COMPUTER DATABASES IN CLASSIFICATION AND CHARACTERISTICS OF PROTEINS AS A SOURCE OF BIOACTIVE PEPTIDES
 
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Pol. J. Food Nutr. Sci. 2010;60(2):139–146
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ABSTRACT:
Classification of proteins as precursors of bioactive peptides is presented in this work. To achieve this aim, the worldwide available computer databases such as BIOPEP, CATH, PDB, and SCOP were applied. The main qualitative criterion to classify the proteins was the integrated coefficient of biological activity of protein (C) defined as a square root of the sum of squares of (A) for different activities divided by the number of activities, where (A) denotes the frequency of occurrence of fragments with a given activity in a protein sequence and is described as the number of fragments with a given activity divided by the number of amino acid residues of a protein chain taken for an analysis. Taking into consideration the coefficient (C) calculated for 126 animal and plant proteins, three families were distinguished. In the family containing proteins - the poorest source of bioactive fragments, were e.g. leguminlike chains of pumpkin, ginkgo biloba isolated from primary endosperm, vicia faba, and faba bean. Proteins being the best source of bioactive fragments (e.g. proteins derived from milk, bovine and chicken meat and wheat) were classified into the 1st family. It was found out that such a family classification is not identical with protein classification according to the criteria proposed and applied in the other computer databases. However, some proteins contained similar bioactive fragments within the sequence chains as well as possessed similar functions or structural motifs (e.g. TIM barrel motif). It can be presumed about the evolutionary similarity of proteins as a source of bioactive peptides.