Variation in structural location and amino acid conservation of functional sites in protein domain families

Background: The functional sites of a protein present important information for determining its cellular function and are fundamental in drug design. Accordingly, accurate methods for the prediction of functional sites are of immense value. Most available methods are based on a set of homologous sequences and structural or evolutionary information, and assume that functional sites are more conserved than the average. In the analysis presented here, we have investigated the conservation of location and type of amino acids at functional sites, and compared the behaviour of functional sites between different protein domains. Results: Functional sites were extracted from experimentally determined structural complexes from the Protein Data Bank harbouring a conserved protein domain from the SMART database. In general, functional (i.e. interacting) sites whose location is more highly conserved are also more conserved in their type of amino acid. However, even highly conserved functional sit...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Birgit Pils, Richard R. Copley, Jörg Schultz
• Keywords: Amino Acids, BMCBI 2005, Functional Sites, Protein