A Comparative Analysis of Protein Interfaces

Jing      Hu; Changhui      Yan

Abstract

Proteins perform various functions through interacting with other molecules. Analyzing the characteristics of residues on the interaction interfaces provides insights into the mechanisms of these interactions. In this study, we analyze the characteristics of five different interfaces: protein-protein interfaces, protein-DNA interfaces, protein-RNA interfaces, protein-carbohydrate interfaces, and protein-ligand interfaces. The analysis reveals that these interfaces are different in residue composition. These differences in residue composition reflect the differences in the mechanisms that facility different types of interactions. Regardless of the differences in residue composition, all of the five types of interfaces are more conservative than the non-interface protein surfaces. Additionally, our results also show that it is important to consider the effect of solvent accessibility when investigating residues propensities for different parts of the proteins.

Keywords: Interface propensity, interface residues, non-interface surfaces, protein cores, residue compositions, sequence entropy, propensity, residues, non-interface, protein, sequence, Protein Interfaces, DNA, RNA, (PDB), hydropho-bicity, NACCESS, (RIP), (rASA), (NIP), pro-tein-DNA, protein-RNA, Trp, Tyr, His, HSSP, PseAAc, van der Walls