Comparative analysis of SH2 domain structures

Abstract

Src Homology 2 (SH2) is the compact globular domains, which is involved in intracellular signaling pathways and play an important role in mediating specific protein-protein interactions. It consists of about 100 amino acids and include sevens β-sheets and two α-helices. The SH2 domains comprise two highly conservative parts of binding pocket – pTyr and pTyr +3. The knowledge of the protein complexes structure is an important step forward to understanding of the mechanisms of their functioning. The binding site of SH2 domains and surrounding to binding site sequences were analyzed by using in silico methods. All SH2 domains were divided into the groups by sequence similarity. The parts of sequences which are common to all domains and the unique parts of certain domains were found within the framework of conservation and similarity analysis of SH2 domains. Furthermore, the surface area analysis displays that the highly conservative structures occupy the smallest area. These results indicate the ability of the SH2 domains to recognize not only linear phosphopeptide sequences. It opens new insights on the interpretation of possible mechanisms of interaction between SH2 domains and ligands/protreins (e. g. possibility of binding between protein or ligand with SH2 domain not only within binding site area).

Keywords

• SH2 domain
• binding site
• conservativeness