Piotr Minkiewicz

University of Warmia and Mazury in Olsztyn · Department of Food Biochemistry

We live in the Big Data Era which affects many aspects of science, including research on bioactive peptides derived from foods, which during the last few decades have been a focus of interest for scientists. These two issues, i.e., the development of computer technologies and progress in the discovery of novel peptides with health-beneficial proper...

The aim of this publication is to discuss role and examples of applications and challenges for computer tools applied in food peptidomics, research area merging proteomics and metabolomics, focused on the entire set of peptides in a raw material or product. It encompasses the characterization of a peptidome, its properties, bioactivity and fate dur...

The BIOPEP-UWM database has recently become a standard tool supporting food peptidomics. The BIOPEP-UWM website provides an access to the databases annotating the following groups of compounds: proteins, bioactive peptides, allergenic proteins and their epitopes, sensory peptides and amino acids, peptides with bioactivity predicted in silico as wel...

Citation: Hrynkiewicz, M.; Iwaniak, A.; Minkiewicz, P.; Darewicz, M.; Płonka, W. Analysis of Structure-Activity Relationships of Food-Derived DPP IV-Inhibitory Di-and Tripeptides Using Interpretable Descriptors. Appl. Sci. 2023, 13, 12935. This study aimed to analyze the structural requirements for di- and tripeptides exhibiting a DPP IV-inhibitor...

Bovine casein is one of the most known precursors of bioactive peptides among food proteins. Thus far in silico investigations addressing casein took no account of the impact of modifications of amino acid residues on the feasibility of bioactive peptide release. The present study aimed to determine the effect of such modification on the possibilit...

Citation: Szymczak, M.; Kamiński, P.; Turło, M.; Bucholska, J.; Mogut, D.; Minkiewicz, P.; Mizielińska, M.; Stobińska, M. Effect of Marinating Abstract: The temperature has a significant effect on cathepsin activity, but the effect of temperature on the ripening of marinades, and the formation of protein hydrolysis products, is less studied than ot...

In recent years, peptides have spurred increased interest as one of the most important classes of bioactive food components [...]

The aim of this study was to characterize the digests and peptides derived from oat kernel proteins in terms of their major enzyme inhibitory activities related to the prevention of cardiomet-abolic syndrome. It also entailed the characteristics of antioxidant bioactivity of the analyzed material. The study was carried out using coupled in silico a...

For many years, proteins and peptides have been attracting scientists’ attention as two of the most important classes of food components [...]

This study is the first to present an integrated approach involving in silico and in vitro protocols that was pursued to analyse an antioxidative potency of Gouda cheese with modified content of β-casein. Firstly, the predictions of the presence of antioxidant peptides in the casein sequences were computed using the BIOPEP-UWM database. Then, the a...

The novel BIOPEP-UWM Virtual database is designed as a repository of peptide sequences whose bioactivity or taste information was the result of in silico predictions. It is a tool complementary to the existing BIOPEP-UWM database summarizing the results of experimental data on bioactive peptides. The layout and organization of the new database are...

The aim of the study presented here was to determine if there is a correlation between the presence of specific protein domains within tree nut allergens or tree nut allergen epitopes and the frequency of bioactive fragments and the predicted susceptibility to enzymatic digestion in allergenic proteins from tree nuts of cashew (Anacardium occidenta...

One of the strategies for detecting allergens in food is application of peptide markers, which are fragments of polypeptide chains of allergenic proteins. Stability of such markers during food processing (including heating) is an important criterion of their selection. The aim of the study was to identify fragments of tropomyosins, that are detecta...

The contemporary scientific world more often uses the information found in databases of molecules. It is the result of the progress in the development of information technologies and the huge amounts of data requiring to be stored, categorized, and classified. This chapter presents the general overview of databases including their classification an...

In silico and in vitro methods were used to analyze ACE- and DPP-IV-inhibiting potential of Gouda cheese with a modified content of beta-casein. Firstly, the BIOPEP-UWM database was used to predict the presence of ACE and DPP-IV inhibitors in casein sequences. Then, the following Gouda cheeses were produced: with decreased, increased, and normative...

Phosphorylation represents one of the most important modifications of amino acids, peptides, and proteins. By modifying the latter, it is useful in improving the functional properties of foods. Although all these substances are broadly annotated in internet databases, there is no unified code for their annotation. The present publication aims to de...

The potential of collagens to release biopeptides was evaluated using the BIOPEP-UWM-implemented quantitative criteria including the frequency of the release of fragments with a given activity by selected enzyme(s) (AE), relative frequency of release of fragments with a given activity by selected enzyme(s) (W), and the theoretical degree of hydroly...

The aim of this study was to analyze soybean proteins as sources of peptides likely to be bitter using fragmentomic and hybrid approaches involving in silico and in vitro studies. The bitterness of peptides (called parent peptides) was theoretically estimated based on the presence of bitter-tasting motifs, particularly those defined as bitter-tasti...

The aim of this study was to employ a hybrid approach combined with a fragmentomic idea of research used to analyze bovine milk protein hydrolysates as a source of peptides with a potential bitter taste. Firstly, selected sequences of bovine milk proteins were in silico hydrolyzed using bromelain, ficin, papain, and proteinase K. Hydrolysis was sim...

Współczesny świat boryka się z problemami, które zagrażają bezpieczeństwu żywnościowemu, m.in.: malejącymi zasobami wody, wysokimi kosztami produkcji białka zwierzęcego i wzrostem liczby ludności. Poszukuje się surowców żywnościowych, których produkcja/hodowla będzie tania, wydajna i jednocześnie dostarczająca ludziom odpowiedniej ilości składników...

The BIOPEP-UWM™ database of bioactive peptides (formerly BIOPEP) has recently become a popular tool in the research on bioactive peptides, especially on these derived from foods and being constituents of diets that prevent development of chronic diseases. The database is continuously updated and modified. The addition of new peptides and the introd...

Since the definition of bioactive peptides has been firstly published, the knowledge about these molecules is still being improved. It stems from the progress in research methods development including, e.g., the achievements of the bio-and cheminformatics. Hence, other protocols are used to analyze biopeptides apart from the classical (experimental...

Forward and backward stepwise regression (FR and BR, respectively) was applied for the structure–bioactivity prediction of angiotensin converting enzyme (ACE)-inhibitory/bitter-tasting dipeptides. The datasets used in this study consisted of 28 sequences and numerical variables reflecting dipeptides’ physicochemical nature. The data were acquired f...

Diet is considered to be a significant factor in cancer prevention and therapy. Many food components reveal anticancer activity. The increasing number of experiments concerning the anticancer potential of chemical compounds, including food components, is a challenge for data searching. Specialized databases provide an opportunity to overcome this p...

This paper presents the use of principal component analysis (PCA) to study the effect of specific physicochemical attributes on bitterness of di- and tripeptides originating from food proteins. Peptide sequences were derived from the BIOPEP-UWM database of sensory peptides and amino acids. Descriptors defining the physicochemical properties of amin...

Allergies and/or food intolerances are a growing problem of the modern world. Diffi culties associated with the correct diagnosis of food allergies result in the need to classify the factors causing allergies and allergens themselves. Therefore, internet databases and other bioinformatic tools play a special role in deepening knowledge of biologica...

A simple equation to calculate the oxidation states (oxidation numbers) of individual atoms in molecules and ions may be introduced instead of rules associated with words alone. The equation includes two of three categories of bonds, classified as proposed by Goodstein: number of bonds with more electronegative atoms and number of bonds with less e...

Multiple linear regression (MLR) models were constructed to explain the bitter taste of di‐ and tripeptides based on their chemical nature (structure). Sequences (51 di‐ and 51 tripeptides) were derived from the BIOPEP‐UWM database of sensory peptides and amino acids. The measure of their bitterness was Rcaf., that is, bitterness relative to that o...

Metabolic syndrome (MSyn) includes physiological, biochemical, clinical, and metabolic abnormalities, leading to an increase in health problems like obesity, dyslipidemia, cardiovascular diseases, and diabetes, which contribute to an increase in mortality rate. One of the main factors having a key impact on our health is the food we consume. Thus,...

Contemporary peptide science exploits methods and tools of bioinformatics, and cheminformatics. These approaches use different languages to describe peptide structures—amino acid sequences and chemical codes (especially SMILES), respectively. The latter may be applied, e.g., in comparative studies involving structures and properties of peptides and...

W obecnych czasach, gdy wiele osób cierpi na różnego rodzaju alergie i nietolerancje pokarmowe, producenci wychodzą konsumentom naprzeciw i wprowadzają nowe produkty, które oprócz tego, że zaspokajają potrzeby spożywających je osób, są również dla nich bezpieczne i stanowią alternatywę dla tradycyjnych produktów. Produkty, których spożycie niesie z...

Celem pracy było określenie potencjalnej aktywności dipeptydów powstających w wyniku symulowanej proteolizy białek pochodzenia zwierzęcego oraz przydatności poszczególnych baz danych w tego typu analizach. Wykonano symulację proteolizy 14 białek mleka, mięsa i jaj przy pomocy pepsyny (EC 3.4.23.1) (pH = 1,3), trypsyny (EC 3.4.21.4) lub chymotrypsyn...

Celem pracy było określenie stopnia podobieństwa sekwencji oraz potencjalnej reaktywności krzyżowej między kurzą parwalbuminą alfa (łac. Gallus gallus domesticus; UniProt ID: P80026; Gal d 8) a parwalbuminami innych zwierząt za pomocą wybranych narzędzi bioinformatycznych. Analizy podobieństwa sekwencji aminokwasowej kurzej parwalbuminy alfa oraz r...

Smak jest jednym z głównych zmysłów wpływających na jakość żywności oraz decydującym o jej atrakcyjności. O smaku żywności decyduje obecność wielu związków smakowych, w tym peptydy. Analiza składników żywności coraz częściej obejmuje stosowanie metod in silico do przewidywania sposobu „zachowania” biocząsteczek w określonych tj. symulowanych warun...

Carp muscle tissue is a valuable source of biologically active constituents known to positively influence human health. In this study, carp protein digests/hydrolysates generated by human/porcine digestive enzymes were analysed for their angiotensin I-converting enzyme inhibitory (ACEi) activity. The ex vivo digests and in vitro hydrolysates were u...

At present two-dimensional polyacrylamide gel electrophoresis (2-DE) is the most widely used proteomic tool, which enables simultaneous separation of even thousands of proteins with a high degree of resolution. The quality of 2-DE separation depends on the type of biological material used as a protein source. The presence of interfering compounds (...

Internet databases of small molecules, their enzymatic reactions, and metabolism have emerged as useful tools in food science. Database searching is also introduced as part of chemistry or enzymology courses for food technology students. Such resources support the search for information about single compounds and facilitate the introduction of seco...

Biologicznie aktywne peptydy pochodzące z żywności, to fragmenty sekwencji aminokwasowych, które stają się aktywne po ich uwolnieniu z białek prekursorowych. Powstają one podczas procesów trawienia, fermentacji lub procesów prowadzonych in vitro. Z białek ryb wyizolowano szereg peptydów bioaktywnych, w tym m.in. peptydy-inhibitory enzymu konwertują...

Taste is one of the factors based on which the organism makes the selection of what to ingest. It also protects humans from ingesting toxic compounds and is one of the main attributes when thinking about food quality. Five basic taste sensations are recognized by humans: bitter, salty, sour, sweet, and umami. The taste of foods is affected by some...

Peptides and amino acids belong to compounds that influence the taste of foods. The aim of this study was to develop a database of sensory peptides and amino acids. Information about the taste of the analyzed compounds was obtained from sensory studies described in the literature. The database of sensory peptides and amino acids has identical struc...

The objective of this study was to identify fish protein markers for detecting multiple species based on a comparative proteomic approach that relies on fragments with identical sequences. The resulting possibilities and challenges were discussed in view of the results noted for peptides from carp and herring proteins. A bioinformatics analysis was...

The presence of specific peptides with antioxidant properties released during carp protein ex vivo and in vitro hydrolysis by human/porcine digestive enzymes, respectively, were examined. Based on the results of the in silico data analysis, antioxidant peptides were selected for subsequent identification in the digests/hydrolysates. Carp proteins w...

Bioaktywne peptydy obecne w żywności mogą przyczynić się do zmniejszenia występowania chorób przewlekłych. W produktach spożywczych peptydy zazwyczaj są uwalniane poprzez hydrolizę enzymatyczną białek. W pracy przedstawiono wybrane metody analityczne, chemometryczne i bioinformatyczne, stosowane w badaniach molekularnych i biologicznych właściwości...

A common subsequence is a fragment of the amino acid chain that occurs in more than one protein. Common subsequences may be an object of interest for food scientists as biologically active peptides, epitopes, and/or protein markers that are used in comparative proteomics. An individual bioactive fragment, in particular the shortest fragment contain...

Białka żywności charakteryzują się wieloma właściwościami odżywczymi i biologicznymi. Biologicznie aktywne peptydy to fragmenty sekwencji aminokwasowych białek żywności, które stają się aktywne po uwolnieniu. Zwykle są one uwalniane podczas procesów trawienia, fermentacji (dzięki aktywności proteolitycznej mikroorganizmów) lub procesów enzymatyczny...

Bioactive peptides are often studied by applying computer analysis prior to in vitro and in vivo protocols. This has been made possible by progresses in the development of new computer technologies for chemical data processing. The chemical data analysis involves multivariate methods which are the core of chemometrics/cheminformatics. This review p...

Internet databases serve as an important source of information on chemical compounds that students can readily investigate, including those studying food science and food technology. This Activity provides a brief introduction to the application of chemical information resources with a focus on conducting structure-based searches.Keywords: Agricult...

The presence of common epitopes among tropomyosins of invertebrates, including arthropods e.g. edible ones, may help to explain the molecular basis of cross-reactivity between allergens. The work presented is the first survey concerning global distribution of epitopes from Pen a 1.0102 in universal proteome. In the group of known tropomyosin epitop...

In the digestive tract in humans, bioactive peptides, i.e. protein fragments impacting the physiological activity of the body, may be released during the digestion of food proteins, including those of fish. The aim of the study was to establish the method of human ex vivo digestion of carp muscle tissue and evaluate the angiotensin I-converting enz...

Supplement to the publication: The occurrence of sequences identical with epitopes from the allergen Pen a 1.0102 among food and non-food proteins. Piotr Minkiewicz, Jolanta Sokołowska, Małgorzata Darewicz Polish Journal of Food and Nutrition Sciences, 2015, vol. 65, issue 1 DOI: 10.1515/pjfns-2015-0002 List of proteins containing fragments identi...

Streszczenie. Niepożądane reakcje organizmu człowieka związane ze spożyciem żywności to nietolerancje pokarmowe lub alergie. Immunologiczna odpowiedź organizmu na składniki żywności jest wywoływana przez wiele czynników. Alergia objawia się w postaci wielu niespecyfi cznych reakcji. Epitopy białek, odpowiadające za oddziaływania z przeciwciałami dz...

http://www.mdpi.com/1422-0067/15/8/14077 The objectives of the present study were two-fold: first, to detect whether salmon protein fractions possess angiotensin I-converting enzyme (ACE) inhibitory properties and whether salmon proteins can release ACE inhibitory peptides during a sequential in vitro hydrolysis (with commercial porcine enzymes) an...

Białka żywności są źródłem peptydów o różnych aktywnościach biologicznych. Mogą m. in. oddziaływać na funkcjonowanie układu krążenia. Do tej grupy biopeptydów można zaliczyć peptydy obniżające ciśnienie krwi (inhibitory enzymu konwertującego angiotensynę - ACE), przeciwkrzepliwe oraz redukujące poziom cholesterolu. Spośród peptydów o wymienionych a...

Nadciśnienie tętnicze jest chorobą cywilizacyjną występującą u pacjentów na całym świecie, szczególnie w krajach o wysokim poziomie rozwoju gospodarczego. Wpływ na występowanie tej choroby ma wiele czynników, takich jak m. in.: wiek pacjenta, predyspozycje genetyczne, styl życia, masa ciała. Dwa ostatnie związane są dietą. Składnikami żywności, któ...

Milk proteins possess a wide range of nutritional and biological properties. They are used as a source of energy, amino acids, vitamins, and minerals which are needed for the growth and development of organisms. Milk proteins contain physiologically active peptides encrypted in the protein sequences. Peptides with biological activity are produced d...

This work is a literature overview on angiotensin-converting enzyme (ACE) inhibitory/antihypertensive peptides in food protein sources. The following aspects related to peptides with the above-mentioned bioactivity are discussed: (i) mechanism of action of ACE, (ii) the structural character of ACE inhibitors/antihypertensive peptide sequences deter...

Według aktualnych poglądów każde białko, oprócz swej podstawowej funkcji, może pełnić rolę prekursora biologicznie aktywnych peptydów. Bioaktywne motywy w łańcuchach białek są definiowane jako te fragmenty, które pozostają nieaktywne w sekwencjach swoich prekursorów, natomiast po uwolnieniu przez enzymy proteolityczne mogą oddziaływać z odpowiednim...

Bioinformatics and cheminformatics tools such as databases play an increasingly important role in modern science. They are commonly used in biological and medical sciences and they have many applications in food science. Databases listing biologically-active compounds contribute to the design of functional foods and nutraceuticals. Databases of tox...

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. MetaComBio provides links to freely available resources.

The objective of this study was to analyse allergenic proteins by identifying their molecular biomarkers for detection in food using bioinformatics tools. The protein and epitope sequences were from BIOPEP database, proteolysis was simulated using BIOPEP program and UniProt database screening via BLAST and FASTA programs. The biomarkers of food pro...

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 o...

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...

Celem niniejszej pracy było opracowanie metody identyfikacji frakcji niskocząsteczkowych produktów hydrolizy bydlęcej kazeiny-beta przez plazminę za pomocą wysokosprawnej chromatografii cieczowej z odwróconymi fazami (RP-HPLC) w połączeniu ze spektroskopią w nadfiolecie (UV). Bydlęcą kazeinę-beta poddano hydrolizie przez plazminę. Supernatant pozo...

The objective of the present research study was to develop a method to identify low-molecular weight fraction of bovine β-casein hydrolysis products by plasmin using a reversed-phase high-performance liquid chromatography (RP-HPLC) method on-line with an ultraviolet (UV) spectroscopy method. The bovine β-casein was hydrolysed by the plasmin. The su...

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. Ca...

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, suc...

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 multicompo...

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 profile...

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 tha...

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...

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, conducte...

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 th...

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,...

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 a...

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...

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 ac...

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. Proli...

Studies were carried out to identify and detect potentially toxic proteins of wheat. The gliadin fractions were subjected to chromatographic and spectroscopic analyses to develop the relevant discriminants. The spectral analysis showed that these proteins differ considerably in their tryptophan-to-tyrosine molar ratios. A standard curve was used. T...

The aim of the present review was to describe the application of diode-array detectors for the identification of HPLC-separated chemical compounds on the basis of their UV/Vis spectra. Diode-array detectors serve to identify compounds containing conjugated double bonds, especially aromatic compounds, and to evaluate their purity. This group of comp...

Modified ß-casein forms were prepared with acid/alkaline phosphatase. The choice between acid and alkaline phosphatases was critical for the physico-chemical properties of ß-casein. Removal of phosphoryl groups fromß-casein via alkaline phosphatase increased the retention time measured using RP-HPLC and did not change the second-derivative UV spect...

The computer simulation of the distribution of biologically active fragments and bonds which are predicted to be susceptible to the action of endopeptidases of known specificity, hydropathy index and prediction of secondary structures were performed. The average values of hydropathy index calculated for bioactive fragments of selected animal protei...

The concept of this study was based on the assumption that protein standards obtained using the same method may reveal heterogeneity explainable by changes in the disulphide bonding pattern. Two lots of bovine α-lactalbumin standard were subjected to reversed-phase high-performance liquid chromatography (RP-HPLC). One of them was homogenous. The ot...