Quantifying similarities in proteins using features based on hydropathy distribution along the protein sequence

Josef Panek1
1j.panek@imb.uq.edu.au, University of Queensland

The distribution of hydrophobic and polar properties of amino acids along a protein sequence has recently been assigned increasing significance for defining structure and function of proteins. This work uses modelling of the hydropathy distribution in proteins to explore relationships between functional specifity of proteins and distribution of hydropathy through constituing residues in proteins. The approach presented uses features based on the hydropathy of amino acids to model the hydropathy distribution in proteins. A feature space based on the proposed features is employed to indentify functional groups of proteins, based on similarities in the hydropathy distribution in proteins. The feature space also makes it possible to identify those elements of the hydropathy distribution that are specific for the functional protein groups. An example is used for demonstration, for which experimental biological information allows to evaluate the biological meaning of the conclusions, achieved using the presented method.