Structural entropy to characterize small proteins (70 aa) and their interactions

Abstract

Proteins composed of short polypeptide chains (about 70 amino acid residues) participating in ligand-protein and protein-protein (small size) complex creation were analyzed and classified according to the hydrophobicity deficiency/excess distribution as a measure of structural and functional specificity and similarity. The characterization of this group of proteins is the introductory part to the analysis of the so called 'Never Born Proteins' (NBPs) in search of protein compounds of biological activity in pharmacological context. The entropy scale (classification between random and deterministic limits) estimated according to the hydrophobicity irregularity organized in ranking list allows the comparative analysis of proteins under consideration. The comparison of the hydrophobicity deficiency/excess appeared to be useful for similarity recognition, examples of which are shown in the paper. The influence of mutations on structure and hydrophobicity distribution is discussed in detail. © 2009 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.