BIOPEP-PBIL Tool for the Analysis of the Structure of Biologically Active Motifs Derived from Food Proteins
Anna Iwaniak* and Jerzy Dziuba
University of Warmia and Mazury in Olsztyn, Chair of Food Biochemistry, Pl. Cieszynski 1, PL-10-726 Olsztyn-Kortowo, Poland
Article history:
Received January 21, 2010
Accepted May 26, 2010
Key words:
databases, proteins, bioactive peptides, bioinformatics
Summary:
This work describes a flexible technique for the analysis of protein sequences as a source of motifs affecting bodily functions. The BIOPEP database, along with the Pôle Bioinformatique Lyonnais (PBIL) server, were applied to define which activities of peptides dominated in their protein precursors and which structure of the protein contained the most of the revealed activities. Such an approach could be helpful in finding some structural requirements for peptide(s) to be regarded as biologically active (bioactive). It was found that apart from the activities of peptides that commonly occur in the majority of proteins (e.g. ACE inhibitors), all analyzed proteins can be a source of motifs involved in e.g. activation of ubiquitin-mediated proteolysis. This could be important in designing diets for patients who suffer from neural diseases. The structure and bioactivity analyses revealed that if peptides were to be 'bioactive', it is essential that they assume the position of a coil (or combination of coil and α-helix) in the sequence of their protein precursors. However, it is recommended to consider the factors such as the length of peptide chains, the number of peptides in the database as well as the repeatability of the occurrence of characteristic amino acids, both in the peptide and in the protein when studying the bioactivity and structure of biomolecules.
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