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“Fuzzy oil drop” model applied to individual small proteins built of 70 amino acids

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Abstract

The proteins composed of short polypeptides (about 70 amino acid residues) representing the following functional groups (according to PDB notation): growth hormones, serine protease inhibitors, antifreeze proteins, chaperones and proteins of unknown function, were selected for structural and functional analysis. Classification based on the distribution of hydrophobicity in terms of deficiency/excess as the measure of structural and functional specificity is presented. The experimentally observed distribution of hydrophobicity in the protein body is compared to the idealized one expressed by a three-dimensional Gauss function. The differences between these two distributions reveal the specificity of structural/functional characteristics of the protein. The residues of hydrophobicity deficiency versus the idealized distribution are assumed to indicate cavities with the potential to bind ligands, while the residues of hydrophobicity excess are interpreted as potentially participating in protein-protein complexation. The distribution of hydrophobicity irregularity seems to be specific for particular structures and functions of proteins. A comparative analysis of such profiles is carried out to identify the potential biological activity of proteins of unknown function.

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Acknowledgments

The Authors are very grateful to Prof. Leszek Konieczny (Institute of Medical Biochemistry - Collegium Medicum - Jagiellonian University - Krakow - Poland) for our fruitful discussion. This research was supported by Collegium Medicum grants 501/P/266/L. This study has also been financially supported by the European Commission in the frame of the EUChinaGRID project (contract number: 026634).

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The tools applied for the calculations presented in this paper are available at http://www.bioinformatics.cm-uj.krakow.pl/activesite.

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Authors and Affiliations

  1. Department of Bioinformatics, Telemedicine Jagiellonian University - Collegium Medicum, Lazarza 16, 31-530, Krakow, Poland

    Katarzyna Prymula, Kinga Sałapa & Irena Roterman

  2. Faculty of Chemistry, Jagiellonian University, Ingardena 3, 30-060, Krakow, Poland

    Katarzyna Prymula

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  1. Katarzyna Prymula
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  2. Kinga Sałapa
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  3. Irena Roterman
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Correspondence to Irena Roterman.

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Prymula, K., Sałapa, K. & Roterman, I. “Fuzzy oil drop” model applied to individual small proteins built of 70 amino acids. J Mol Model 16, 1269–1282 (2010). https://doi.org/10.1007/s00894-009-0639-2

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  • DOI: https://doi.org/10.1007/s00894-009-0639-2

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