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. 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.
Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland. minkiew@uwm.edu.pl.
Piotr
P
Minkiewicz
Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland. darewicz@uwm.edu.pl.
Małgorzata
M
Darewicz
Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland. ami@uwm.edu.pl.
Anna
A
Iwaniak
Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland. jolanta_sokolowska133@wp.pl.
Jolanta
J
Sokołowska
Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland. pointer86@wp.pl.
Piotr
P
Starowicz
Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland. justyna.bucholska@uwm.edu.pl.
Justyna
J
Bucholska
Department of Food Biochemistry, University of Warmia and Mazury in Olsztyn, Plac Cieszyński 1, Olsztyn-Kortowo 10-726, Poland. monika.protasiewicz@uwm.edu.pl.
Monika
M
Hrynkiewicz
D000485:Allergens / Q000737:chemistry / Q000276:immunology; D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D000818:Animals; D015415:Biomarkers; D030562:Databases, Protein; D000939:Epitopes / Q000737:chemistry / Q000276:immunology; D005524:Food Technology; D006801:Humans; D013058:Mass Spectrometry / Q000379:methods; D010455:Peptides / Q000737:chemistry / Q000276:immunology; D020543:Proteome; D040901:Proteomics / Q000379:methods
D000485:Allergens; D015415:Biomarkers; D000939:Epitopes; D010455:Peptides; D020543:Proteome
allergens; biologically active peptides; biomarkers; databases; epitopes