Prediction of Polypeptide Fragments Exposed to the Solvent

Article type: Research Article

Authors: Carugo, Oliviero^;

Affiliations: Department of General Chemistry of the Pavia University, Viale Taramelli 12, I-27100 Pavia, Italy | International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34012 Trieste, Italy. E-mail: carugo@embl-heidelberg.de

Abstract: A method is presented to predict those polypeptide segments within a globular protein that are more likely to be exposed to the solvent. The protein amino acidic sequence is the only information needed by this new algorithm. It uses a consensus hydrophobicity scale, derived from 28 known scales, and it is based on the comparison between the average hydrophobicity of a polypeptide fragment and the average hydrophobicity expected for a segment containing the same number of residues. The latter values are pre-computed from a non-redundant set of single chain protein structural domains. The comparison between the two average values results in a t value that readily provides the prediction with a statistical significance. A jack-knife validation analysis indicates that the protein segment predicted to be the most solvent exposed is actually solvent exposed and amongst the fragments that are most exposed. The source of a stand-alone program, written in C language, that allows the prediction of the most likely solvent exposed segment in a globular protein is available from the author.

Keywords: accessibility prediction, epitope, hydrophobicity, modelling, protein structure, solvent accessibility, structure prediction

Journal: In Silico Biology, vol. 3, no. 4, pp. 417-428, 2003