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Entropy 2009, 11(1), 62-84; doi:10.3390/e11010062

Structural Entropy to Characterize Small Proteins (70 aa) and Their Interactions

1
Department of Bioinformatics and Telemedicine, Collegium Medicum - Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland
2
Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Krakow, Poland
*
Author to whom correspondence should be addressed.
Received: 26 November 2008 / Accepted: 19 February 2009 / Published: 20 February 2009
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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.
Keywords: biological activity; hydrophobicity deficiency; hydrophobicity excess; ligand binding; mutation biological activity; hydrophobicity deficiency; hydrophobicity excess; ligand binding; mutation
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Prymula, K.; Roterman, I. Structural Entropy to Characterize Small Proteins (70 aa) and Their Interactions. Entropy 2009, 11, 62-84.

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