Study of Characterization of Promiscuous Binding Sites in Protein-Small Molecule Complexes

Abstract

An exhaustive comparison of different proteins has provided new insights into the characteristics of many proteins, leading to understanding their molecular and biological functions. Although many research works have so far characterized binding sites (BS) in proteins, only a few research-works about promiscuous BS which can accommodate different ligands or compounds have been presented and the knowledge is still limited. Thus, in this study, the promiscuous BS in protein-small molecule complexes from the Protein Data Bank (PDB) were exhaustively compared with the non-promiscuous BS to reveal physicochemical and structural properties of their BS. As a result, aliphatic, aromatic, and sulfur-containing amino acids (AA) were more likely to appear in promiscuous BS, indicating that they tend to be more hydrophobic than non-promiscuous BS. Furthermore, the number of AA and the accessible surface area of promiscuous BS tended to be larger than those of non-promiscuous BS. In addition, the significant difference of a-helix between promiscuous BS and non-promiscuous BS was observed.