Protein interactions and ligand binding: From protein subfamilies to functional specificity

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 107; no. 5; pp. 1995 - 2000
• Main Authors: Rausell, Antonio, Juan, David, Pazos, Florencio, Valencia, Alfonso
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 02.02.2010; National Acad Sciences
• Subjects: Amino Acid Sequence; Animals; Binding Sites; Biochemistry; Biological Sciences; Biophysical Phenomena; Conserved Sequence; Databases, Protein; Datasets; Evolution; Evolution, Molecular; Family structure; Humans; Ligands; Models, Molecular; Molecular evolution; Molecules; Multiprotein Complexes; Nucleic acids; Protein Conformation; Protein Interaction Domains and Motifs; protein-protein interactions; Proteins; Proteins - chemistry; Proteins - classification; Proteins - genetics; Proteins - metabolism; Sequence Homology, Amino Acid; Studies; Substrate specificity
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.0908044107

The divergence accumulated during the evolution of protein families translates into their internal organization as subfamilies, and it is directly reflected in the characteristic patterns of differentially conserved residues. These specifically conserved positions in protein subfamilies are known as "specificity determining positions" (SDPs). Previous studies have limited their analysis to the study of the relationship between these positions and ligand-binding specificity, demonstrating significant yet limited predictive capacity. We have systematically extended this observation to include the role of differential protein interactions in the segregation of protein subfamilies and explored in detail the structural distribution of SDPs at protein interfaces. Our results show the extensive influence of protein interactions in the evolution of protein families and the widespread association of SDPs with protein interfaces. The combined analysis of SDPs in interfaces and ligand-binding sites provides a more complete picture of the organization of protein families, constituting the necessary framework for a large scale analysis of the evolution of protein function.