ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information

Experimental approaches for the identification of functionally important re gions on the surface of a protein involve mutagenesis, in which exposed res idues are replaced one after another while the change in binding to other p roteins or changes in activity are recorded. However, practical considerati ons limit the use of those methods to small-scale studies, precluding a ful l mapping of all the functionally important residues on the surface of a pr otein. We present here an alternative approach involving the use of evoluti onary data in the form of multiple-sequence alignment for a protein family to identify hot spots and surface patches that are likely to be in contact with other proteins, domains, peptides, DNA, RNA or ligands. The underlying assumption in this approach is that key residues that are important for bi nding should be conserved throughout evolution, just like residues that are crucial for maintaining the protein fold, i.e. buried residues. A main lim itation in the implementation of this approach is that the sequence space o f a protein family may be unevenly sampled, e.g. mammals may be overly repr esented. Thus, a seemingly conserved position in the alignment may reflect a taxonomically uneven sampling, rather than being indicative of structural or functional importance. To avoid this problem, we present here a novel m ethodology based on evolutionary relations among proteins as revealed by in ferred phylogenetic trees, and demonstrate its capabilities for mapping bin ding sites in SH2 and PTB signaling domains. A computer program that implem ents these ideas is available freely at: http://ashtoret.tau.ac.il/ similar to rony (C) 2001 Academic Press.