Publications
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    Dataset: Link to MetaComBio website
    Małgorzata Darewicz, Anna Iwaniak, Piotr Minkiewicz
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    ABSTRACT: MetaComBio (Meta Compound Bioactivity) is a website containing links to chemical databases describing carbohydrates, flavor and aroma enhancing compounds, haptens, lipids, toxic compounds and other substances important for food quality and safety.
  • Article: Peptides, specific proteolysis products as molecular markers of allergenic proteins – in silico studies
    Marta Dziuba, Piotr Minkiewicz, Marianna Dąbek
    Acta Scientiarum Polonorum, Technologia Alimentaria 01/2013; 12:101-112.
  • Article: Epitopic hexapeptide sequences from Baltic cod parvalbumin beta (allergen Gad c 1) are common in the universal proteome.
    Piotr Minkiewicz, Justyna Bucholska, Małgorzata Darewicz, Justyna Borawska
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    ABSTRACT: The aim of this study was to analyze the distribution of hexapeptide fragments considered as epitopes of Baltic cod parvalbumin beta (allergen Gad c 1) in the universal proteome. Cod (Gadus morhua subsp. callarias) parvalbumin hexapeptides cataloged in the Immune Epitope Database were used as query sequences. The UniProt database was screened using the WU-BLAST 2 program. The distribution of hexapeptide fragments was investigated in various protein families, classified according to the presence of the appropriate domains, and in proteins of plant, animal and microbial species. Hexapeptides from cod parvalbumin were found in the proteins of plants and animals which are food sources, microorganisms with various applications in food technology and biotechnology, microorganisms which are human symbionts and commensals as well as human pathogens. In the last case possible coverage between epitopes from pathogens and allergens should be avoided during vaccine design.
    Peptides 08/2012; 38(1):105-109. · 2.43 Impact Factor
  • Chapter: Database of biologically active proteins and peptides
    Bartłomiej Dziuba, Piotr Minkiewicz, Małgorzata Darewicz
    01/2012: pages 317-359; , ISBN: 978-1-4200-9341-4
  • Article: Zastosowanie drugich i czwartych pochodnych widm UV do identyfikacji niskocząsteczkowych frakcji produktów hydrolizy kazeiny-beta przez plazminę
    Małgorzata Darewicz, Piotr Minkiewicz, Marta Dziuba, Tomasz Panfil
    Zywnosc: Nauka, Technologia, Jakosc 01/2012; · 0.16 Impact Factor
  • Article: Evaluation of In Silico Prediction Possibility of Epitope Sequences Using Experimental Data Concerning Allergenic Food Proteins Summarised in BIOPEP Database
    Piotr Minkiewicz, Jerzy Dziuba, Małgorzata Darewicz, Justyna Bucholska, Damir Mogut
    [show abstract] [hide abstract]
    ABSTRACT: 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 signifi cantly 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).
    Polish Journal of Food and Nutrition Sciences 01/2012; 62(3):151-157.
  • Article: The Preventive Potential of Milk and Colostrum Proteins and Protein Fragments
    Małgorzata Darewicz, Bartłomiej Dziuba, Piotr Minkiewicz, Jerzy Dziuba
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    ABSTRACT: 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.
    Food Reviews International 10/2011; 27(4):357-388. · 1.45 Impact Factor
  • Article: Bovine meat proteins as potential precursors of biologically active peptides--a computational study based on the BIOPEP database.
    P Minkiewicz, J Dziuba, J Michalska
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    ABSTRACT: 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 (A(E)), 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.
    Food Science and Technology International 02/2011; 17(1):39-45. · 0.68 Impact Factor
  • Article: Determination of theoretical retention times for peptides analyzed by reversed- -phase high-performance liquid chromatography
    Dziuba Jerzy, Minkiewicz Piotr, Mogut Damir
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    ABSTRACT: Background. Peptides are important components of foods mainly due to their biological activity. The basic method of their identification is reversed phase high-performance liquid chromatography coupled with electrospray-ionization mass spectrometry (RP-HPLC-ESI-MS). Retention time (tR) prediction in silico is very helpful in analysis of multicomponent peptide mixtures. One of problems associated with RP-HPLC-ESI-MS is deterioration of mass spectra quality by trifluoroacetic acid (TFA). This problem can be avoided through the use of chromatographic columns designed for work with low TFA concentrations in mobile phase. The objective of this study was to determine the correlations between peptide retention times predicted with the use of a program available on-line and experimental retention times obtained using the column working with low TFA concentrations. Material and methods. The set of synthetic peptides and bovine α-lactalbumin fragments (18 peptides) was used in the experiment. Theoretical retention times were calculated using Sequence Specific Retention Calculator (SSRC) program. The experimental retention times were measured via RP-HPLC-ESI-MS method using column working with low TFA content. The dependence between theoretical and experimental tR was expressed via empirical equations. Results. The best correlation between theoretical and experimental retention times of peptides containing at least four amino acid residues has been obtained when third order polynomial (R² = 0.9536). Prediction quality for di- and tripeptides was significantly lower. The method described can be applied for cysteine-containing peptides although our sample preparation procedure did not include modification of this amino acid, taken into attention by SSRC program. Conclusions. The results of this study validate the usefulness of a third degree polynomial as a simple function describing the correlation between peptide retention times predicted by an on-line application and experimental retention times. The above function can effectively predict retention times in situations when experimental conditions differ from the computational environment (various columns, mobile phase composition, use or resignation from chemical modifications during sample preparation, various HPLC equipments). On-line available tR predicting application with correction based on user’s own data may be a useful tool in food peptidomics.
    Acta Scientiarum Polonorum : Technologia Alimentaria. 01/2011;
  • Article: 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
    Piotr Minkiewicz, Jerzy Dziuba, Izabela Gładkowska-Balewicz
    [show abstract] [hide abstract]
    ABSTRACT: 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 sequenceidentity. The absence of common linear epitopes with known allergens cannot be treated as the evidence that a given protein is not allergenic.
    Polish Journal of Food and Nutrition Sciences 01/2011; 61(2):153-158.
  • Chapter: Milk Proteins
    Jerzy Dziuba, Piotr Minkiewicz, Małgorzata Darewicz, Bartłomiej Dziuba
    01/2010: pages 79-107; , ISBN: 978-1-4200-4631-1
  • Source
    Article: Online Programs and Databases of Peptides and Proteolytic Enzymes–A Brief Update for 2007–2008
    Piotr Minkiewicz, Jerzy Dziuba, Małgorzata Darewicz, Anna Iwaniak, Justyna Michalska
    [show abstract] [hide abstract]
    ABSTRACT: Bioinformatics methods have become one of the most important tools in peptide sci-ence. The number of available peptide databases is growing rapidly. The number of online programs able to process peptide sequences to extract information concerning their struc-ture, physicochemical and biological properties is also increasing. Many of such programs were designed to manipulate protein sequences, but they have no built-in restrictions dis-abling their application to process oligopeptides containing less than 20 amino acid resi-dues. Publications addressing these programs cannot be found in literature databases using the keyword 'peptide' or 'peptides', in connection with the term 'bioinformatics' or related terms, thus a reference source summarizing data from such publications seems necessary. This paper provides a brief review of bioactive peptide databases and sequence alignment programs enabling the search for peptide motifs, determination of physicochemical pro-perties of amino acid residues, prediction of peptide structure, the occurrence of posttrans-lational glycosylation and immunogenicity, as well as the support of peptide design process. The review also includes databases and programs providing information about proteolytic enzymes. The databases and programs discussed in this paper were developed or updated between September 2007 and December 2008.
    Food Technology and Biotechnology 05/2009; 47(4):345-355. · 1.20 Impact Factor
  • Article: Reproducibility of two-dimensional electrophoresis gel image of pea (Pisum sativum L.) seed proteins evaluated using scatter plots – a short report
    Jerzy Dziuba, Piotr Minkiewicz, Dorota Nałęcz, Marta Dziuba, Iwona Szerszunowicz
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    ABSTRACT: The aim of this study was to evaluate plots showing a linear correlation between the parameters characterising protein content in the spots obtained using two-dimensional electrophoresis (scatter plots). The correlation coefficient of normalized spot volume may be used to determine regions with increased reproducibility. In our experiment, conducted using pea seed proteins, the correlation coefficient reached 0.980 in such regions, compared with 0.917 noted for the entire gel surface. The correlation coefficient calculated based on scatter plots may serve as a tool for the preliminary selection of regions characteristic of a given proteome.
    Polish Journal of Food and Nutrition Sciences 01/2009; 59:141-144.
  • Chapter: Otrzymywanie biologicznie i funkcjonalnie aktywnych peptydów
    Piotr Minkiewicz, Jerzy Dziuba
    01/2009: pages 110-140; , ISBN: 978-83-204-3582-5
  • Article: Identification of oat (Avena sativa) and buckwheat (Fagopyrum esculentum) proteins and their prolamin fractions using two-dimensional polyacrylamide gel electrophoresis
    Dorota Nałęcz, Jerzy Dziuba, Piotr Minkiewicz, Marta Dziuba, Iwona Szerszunowicz
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    ABSTRACT: Total (non-fractionated) kernel proteins and the prolamin fraction (soluble in 75% ethanol) were extracted from oat (Avena sativa) var. Flämingstern kernel and from buckwheat (Fagopyrum esculentum) var. Kora kernel. As for buckwheat, extraction was effective only after kernel dehulling which allowed the removal of tannins and phenolic compounds that form complexes with proteins during extraction. The extracted proteins were analyzed using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). Gels of the prolamin fractions of oat and buckwheat were used as reference gels in order to detect prolamins on gels of total kernel proteins. The occurrence of 26 and 29 spots corresponding to prolamins was found on gels of total oat proteins and on gels of total buckwheat proteins, respectively. The electrophoretic images of oat and buckwheat prolamins revealed organized subregions containing spots with similar isoelectric points (pI) and various molecular weights (MW), mostly on oat prolamin gels and spots of similar molecular weights with various isoelectric points, mostly on buckwheat prolamin gels. Such organized subregions can be used as identifiers for the occurrence of prolamin fractions in total proteins (particularly as regards buckwheat proteins).
    European Food Research and Technology 01/2009; 230(1):71-78. · 1.57 Impact Factor
  • Article: Food Peptidomics
    Piotr Minkiewicz, Jerzy Dziuba, Mal/ gorzata Darewicz, Anna Iwaniak, Marta Dziuba, Dorota Nal/eu cz
    [show abstract] [hide abstract]
    ABSTRACT: The aim of this review is to discuss the definition of food peptidomics and highlight the role of this approach in food and nutrition sciences. Similar to living organisms, food peptidome may be defined as the whole peptide pool present in a food product or raw material. This definition also covers peptides obtained during technological processes and/or storage. The area of interest of food peptidomics covers research concerning the origin of peptidome, its dynamic changes during processing and/or storage, the influence of its presence, the composition and changes in the pool of peptides on the properties of food products or raw materials as well as the methods applied in research into this group of compounds. The area of interests of food peptidomics would include biological activity, functional properties, allergenicity, sensory properties and information on the product or resource authenticity and origin as well as its history and relationships. Research methods applied in food peptidomics, with special emphasis on computational methods, are also summarized.
    Food Technology and Biotechnology 01/2008; 46(1):1-10. · 1.20 Impact Factor
  • Article: Biologically active peptides derived from proteins – a review
    Anna Iwaniak, Piotr Minkiewicz
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    ABSTRACT: Proteins play an important role in body functioning. They can also be a good source of peptides with different activities. Such peptides are defined as biologically active (bioactive peptides). Bioactive peptides interact with proper body receptors and such an effect can be beneficial or not. Biopeptides as components of food with desired features have become an interesting issue for scientific research. Many of bioactive peptides are found in milk and dairy products, plant, animal and microbial proteins. They function mainly as inhibitors of the angiotensin converting enzyme but there is a plenty of peptides derived from other sources that can even prevent chronic diseases. This paper focuses on peptides derived from different sources and their physiological role in the body as well as functional aspects of their application in food production. In this article we concentrate on the peptides exerting the following activities: affecting blood pressure, prolyl endopeptidase inhibitors, coeliac toxic, immunomodulating and opioid.
    Polish Journal of Food and Nutrition Sciences 01/2008; 58:289-294.
  • Article: Celiac Disease—Background, Molecular, Bioinformatics and Analytical Aspects
    Małgorzata Darewicz, Jerzy Dziuba, Piotr Minkiewicz
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    ABSTRACT: 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.
    Food Reviews International 01/2008; 24(3):311-329. · 1.45 Impact Factor
  • Article: BIOPEP database and other programs for processing bioactive peptide sequences.
    Piotr Minkiewicz, Jerzy Dziuba, Anna Iwaniak, Marta Dziuba, Małgorzata Darewicz
    [show abstract] [hide abstract]
    ABSTRACT: This review presents the potential for application of computational tools in peptide science based on a sample BIOPEP database and program as well as other programs and databases available via the World Wide Web. The BIOPEP application contains a database of biologically active peptide sequences and a program enabling construction of profiles of the potential biological activity of protein fragments, calculation of quantitative descriptors as measures of the value of proteins as potential precursors of bioactive peptides, and prediction of bonds susceptible to hydrolysis by endopeptidases in a protein chain. Other bioactive and allergenic peptide sequence databases are also presented. Programs enabling the construction of binary and multiple alignments between peptide sequences, the construction of sequence motifs attributed to a given type of bioactivity, searching for potential precursors of bioactive peptides, and the prediction of sites susceptible to proteolytic cleavage in protein chains are available via the Internet as are other approaches concerning secondary structure prediction and calculation of physicochemical features based on amino acid sequence. Programs for prediction of allergenic and toxic properties have also been developed. This review explores the possibilities of cooperation between various programs.
    Journal of AOAC International 01/2008; 91(4):965-80. · 1.20 Impact Factor
  • Article: Proteins as the source of physiologically and functionally active peptides
    Iwaniak Anna, Minkiewicz Piotr
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    ABSTRACT: The market of functional foods and beverages develops dynamically. Biological activities of many food components which occur naturally become an issue of many scientific and industrial interests. The structural and chemical changes occurring during the proteins processing lead to the release of bioactive peptides. Their multifunctional activity is based on their structure and other factors including e.g. hydrophobicity, charge, or microelements binding properties. This article focuses on peptides with other physiological and functional activities such as antithromobotic, antioxidative, antibacterial and antifungal, sensory, and improving those nutritional value of food.
    Acta Scientiarum Polonorum, Technologia Alimentaria 01/2007; 6(3):5-15.
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