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A New Method for Identification of Protein (Sub)families in a Set of Proteins Based on Hydropathy Distribution in Proteins by Josef Pánek; Ingvar Eidhammer; Rein Aasland is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

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## Abstract Structural similarity among proteins is reflected in the distribution of hydropathicity along the amino acids in the protein sequence. Similarities in the hydropathy distributions are obvious for homologous proteins within a protein family. They also were observed for proteins with related structures, even when sequence similarities were undetectable. Here we present a novel method that employs the hydropathy distribution in proteins for identification of (sub)families in a set of (homologous) proteins. We represent proteins as points in a generalized hydropathy space, represented by vectors of specifically defined features. The features are derived from hydropathy of the individual amino acids. Projection of this space onto principal axes reveals groups of proteins with related hydropathy distributions. The groups identified correspond well to families of structurally and functionally related proteins. We found that this method accurately identifies protein families in a set of proteins, or subfamilies in a set of homologous proteins. Our results show that protein families can be identified by the analysis of hydropathy distribution, without the need for sequence align

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Author

Josef Pánek; Ingvar Eidhammer; Rein Aasland

Publisher

John Wiley and Sons; Wiley (John Wiley & Sons); Wiley-Liss Inc; Wiley (ISSN 0887-3585)

Published

2005

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)