acids in the design of proteolytically stable peptide-based pharmaceuticals.

Single-Walled Carbon Nanotube Dispersion in Tryptic Soy Broth

There has been little research on the dispersion of carbon nanotubes in dispersions of standard microbiological media. We report that tryptic soy broth (TSB) containing casein digest disperses single-walled carbon nanotubes (SWNT) at concentrations similar to those achieved in lysozyme (LSZ), one of the best known biomolecular SWNT dispersants. Similar to LSZ, the proposed mechanism for SWNT dispersion in TSB is favorable π-π stacking interactions with l-tryptophan. This is supported by similar SWNT concentrations in both LSZ and TSB supernatants, and the absence of appreciable dispersion in TSB that does not contain a source of l-tryptophan. Since l-tryptophan alone is insufficient to enable dispersion, it was previously hypothesized that LSZ's macromolecular structure created steric hindrance that was critical for SWNT dispersion. These new results show that intermediately sized l-tryptophan containing species can also enable dispersion. In addition, since TSB is a commonly used growth medium for microbiological research, its dispersive ability presents new research avenues for studying the effect of SWNT on prokaryotic cells without the need to oxidize SWNT or add dispersants that may induce microbial stress.

Process optimisation for preparation of caseinophosphopeptides from Buffalo milk casein and their characterisation

Caseinophosphopeptides (CPPs) are multifunctional bioactive peptides containing phosphorylated seryl residues in their sequence. In the present study, method for the production of CPPs from buffalo milk casein was optimised and characterised for their sequence, calcium solubilising and calcium binding activities. Response surface methodology was used to optimise the conditions for hydrolysis of buffalo casein by trypsin to obtain maximum yield of CPPs. The optimum hydrolysis conditions were as follows: hydrolysis pH 7·5, temperature 37 °C, hydrolysis time 7·0 h. Under these conditions, the experimental yield obtained was 10·04±0·24%, which is slightly lower than value predicted by the model. These CPPs were able to solubilise 1·03±0·08 mg la/mg CPPs in presence of excess phosphate and bind 0·935 mg of Ca/mg of CPPs. Eight phosphopeptides i.e. αs1-CN f (37-58) 2P; αs1-CN f (37-58) 3P; αs1-CN f (35-58) 2P; αs1-CN f (35-58) 3P; αs2-CN f (2-21) 4P; αs2-CN f (138-149) 1P; β-CN f (2-28) 4P and β-CN f (33-48) 1P were identified by LC-MS/MS which contained motif for binding of divalent minerals. The sequences of these CPPs differed from that of derived from bovine casein.

Improvement of the antimicrobial and antioxidant activities of camel and bovine whey proteins by limited proteolysis

The compositions and structures of bovine and camel milk proteins are different, which define their functional and biological properties. The aim of this study was to investigate the effects of enzymatic hydrolysis of camel and bovine whey proteins (WPs) on their antioxidant and antimicrobial properties. After enzymatic treatment, both the antioxidant and the antimicrobial activities of bovine and camel WPs were improved. The significantly higher antioxidant activity of camel WPs and their hydrolysates as compared with that of bovine WPs and their hydrolysates may result from the differences in amounts and/or in accessibilities of antioxidant amino acid residues present in their primary structures and from the prevalence of alpha-lactalbumin and beta-lactoglobulin as proteolytic substrates in camel and bovine whey, respectively. The results of this study reveal differences in antimicrobial and antioxidant activities between WP hydrolysates of bovine and camel milk and the effects of limited proteolysis on these activities.

Functional group and substructure searching as a tool in metabolomics

Background

A direct link between the names and structures of compounds and the functional groups contained within them is important, not only because biochemists frequently rely on literature that uses a free-text format to describe functional groups, but also because metabolic models depend upon the connections between enzymes and substrates being known and appropriately stored in databases.

Methodology

We have developed a database named “Biochemical Substructure Search Catalogue” (BiSSCat), which contains 489 functional groups, >200,000 compounds and >1,000,000 different computationally constructed substructures, to allow identification of chemical compounds of biological interest.

Conclusions

This database and its associated web-based search program (http://bisscat.org/) can be used to find compounds containing selected combinations of substructures and functional groups. It can be used to determine possible additional substrates for known enzymes and for putative enzymes found in genome projects. Its applications to enzyme inhibitor design are also discussed.

MapQuant: Open-source software for large-scale protein quantification

Whole-cell protein quantification using MS has proven to be a challenging task. Detection efficiency varies significantly from peptide to peptide, molecular identities are not evident a priori, and peptides are dispersed unevenly throughout the multidimensional data space. To overcome these challenges we developed an open-source software package, MapQuant, to quantify comprehensively organic species detected in large MS datasets. MapQuant treats an LC/MS experiment as an image and utilizes standard image processing techniques to perform noise filtering, watershed segmentation, peak finding, peak fitting, peak clustering, charge-state determination and carbon-content estimation. MapQuant reports abundance values that respond linearly with the amount of sample analyzed on both low- and high-resolution instruments (over a 1000-fold dynamic range). Background noise added to a sample, either as a medium-complexity peptide mixture or as a high-complexity trypsinized proteome, exerts negligible effects on the abundance values reported by MapQuant and with coefficients of variance comparable to other methods. Finally, MapQuant's ability to define accurate mass and retention time features of isotopic clusters on a high-resolution mass spectrometer can increase protein sequence coverage by assigning sequence identities to observed isotopic clusters without corresponding MS/MS data.

A self-stabilized model of the chymotrypsin catalytic pocket. The energy profile of the overall catalytic cycle

A model of the catalytic triad of chymotrypsin is built assuring the arrangement and properties as they are within the complete enzyme. The model contains 18 amino acid residues of chymotrypsin and its substrate. A total of 135 atoms (including 70 heavy atoms) were subjected to full ab initio geometry optimizations through 127 individual steps along the reaction coordinate of the complete catalytic mechanism. It was shown that the described model of the catalytic apparatus forms a self-stabilized molecule ensemble without the rest of the enzyme and substrate. According to the calculations, the formations of the first and second tetrahedral intermediates in the model have 20.3 and 15.7 kcal/mol activation energy barriers, respectively. Removing elements of the catalytic apparatus such as the (1) catalytic aspartate or (2) the anion hole, as well as (3) inserting a water molecule "early" in the catalytic process, or (4) introducing conformational rigidity of the substrate, results in an increase of the above energy barrier of the first catalytic step in the model by 6.4, 13.7, 3.7, and 4.1 kcal/mol, respectively. Based on the calculated process one can conclude that the catalytic reaction in this model is much more similar to the reaction in the enzyme than to the reference reaction. To our knowledge, this is the first model system that mimics the complete catalytic mechanism.

Crystallographic and biochemical investigations of kumamolisin-As, a serine-carboxyl peptidase with collagenase activity

Kumamolisin-As (previously called ScpA) is the first known example of a collagenase from the sedolisin family (MEROPS S53). This enzyme is active at low pH and in elevated temperatures. In this study that used x-ray crystallographic and biochemical methods, we investigated the structural basis of the preference of this enzyme for collagen and the importance of a glutamate residue in the unique catalytic triad (Ser(278)-Glu(78)-Asp(82)) for enzymatic activity. Crystal structures of the uninhibited enzyme and its complex with a covalently bound inhibitor, N-acetyl-isoleucyl-prolyl-phenylalaninal, showed the occurrence of a narrow S2 pocket and a groove that encompasses the active site and is rich in negative charges. Limited endoproteolysis studies of bovine type-I collagen as well as kinetic studies using peptide libraries randomized at P1 and P1', showed very strong preference for arginine at the P1 position, which correlated very well with the presence of a negatively charged residue in the S1 pocket of the enzyme. All of these features, together with those predicted through comparisons with fiddler crab collagenase, a serine peptidase, rationalize the enzyme's preference for collagen. A comparison of the Arrhenius plots of the activities of kumamolisin-As with either collagen or peptides as substrates suggests that collagen should be relaxed before proteolysis can occur. The E78H mutant, in which the catalytic triad was engineered to resemble that of subtilisin, showed only 0.01% activity of the wild-type enzyme, and its structure revealed that Ser(278), His(78), and Asp(82) do not interact with each other; thus, the canonical catalytic triad is disrupted.

Mutant rat trypsin selectively cleaves tyrosyl peptide bonds

A double mutant of rat trypsinogen (Asp189Ser, DeltaAsp223) was constructed by site-directed mutagenesis. The recombinant protein was produced in Escherichia coli under the control of a periplasmic expression vector. The purified and enterokinase-activated enzyme was characterized by synthetic fluorogenic tetrapeptide and natural polypeptide substrates and by a recently developed method. In case of this latter method the specificity profile of the enzyme was examined by simultaneous digestion of a mixture of oligopeptide substrates each differing only at the P(1) site residue, and the results were analyzed by high-performance liquid chromatography. All these assays unanimously demonstrated that the recombinant proteinase lacks trypsin-like activity but acquired a rather unique selectivity: it preferentially hydrolyses peptide bonds C-terminal to tyrosyl residues. This narrow specificity should be useful in peptide-analytical applications such as sequence-specific fragmentation of large proteins prior to sequencing.

Regulation of the yeast amphiphysin homologue Rvs167p by phosphorylation

The yeast amphiphysin homologue Rvs167p plays a role in regulation of the actin cytoskeleton, endocytosis, and sporulation. Rvs167p is a phosphoprotein in vegetatively growing cells and shows increased phosphorylation upon treatment with mating pheromone. Previous work has shown that Rvs167p can be phosphorylated in vitro by the cyclin-dependent kinase Pho85p complexed with its cyclin Pcl2p. Using chymotryptic phosphopeptide mapping, we have identified the sites on which Rvs167p is phosphorylated in vitro by Pcl2p-Pho85p. We have shown that these same sites are phosphorylated in vivo during vegetative growth and that phosphorylation at two of these sites is Pcl-Pho85p dependent. In cells treated with mating pheromone, the MAP kinase Fus3p is needed for full phosphorylation of Rvs167p. Functional genomics and genetics experiments revealed that mutation of other actin cytoskeleton genes compromises growth of a strain in which phosphorylation of Rvs167p is blocked by mutation. Phosphorylation of Rvs167p inhibits its interaction in vitro with Las17p, an activator of the Arp2/3 complex, as well as with a novel protein, Ymr192p. Our results suggest that phosphorylation of Rvs167p by a cyclin-dependent kinase and by a MAP kinase is an important mechanism for regulating protein complexes involved in actin cytoskeleton function.

Natural substrates and inhibitors of mannan-binding lectin-associated serine protease-1 and -2: a study on recombinant catalytic fragments

Mannan-binding lectin-associated serine protease (SP) (MASP)-1 and MASP-2 are modular SP and form complexes with mannan-binding lectin, the recognition molecule of the lectin pathway of the complement system. To characterize the enzymatic properties of these proteases we expressed their catalytic region, the C-terminal three domains, in Escherichia coli. Both enzymes autoactivated and cleaved synthetic oligopeptide substrates. In a competing oligopeptide substrate library assay, MASP-1 showed extreme Arg selectivity, whereas MASP-2 exhibited a less restricted, trypsin-like specificity. The enzymatic assays with complement components showed that cleavage of intact C3 by MASP-1 and MASP-2 was detectable, but was only approximately 0.1% of the previously reported efficiency of C3bBb, the alternative pathway C3-convertase. Both enzymes cleaved C3i 10- to 20-fold faster, but still at only approximately 1% of the efficiency of MASP-2 cleavage of C2. We believe that C3 is not the natural substrate of either enzyme. MASP-2 cleaved C2 and C4 at high rates. To determine the role of the individual domains in the catalytic region of MASP-2, the second complement control protein module together with the SP module and the SP module were also expressed and characterized. We demonstrated that the SP domain alone can autoactivate and cleave C2 as efficiently as the entire catalytic region, while the second complement control protein module is necessary for efficient C4 cleavage. This behavior strongly resembles C1s. Each MASP-1 and MASP-2 fragment reacted with C1-inhibitor, which completely blocked the enzymatic action of the enzymes. Nevertheless, relative rates of reaction with alpha-2-macroglobulin and C1-inhibitor suggest that alpha-2-macroglobulin may be a significant physiological inhibitor of MASP-1.