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Int. J. Mol. Sci. 2015, 16(9), 20748-20773; doi:10.3390/ijms160920748

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

Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland
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Author to whom correspondence should be addressed.
Academic Editor: Bing Yan
Received: 7 July 2015 / Revised: 18 August 2015 / Accepted: 24 August 2015 / Published: 1 September 2015
(This article belongs to the Collection Advances in Proteomic Research)
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Abstract

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. An individual linear epitope may also be present in multiple sequences of precursor proteins. Although recent recommendations for prediction of allergenicity and cross-reactivity include not only sequence identity, but also similarities in secondary and tertiary structures surrounding the common fragment, local sequence identity may be used to screen protein sequence databases for potential allergens in silico. The main weakness of the screening process is that it overlooks allergens and cross-reactivity cases without identical fragments corresponding to linear epitopes. A single peptide may also serve as a marker of a group of allergens that belong to the same family and, possibly, reveal cross-reactivity. This review article discusses the benefits for food scientists that follow from the common subsequences concept. View Full-Text
Keywords: allergens; biologically active peptides; biomarkers; epitopes; databases allergens; biologically active peptides; biomarkers; epitopes; databases
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Minkiewicz, P.; Darewicz, M.; Iwaniak, A.; Sokołowska, J.; Starowicz, P.; Bucholska, J.; Hrynkiewicz, M. Common Amino Acid Subsequences in a Universal Proteome—Relevance for Food Science. Int. J. Mol. Sci. 2015, 16, 20748-20773.

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