Jerzy Dziuba

Bovine Meat Proteins as Potential Precursors of Biologically Active Peptides - a Computational Study based on the BIOPEP Database

The aim of the present study was to perform an in silico evaluation of bovine meat proteins as potential precursors of biologically active peptides, as well as to determine whether such peptides can be released by selected proteolytic enzymes. The sequences of 19 bovine meat proteins were processed using the BIOPEP database and program. The profiles of potential biological activity of protein fragments were determined and the following parameters were calculated: the frequency of occurrence of fragments with given activity (A), the frequency of release of fragments with given activity by selected enzymes (AE), and the relative frequency of release of fragments with given activity by selected enzymes (W). Among the examined proteins, collagen and elastin appear to be the richest potential source of bioactive peptides, in particular of angiotensin-converting enzyme inhibitors, antithrombotic fragments, inhibitors of dipeptidyl peptidase IV and peptides regulating gastric mucosal activity. The high number of bioactive fragments in collagen and elastin is associated with a high content of glycine and proline, amino acids that are most abundant in biologically active fragments. Of the two investigated proteolytic enzymes, Proteinase K — an enzyme with broad specificity (e.g., against peptide bonds formed by the carboxyl groups of proline) can release considerably more biologically active fragments than Proteinase P1 — an enzyme with narrow specificity, not including proline residues.

The Preventive Potential of Milk and Colostrum Proteins and Protein Fragments

This study presents and analyzes the results of in silico, in vitro, and in vivo tests investigating the potential preventive properties of a group of biologically active milk and colostrum proteins and peptides; that is, casein, α-lactalbumin, β-lactoglobulin, lysozyme, lactoferrin, glycomacropeptide, proline-rich peptides, and lactoperoxidase. Casein or its peptides lowers blood pressure, reduces tumor growth, and shows anticoagulant, antimicrobial, and antioxidant activity. Casein hydrolysates decrease the probability of diabetes. α-Lactalbumin and β-lactoglobulin manifest antiviral activity directed against HIV and antibacterial and hypotensive activities. A diet rich in α-lactalbumin has antistress, antidepressive, and anticarcinogenic properties. Lysozyme is used as a supplement in infant formulas and an anti-inflammatory and analgesic agent in neoplastic diseases. Lactoferrin demonstrates an antibacterial, antiviral, fungistatic, antiparasitic, and antithrombotic effect. Glycomacropeptide is characterized by antibacterial, antiviral, and antithrombotic properties. Colostrinin, a proline-rich peptide, is applied in the treatment of neurodegenerative diseases of the brain and autoimmune diseases. Lactoperoxidase is an antimicrobial agent. Studies indicate that milk and colostrum proteins and peptides have many applications in the prevention and treatment of various diseases in patients from all age groups.

Computational Characterisation and Identification of Peptides for in silico Detection of Potentially Celiac-Toxic Proteins

This work reports on in silico analysis of celiac-toxic peptide occurrence in proteins. The toxic properties of celiac disease are linked to the presence of specific amino acid sequences and the properties of their environment. The analysed celiac-toxic peptides were found to be predominated by unordered structures of random coil and β-turns. Proline and glutamine-rich amino acid sequences from hydrophilic β-turns were exposed on the surface of the precursor proteins. The sequence motifs represented by gluten peptide epitopes or tetrapeptides with surroundings seem to represent an immunodominant structure. The application of MS BLAST software enabled identification of a few fragments with high degrees of identity to the toxic peptides in one protein sequence. Rich sources of celiac-disease-potentiating peptides were wheat gliadins, barley hordeins and rye secalins as well as low-molecular weight fractions of glutenin. In addition, amino acid sequences with a high degree of identity to the toxic peptides examined were detected in maize zein, oat avenin, protein of rice, yeast and chicken muscles, as well as β-casein and galanin.

Update of the List of Allergenic Proteins From Milk, Based on Local Amino Acid Sequence Identity with Known Epitopes From Bovine Milk Proteins - a Short Report

Update of the List of Allergenic Proteins From Milk, Based on Local Amino Acid Sequence Identity with Known Epitopes From Bovine Milk Proteins-a Short Report The study involved the screening of protein sequence database nrdb 95 for sequences containing fragments identical with experimentally proven sequential epitopes of bovine milk proteins. Such fragments were found in proteins from milk of the buffalo (Bubalus bubalis), yak (Bos grunniens), goat (Capra hircus) and ewe (Ovis aries). Some proteins, such as α-lactalbumins (from the yak, buffalo and goat) and κ-caseins (from the goat and ewe), have not been previously considered as allergens. They were entered into a new database of allergenic proteins from foods and their epitopes, which is part of the BIOPEP database http://www.uwm.edu.pl/biochemia. The proteins containing fragments identical with linear epitopes from known allergens should also be classified as allergens, based on local sequence identity. The absence of common linear epitopes with known allergens cannot be treated as the evidence that a given protein is not allergenic.

Celiac Disease—Background, Molecular, Bioinformatics and Analytical Aspects

This review summarizes the background of celiac disease (CD), and the available bioinformatic and analytical methods designed to evaluate the molecular aspects of celiac-toxic proteins and peptides. CD is a T-cell-mediated autoimmune disease of the small intestine that is induced by ingestion of gluten proteins from wheat, barley, rye, and, rarely, after consumption of oats. This disease is characterized by malabsorption of nutrients from the intestine. It has been demonstrated that polypeptide chains of gliadin contain repeating amino acid sequences that constitute epitopes for a respective lymphocyte receptor (TCR). It was reported that the optimal length of a polypeptide chain suitable for a TCR is 10 to 15 amino acid residues. Celiac toxic proteins and peptides were characterized by the following methods and techniques: immunochemical, electrophoretic, chromatographic, and mass spectrometric. Characterization of celiac toxic peptides may provide sufficient information to breed out these sequences from wheat, barley or rye, whilst retaining its baking properties. An improved understanding of the immune response to gluten has provided an insight into possible future advances in the treatment of celiac disease.

Proteomic analysis of albumin and globulin fractions of pea (Pisum sativum L.) seeds

BACKGROUND Proteomic analysis is emerging as a highly useful tool in food research, including studies of food allergies. Two-dimensional gel electrophoresis involving isoelectric focusing and sodium dodecyl sulfate polyacrylamide gel electrophoresis is the most effective method of separating hundreds or even thousands of proteins. In this study, albumin and globulin tractions of pea seeds cv. Ramrod were subjected to proteomic analysis. Selected potentially alergenic proteins were identified based on their molecular weights and isoelectric points. MATERIAL AND METHODS Pea seeds (Pisum sativum L.) cv. Ramrod harvested over a period of two years (Plant Breeding Station in Piaski-Szelejewo) were used in the experiment. The isolated albumins, globulins and legumin and vicilin fractions of globulins were separated by two-dimensional gel electrophoresis. Proteomic images were analysed in the ImageMaster 2D Platinum program with the use of algorithms from the Melanie application. The relative content, isoelectric points and molecular weights were computed for all identified proteins. Electrophoregrams were analysed by matching spot positions from three independent replications. RESULTS The proteomes of albumins, globulins and legumin and vicilin fractions of globulins produced up to several hundred spots (proteins). Spots most characteristic of a given fraction were identified by computer analysis and spot matching. The albumin proteome accumulated spots of relatively high intensity over a broad range of pi values of ~4.2-8.1 in 3 molecular weight (MW) ranges: I - high molecular-weight albumins with MW of ~50-110 kDa, II - average molecular-weight albumins with MW of ~20-35 kDa, and III - low molecular-weight albumins with MW of ~13-17 kDa. 2D gel electrophoregrams revealed the presence of 81 characteristic spots, including 24 characteristic of legumin and 14 - of vicilin. CONCLUSIONS Two-dimensional gel electrophoresis proved to be a useful tool for identifying pea proteins. Patterns of spots with similar isoelectric points and different molecular weights or spots with different isoelectric points and similar molecular weights play an important role in proteome analysis. The regions characteristic of albumin, globulin and legumin and vicilin fractions of globulin with typical MW and pi values were identified as the results of performed 2D electrophoretic separations of pea proteins. 2D gel electrophoresis of albumins and the vicilin fraction of globulins revealed the presence of 4 and 2 spots, respectively, representing potentially allergenic proteins. They probably corresponded to vicilin fragments synthesized during post-translational modification of the analysed protein.

Evaluation of In Silico Prediction Possibility of Epitope Sequences Using Experimental Data Concerning Allergenic Food Proteins Summarised in BIOPEP Database

Evaluation of In Silico Prediction Possibility of Epitope Sequences Using Experimental Data Concerning Allergenic Food Proteins Summarised in BIOPEP Database The aim of the study was to evaluate the possibility of predicting potential epitope sequences and location in allergenic proteins from food using EVALLER program by comparison with experimental epitopes summarised in the BIOPEP database of allergenic proteins. Sequences of experimental epitopes from food allergens, present in the BIOPEP database of allergenic proteins were used in the study. Sequences of potential epitopes were found using EVALLER program. The Positive Predictive Value (PPV) has been used as a measure of prediction quality. The potential epitopes fully or partially overlapping with the experimental ones were considered as true positive results whereas these unrelated to the experimental ones as false positive results. The PPV for entire dataset containing 310 potential epitopes was 80.6%. The PPV varied significantly among particular allergen families defined according to the AllFam database. Caseins revealed PPV=100% (with one exception), proteins from tropomyosin family and proteins from papain-like cystein protease family - exceeding 50%. The last two families possess also relatively low frequency of epitope occurrence. The predictive potential was poor (less than 50%) for plant allergens from cupin superfamily. Families such as lipocalins from milk and EF-hand family (parvalbumins) revealed high variability within family. The EVALLER program may be used as a tool for the prediction of epitope location although its potential varies considerably among allergen families. High PPV is associated with a high number of known experimental epitopes (such as in caseins) and/or a high degree of sequence conservation within family (caseins, tropomyosins).