Bioinformatics and bioactive peptides from foods: Do they work together?

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.

Multi-Bioactivity of Protein Digests and Peptides from Oat ( L.) Kernels in the Prevention of the Cardiometabolic Syndrome.

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 cardiometabolic syndrome. It also entailed the characteristics of antioxidant bioactivity of the analyzed material. The study was carried out using coupled in silico and in vitro methods.

An integrated approach to the analysis of antioxidative peptides derived from Gouda cheese with a modified β-casein content.

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 antioxidative bioactivity of six variants of Gouda cheese (with reduced, normative, and increased content of β-casein at the initial and final stage of ripening) was assessed.

Quantitative In Silico Evaluation of Allergenic Proteins from , , and and Their Epitopes as Precursors of Bioactive Peptides.

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 (), pecan (), English walnut () and pistachio () plants. These bioactive peptides are distributed along the length of the protein and are not enriched in IgE epitope sequences. Classification of proteins as bioactive peptide precursors based on the presence of specific protein domains may be a promising approach.

Gouda Cheese with Modified Content of β-Casein as a Source of Peptides with ACE- and DPP-IV-Inhibiting Bioactivity: A Study Based on In Silico and In Vitro Protocol.

In silico and in vitro methods were used to analyze ACE- and DPP-IV-inhibiting potential of Gouda cheese with a modified content of β-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 content of β-casein after 1 and 60 days of ripening each (six variants in total).

Proposal of the Annotation of Phosphorylated Amino Acids and Peptides Using Biological and Chemical Codes.

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.

Characteristics of Biopeptides Released In Silico from Collagens Using Quantitative Parameters.

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) (A), relative frequency of release of fragments with a given activity by selected enzyme(s) (W), and the theoretical degree of hydrolysis (DH). Cow, pig, sheep, chicken, duck, horse, salmon, rainbow trout, goat, rabbit, and turkey collagens were theoretically hydrolyzed using: stem bromelain, ficin, papain, pepsin, trypsin, chymotrypsin, pepsin+trypsin, and pepsin+trypsin+chymotrypsin. Peptides released from the collagens having comparable A and W were estimated for their likelihood to be bioactive using PeptideRanker Score.

BIOPEP-UWM Database of Bioactive Peptides: Current Opportunities.

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 introduction of new information about the existing ones (e.

Understanding the nature of bitter-taste di- and tripeptides derived from food proteins based on chemometric analysis.

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 R , that is, bitterness relative to that of 1 mM caffeine solution (R  = 1.

Structure⁻Activity Prediction of ACE Inhibitory/Bitter Dipeptides-A Chemometric Approach Based on Stepwise Regression.

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 from the BIOPEP-UWM, Biological Magnetic Resonance Databank, ProtScale, and AAindex databases.

Free Accessible Databases as a Source of Information about Food Components and Other Compounds with Anticancer Activity⁻Brief Review.

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.

Peptides Derived from Foods as Supportive Diet Components in the Prevention of Metabolic Syndrome.

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, scientists work towards the discovery of novel bioactive compounds with therapeutic potential to address MSyn.

Annotation of Peptide Structures Using SMILES and Other Chemical Codes-Practical Solutions.

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.

Food protein-originating peptides as tastants - Physiological, technological, sensory, and bioinformatic approaches.

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.

2-DE Separation and Identification of Oat (Avena sativa L.) Proteins and Their Prolamin Fractions.

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 (e.

The Use of Peptide Markers of Carp and Herring Allergens as an Example of Detection of Sequenced and Non-Sequenced Proteins.

The objective of this study is to identify fish protein markers for detecting multiple species based on a comparative proteomic approach that relies on fragments with identical sequences. The possibilities and challenges of the use of peptides obtained from carp () and herring () proteins are discussed. A bioinformatic analysis was followed by an LC-MS/MS experiment to identify markers predicting the presence of fish allergenic proteins.

Internet Databases of the Properties, Enzymatic Reactions, and Metabolism of Small Molecules-Search Options and Applications in Food Science.

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 secondary analyses of large datasets.

European Carp (Cyprinus carpio L.) Protein-Derived Ex Vivo Digests and In Vitro Hydrolysates Differ in the ACE I Inhibitory Activity and Composition of Released ACE Inhibitory Peptides.

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 used in a screening for ACEi peptides as well.

BIOPEP database of sensory peptides and amino acids.

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.

Antioxidant properties of carp (Cyprinus carpio L.) protein ex vivo and in vitro hydrolysates.

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

Common Amino Acid Subsequences in a Universal Proteome--Relevance for Food Science.

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 containing two or three amino acid residues, may occur in many protein sequences.

Angiotensin I-converting enzyme (ACE) inhibitory activity and ACE inhibitory peptides of salmon (Salmo salar) protein hydrolysates obtained by human and porcine gastrointestinal enzymes.

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) and ex vivo digestion (with human gastrointestinal enzymes). Secondly, to evaluate the ACE inhibitory activity of generated hydrolysates. A two-step ex vivo and in vitro model digestion was performed to simulate the human digestion process.

[Biologically active peptides derived from food proteins as the food components with cardioprotective properties].

Food proteins are the source of peptides with many biological activities. One of them is their impact on blood circulatory system. This group of peptides includes the ones with the ability to reduce the blood pressure (inhibitors of angiotensin converting enzyme--ACE), antithrombotic, and to lower the cholesterol level.

Food-Originating ACE Inhibitors, Including Antihypertensive Peptides, as Preventive Food Components in Blood Pressure Reduction.

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 determined by different methods, including quantitative structure-activity relationship studies, (iii) their food sources, (iv) absorption of peptides, (v) in vitro and in vivo approaches involved in the production and potential release of peptide ACE inhibitors as well as in silico methods applied in research concerning peptides.

Peptides, specific proteolysis products, as molecular markers of allergenic proteins - in silico studies.

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 proteins were proposed: for example for whey proteins - TPEVDDEALEKFDKALKALPMHIR (β-Lg: fragment 141-164), chicken egg - AAVSVDCSEYPKPDCTAEDRPL (ovomucoid: 156-177), wheat - KCNGTVEQVESIVNTLNAGQIASTDVVEVVVSPPY (triose phosphate isomerase: 12-46) and peanuts - QARQLKNNNPFKFFVPPFQQSPRAVA (arachin: 505-530).