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

• Autorzy: Dziuba M. , Minkiewicz P. , Dabek M.

Warianty tytułu

PL

Peptydy, produkty specyficznej proteolizy jako molekularne markery alergennych białek - badania in silico

• Języki publikacji: EN

Abstrakty

EN

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 - TPEVD- DEALEKFDKALKALPMHIR (β-Lg: fragment 141-164), chicken egg - AAVSVDCSEYPKPDCTAEDRPL (ovomucoid: 156-177), wheat - KCNGTVEQVESIVNTLNAGQIASTDVVEVWSPPY (triose phosphate isomerase: 12-46) and peanuts - QARQLKNNNPFKFFVPPFQQSPRAVA (arachin: 505-530). The results are annotated in the BIOPEP database of allergenic proteins and epitopes, available at http://www.uwm.edu. pl/biochemia. The epitope-receptor interactions are attributed to the epitope’s sequence and suggest that in silico proteolysis products showing the highest degree of sequence identity with an epitope or its part are characteristic of a given protein or a group of cross-reactive homologs. The protein markers from basic food groups were proposed based on the above assumption.

PL

Celem przeprowadzonych badań była charakterystyka produktów specyficznej proteolizy białek alergennych jako molekularnych biomarkerów ich obecności w żywności. Wykorzystano sekwencje białek i epitopów znajdujące się w bazie BIOPEP oraz przeprowadzono symulację proteolizy w tej bazie. Użyto programów BLAST i FASTA do przeszukiwania zasobów bazy UniProt. Wytypowano biomarkery białek żywności, między innymi: serwatkowych - TPEVDDEALEKFDKALKALPMHIR (fr. b-Lg 141-164), jaja kurzego - AAVSVDCSEYPKPDCTAEDRPL (fr. owomukoidu 156-177), pszenicy - KCNGTVEQVESI- VNTLNAGQIASTDWEWVSPPY (fr. izomerazy fosforanu triozy 12-46) i orzeszków arachidowych - QARQLKNNNPFKFFVPPFQQSPRAVA (fr. arachin 505-530). Wyniki zostały zamieszczone w podbazie alergennych białek i ich epitopów bazy BIOPEP dostępnej na stronie http://www.uwm.edu.pl/biochemia. Specyficzność biologicznego oddziaływania epitopu z receptorem wynika między innymi z określonej chemicznej struktury tego epitopu. Na tej podstawie przyjęto, że produkty proteolizy in silico białek alergennych, nakładające się maksymalnie z sekwencjami epitopów, są charakterystyczne dla grup białek alergennych.

• Wydawca: -
• Czasopismo: Acta Scientiarum Polonorum. Technologia Alimentaria
• Rocznik: 2013
• Tom: 12
• Numer: 1
• Opis fizyczny: p.101-112,fig.,ref.

Twórcy

autor

Dziuba M.

• Chair of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszynski 1, 10-726 Olsztyn, Poland

autor

Minkiewicz P.

• Chair of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszynski 1, 10-726 Olsztyn, Poland

autor

Dabek M.

• Chair of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszynski 1, 10-726 Olsztyn, Poland

Bibliografia

• Agabriel C., Robert R, Bongrand P., Sarles J., Vitte J., 2010. Fish allergy: In Cyp c 1 we trust. Allergy 65, 1483-1484.
• Al-Shahib A., Misra R., Ahmod N., Fang M., Shah H., Gharbia S., 2010. Coherent pipeline for biomarker discovery using mass spectrometry and bioinformatics. BMC Bioinformatics 11, art. no. 437.
• Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J., 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
• Ansari P., Stoppacher N., Rudolf J., Schuhmacher R., Baumgartner S., 2011. Selection of possible marker peptides for the detection of major ruminant milk proteins in food by liąuid chromatography-tandem mass spectrometry. Anal. Bioanal. Chem. 399, 1105-1115.
• Besler M., 2001. Determination of allergens in foods. Trends Anal. Chem. 20, 662-672.
• Bucholska J., 2012. Identification of markers of potential allergens and bioactive peptides present in fish proteins. Univ. Warmia Mazury Olsztyn, Poland.
• Cuollo M., Caira S., Fierro O., Pinto G., Picariello G., Addeo F., 2010. Toward milk speciation through the monitoring of casein proteotypic peptides. Rapid Commun. Mass Spectr. 24, 1687-1696.
• Dziuba J., Iwaniak A., 2006. Database of Protein and Bioactive Peptide Sequences. In: Nutraceutical proteins and peptides in health and disease. Eds Y. Mine, F. Shahidi. CRC - Taylor & Francis Boca Raton, 543-563.
• Dziuba M., Dziuba B., 2010. In Silico analysis of bioactive peptides. In: Bioactive proteins and peptides as functional foods and nutraceuticals. Eds Y. Mine, E.C.Y. Li- -Chan, B. Jiang. Blackwell Publ. Oxford, UK, 324-340.
• Faeste C.K, Ronnin H.T., Christians U., Granum P.E., 2011. Liquid chromatography and mass spectrometry in food allergen detection. J. Food Protect. 74, 316-345.
• Federhen S., 2012. The NCBI taxonomy database. Nucleic AcidsRes. 40, 136-143.
• Gendel S.M., 2009. Allergen databases and allergen semantics. Reguł. Toxicol. Pharmacol. (3 Suppl.) 54, 7-10.
• Ivanciuc O., Schein C., Garcia T., Oezguen N., Negi S.S., Braun W., 2009. Structural analysis of linear and conformational epitopes of allergens. Regul. Toxicol. Pharmacol. (3 Suppl.) 54, 11-19.
• Kanduc D., 2008. Correlating low-similarity peptide sequences and allergenic epitopes. Curr. Pharmaceut. Design. 14, 289-295.
• King T.P., Hoffman D., Lowenstein H., Marsh D.G., Platts- -Mills T.A.E., Thomas W., 1995. Allergen nomencla- ture. J. Aller. Clin. Immunol. 96, 5-14.
• Kleter G.A., Peijnenburg A.A., 2002. Screening of transgenic proteins expressed in transgenic food crops for the presence of short amino acid sequences identical to potential, IgE-binding linear epitopes of allergens. BMC Struct. Biol. 2, 8.
• Korber B., LaBute M., Yusim K., 2006. Immunoinformatics comes of age. PLoS Comput. Biol. 2, 484-492.
• Mari A., Rasi C., Palazzo P., Scala E., 2009. Allergen databases: current status and perspectives. Curr. Aller. Asthma Rep. 9, 376-383.
• Martinez Barrio A., Soeria-Atmadja D., Nistér A., Gustafsson M.G., Hammerling U., Bongcam-Rudloff E., 2007. EYALLER: a web server for in silico assessment of potential protein allergenicity. Nucleic Acids Res. 35, 694-700.
• Minkiewicz R, Dziuba J., Darewicz M., Bucholska J., Mogut D., 2012. Evaluation of in silico prediction possibility of potential epitope seąuences using experimental data conceming allergenic food proteins summarized in BIOPEP database. Pol. J. Food Nutr. Sci. 62,151-157.
• Minkiewicz P., Dziuba J., Gładkowska-Balewicz I., 2011. 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. Pol. J. Food Nutr. Sci. 61, 153-158.
• Minkiewicz P., Dziuba J., Iwaniak A., Dziuba M., Darewicz M., 2008. BIOPEP database and other programs for processing bioactive peptide sequences. J. AOAC Int. 91,965-980.
• Mogut D., 2012. Identification of peptidic markers of allergenic milk proteins. Univ. Warmia Mazury Olsztyn, Poland [in press],
• Monaci L., Losito I., Palmisano F., Visconti A., 2010. Identification of allergenic milk proteins markers in fined white wines by capillary liquid chromatography-elec- trospray ionization-tandem mass spectrometry. J. Chromatogr.A, 1217, 4300-4305.
• Nakamura R., Teshima R., Talagi K., Sawada J.I., 2005. Development of Allergen Database for Food Safety (ADFS): an integrated database to search allergens and predict allergenicity. Buli. Natl. Inst. Health Sci. 123, 32-36.
• Pearson W.R., 2000. Flexible sequence similarity searching with the FASTA3 program package. Methods Mol. Biol. 132, 185-219.
• Picariello G., Mamone G., Addeo F., Ferranti P., 2011. The frontiers of mass spectrometry-based techniques in food allergenomics. J. Chromatogr. A, 1218, 7386-7398.
• Radauer C., Bublin M., Wagner S., Mari A., 2008. Allergens are distributed into few protein families and possess a restricted number of biochemical functions. I. Aller. Clin. Immunol. 121, 847-852.
• Saha S., Raghava G.P.S., 2006. AlgPred: prediction of allergenic proteins and mapping of IgE epitopes. Nucleic Acids Res. 34, 202-209.
• Sayers E.W., Barrett T., Benson D.A., Bolton E., Bryant S.H., Canese K., et al., 2012. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 40, 13-25.
• Schnell S., Herman R.A., 2009. Should digestion assays be used to estimate persistence of potential allergens in tests for safety of novel food proteins? Clin. Mol. Allergy 7, art. no. 1.
• The UniProt Consortium, 2012. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 40, 71-75.
• Tomar N., De R.K., 2010. Immunoinformatics: An integrated scenario. Immunology 131, 153-168.
• Vita R., Zarębski L., Greenbaum J.A., Emami H., Hoof I., Salimi N., Damble R., Sette A., Peters B., 2010. The Immune Epitope Database 2.0. Nucleic Acids Res. 38, 854-862.
• Wickham M., Faulks R., Mills C., 2009. In vitro digestion methods for assessing the effect of food structure on allergen breakdown. Mol. Nutr. Food Res. 53, 952-958.

Uwagi

PL

Rekord w opracowaniu