Glycosylation of proteins in healthy and pathological human renal tissues

Cancer development is connected with improper glycosylation of proteins. There are alterations in synthesis and expression of sugar structures. These changes can be important not only at early steps of tumor development but also in next stages connected with cancer invasiveness and its ability to form metastases. Oligosaccharide structures of glycans in tumors deviate from normal cells. Particularly relatively increased degrees of branching and sialylation of N-glycans, enhanced presentation of short-chain mucin-type O-glycans with sialylation and alterations in the expression of blood group ABO and Lewis epitopes can be observed. The main aim of our study was to assess changes in glycosylation of proteins in healthy, intermediate and cancer renal tissues. The study was performed on tissues taken from 15 clinical patients. The relative amounts of sugar structures of proteins with molecular mass above 30 kDa were determined by ELISA test with biotinylated lectins highly specific to proper sugar antigens. Higher expresion of all examined structures was revealed in cancer tissues. Increased levels of sialic acid, fucose, T and Tn antigens, in comparison with healthy state, are characteristic alterations of cancers cell

Programi i baze podataka o peptidima i proteolitičkim enzimima na internetu – kratak osvrt na 2007. i 2008. godinu

Bioinformatics methods have become one of the most important tools in peptide science. The number of available peptide databases is growing rapidly. The number of online programs able to process peptide sequences to extract information concerning their structure, physicochemical and biological properties is also increasing. Many of such programs were designed to manipulate protein sequences, but they have no built-in restrictions disabling their application to process oligopeptides containing less than 20 amino acid residues. Publications addressing these programs cannot be found in literature databases using the keyword \u27peptide\u27 or \u27peptides\u27, in connection with the term \u27bioinformatics\u27 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 properties of amino acid residues, prediction of peptide structure, the occurrence of posttranslational 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.Bioinformatičke metode postale su jedan od najvažnijih alata u području istraživanja peptida. Sve je veći broj dostupnih baza podataka o peptidima, a i „online” programa koji obradom aminokiselinskih sljedova daju informacije o strukturi peptida te njihovim fizikalno-kemijskim i biološkim svojstvima. Mnogi od tih programa dizajnirani su za obradu aminokiselinskih sljedova proteina, ali nemaju ugrađenu restrikciju njihove primjene na oligopeptide koji sadrže manje od 20 aminokiselinskih ostataka. Radovi o takvim programima ne mogu se pronaći u bazama publikacija uporabom ključnih riječi „peptid” ili „peptidi”, u kombinaciji s pojmom „bioinformatika” ili sličnim terminima. Stoga je važno sažeti rezultate objavljenih radova u jednom izvoru. U ovom je radu dan kratak pregled baza podataka o bioaktivnim peptidima i programima za analizu aminokiselinskoga slijeda koji omogućuju: pronalazak peptidnih motiva; određivanje fizikalno-kemijskih svojstava aminokiselinskih ostataka; predviđanje strukture peptida, pojave posttranslacijske glikozilacije i imunogenosti; te programsku podršku za dizajn peptida. Također su prikazani programi i baze podataka o proteolitičkim enzimima. Svi navedeni programi i baze razvijeni su i ažurirani od rujna 2007. do prosinca 2008

Analiza peptida iz hrane

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.Ovaj revijalni prikaz razmatra definiciju pojma „food peptidomics“, tj. istraživanje peptida iz hrane i njihovu ulogu u prehrambenoj tehnologiji i nutricionizmu. Slično živim organizmima, „peptidome“ hrane obuhvaća sve peptide u prehrambenom proizvodu ili sirovini, a i one proizvedene tijekom prerade i/ili njihova skladištenja. Ova grana znanosti obuhvaća istraživanje podrijetla peptida, dinamičnosti njihove promjene pri preradi i/ili skladištenju, utjecaja peptida, njihova sastava i promjene sastava na svojstva prehrambenih proizvoda i sirovina, te metode istraživanja. To uključuje ispitivanje njihove biološke aktivnosti, funkcionalnih, alergenskih i senzorskih svojstava, informacije o autentičnosti i porijeklu proizvoda ili izvora, te povijesni razvoj i odnose. U radu su opisane metode istraživanja peptida, s posebnim naglaskom na računske metode

Analiza peptida iz hrane

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.Ovaj revijalni prikaz razmatra definiciju pojma „food peptidomics“, tj. istraživanje peptida iz hrane i njihovu ulogu u prehrambenoj tehnologiji i nutricionizmu. Slično živim organizmima, „peptidome“ hrane obuhvaća sve peptide u prehrambenom proizvodu ili sirovini, a i one proizvedene tijekom prerade i/ili njihova skladištenja. Ova grana znanosti obuhvaća istraživanje podrijetla peptida, dinamičnosti njihove promjene pri preradi i/ili skladištenju, utjecaja peptida, njihova sastava i promjene sastava na svojstva prehrambenih proizvoda i sirovina, te metode istraživanja. To uključuje ispitivanje njihove biološke aktivnosti, funkcionalnih, alergenskih i senzorskih svojstava, informacije o autentičnosti i porijeklu proizvoda ili izvora, te povijesni razvoj i odnose. U radu su opisane metode istraživanja peptida, s posebnim naglaskom na računske metode

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. Salmon proteins were degraded more efficiently by porcine enzymes than by human gastrointestinal juices and sarcoplasmic proteins were digested/hydrolyzed more easily than myofibrillar proteins. The ex vivo digested myofibrillar and sarcoplasmic duodenal samples showed IC50 values (concentration required to decrease the ACE activity by 50%) of 1.06 and 2.16 mg/mL, respectively. The in vitro hydrolyzed myofibrillar and sarcoplasmic samples showed IC50 values of 0.91 and 1.04 mg/mL, respectively. Based on the results of in silico studies, it was possible to identify 9 peptides of the ex vivo hydrolysates and 7 peptides of the in vitro hydrolysates of salmon proteins of 11 selected peptides. In both types of salmon hydrolysates, ACE-inhibitory peptides IW, IY, TVY and VW were identified. In the in vitro salmon protein hydrolysates an ACE-inhibitory peptides VPW and VY were also detected, while ACE-inhibitory peptides ALPHA, IVY and IWHHT were identified in the hydrolysates generated with ex vivo digestion. In our studies, we documented ACE inhibitory in vitro effects of salmon protein hydrolysates obtained by human and as well as porcine gastrointestinal enzymes

BIOPEP-UWM Virtual—A Novel Database of Food-Derived Peptides with In Silico-Predicted Biological Activity

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 identical to those of the existing BIOPEP-UWM database of bioactive peptides. The peptide data record includes the following information: name; sequence and function information (understood as information about the predicted target biomacromolecule); bibliographic data with the reference paper describing the peptide; additional information, including the peptide structure, annotated using chemical codes as well as the specification of the method used for bioactivity prediction; information about other activities discovered experimentally or predicted using computational methods; peptide taste (if available); and a database reference tab providing information about compound annotations in other databases (if available)

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.g., in comparative studies involving structures and properties of peptides and peptidomimetics. Progress in peptide science “in silico” may be achieved via better communication between biologists and chemists, involving the translation of peptide representation from amino acid sequence into SMILES code. Recent recommendations concerning good practice in chemical information include careful verification of data and their annotation. This publication discusses the generation of SMILES representations of peptides using existing software. Construction of peptide structures containing unnatural and modified amino acids (with special attention paid on glycosylated peptides) is also included. Special attention is paid to the detection and correction of typical errors occurring in SMILES representations of peptides and their correction using molecular editors. Brief recommendations for training of staff working on peptide annotations, are discussed as well

BIOPEP-UWM Virtual—A Novel Database of Food-Derived Peptides with In Silico-Predicted Biological Activity

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 identical to those of the existing BIOPEP-UWM database of bioactive peptides. The peptide data record includes the following information: name; sequence and function information (understood as information about the predicted target biomacromolecule); bibliographic data with the reference paper describing the peptide; additional information, including the peptide structure, annotated using chemical codes as well as the specification of the method used for bioactivity prediction; information about other activities discovered experimentally or predicted using computational methods; peptide taste (if available); and a database reference tab providing information about compound annotations in other databases (if available)

Quantitative In Silico Evaluation of Allergenic Proteins from Anacardium occidentale, Carya illinoinensis, Juglans regia and Pistacia vera 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 (Anacardium occidentale), pecan (Carya illinoinensis), English walnut (Juglans regia) and pistachio (Pistacia vera) 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. Proteins possessing a vicilin, N-terminal family domain, or napin domain contain a relatively low occurrence of bioactive fragments. In contrast, proteins possessing the cupin 1 domain without the vicilin N-terminal family domain contain a relatively high total frequency of bioactive fragments and predicted release of bioactive fragments by the joint action of pepsin, trypsin, and chymotrypsin. This approach could be utilized in food science to simplify the selection of protein domains enriched for bioactive peptides

Rainbow trout proteins as potential source of biologically active peptides

Bioaktywne peptydy pochodzące z białek żywności mogą pełnić funkcje regulatorów układu sercowo-naczyniowego, nerwowego czy pokarmowego. Do najlepiej znanych bioaktywnych peptydów należą fragmenty białek o właściwościach przeciwnadciśnieniowych, z których większość to inhibitory enzymu konwertującego angiotensynę I (inhibitory ACE). Celem badań było określenie profilu potencjalnej aktywności biologicznej wybranych białek pstrąga tęczowego (Oncorhynchus mykiss) przy użyciu narzędzi bioinformatycznych dostępnych w bazie BIOPEP. Materiał i metody. Sekwencje aminokwasowe 7 białek pochodzących z tkanki mięśniowej pstrąga pobrano z bazy danych UniProt. Dla każdej z wybranych sekwencji wyznaczono częstotliwość występowania biologicznie aktywnych fragmentów (parametr A) oraz potencjalną aktywność biologiczną (parametr B) białek. Następnie przeprowadzono symulowaną proteolizę in silico z wykorzystaniem 6 enzymów proteolitycznych. Wyniki. Największą liczbę sekwencji biopeptydów (1999) zidentyfikowano w kolagenie pstrąga, w tym najwięcej fragmentów o aktywności inhibitora ACE. Białko to charakteryzowało się największą wartością parametrów A (0,7316) i B (0,1651) dla peptydów o aktywności inhibitora ACE ze wszystkich przebadanych sekwencji. Ficyna i papaina uwalniały największą liczbę bioaktywnych fragmentów z badanych białek pstrąga tęczowego. Wnioski. Na podstawie otrzymanych wyników można stwierdzić, że kolagen jest najbogatszym źródłem peptydów bioaktywnych z przebadanych sekwencji aminokwasowych białek pstrąga tęczowego. Ficyna i papaina mogą być wykorzystane do produkcji hydrolizatów lub peptydów o potencjalnej aktywności biologicznej z tkanki mięśniowej pstrąga.Bioactive peptides derived from food proteins are considered as regulators of the cardiovascular, nervous, and digestive systems. Peptides with antihypertensive activity are the best recognized bioactive peptides, of which angiotensin I-converting enzyme inhibitors (ACE inhibitors) are the most known. The aim of presented study was to determine the profile of the potential biological activity of a selected rainbow trout (Oncorhynchus mykiss) protein using bioinformatics tools from the Bioactive Proteins and Peptides database – BIOPEP. Material and methods. Amino acid sequences of 7 proteins originated from trout meat tissue were taken from the UniProt database. The frequency of occurrence of bioactive fragments in protein sequence (parameter A) and potential biological activity of protein (parameter B) were determined for all selected proteins using a procedure built into the BIOPEP database. Then, in silico proteolysis was performed using 6 proteolytic enzymes, which acted separately. Results. It was found that the largest number of bioactive peptides sequences (1,999) was hidden in trout collagen, including the largest number of ACE inhibitors. Collagen was characterized by the highest value of the parameter A (0.7316) and B (0.1651) for fragments with ACE inhibitory activity. Ficin and papain released the largest number of bioactive fragments from the trout proteins tested. Conclusions. Based on these results, it can be concluded that collagen is the richest source of bioactive peptides when compared with the trout proteins studied. Ficin and papain can be used to produce hydrolysates or peptides with potential biological activity from trout meat tissue