Contribution of aromatic cluster to protein-ligand interaction

Abstract

The interactions between aromatic residues in protein structures have been extensively studied. It was shown that aromatic clusters formed by three or more aromatic rings were found in many protein structures and they were important for structure stability, folding, protein-protein recognition, and ligand binding. In drug design, we have a strong interest in protein-ligand interactions. Previously, we found that there were aromatic clusters formed by three or more aromatic rings in protein-ligand complexes as well as in protein structures. To reveal attractive and repulsion interactions in aromatic clusters and between aromatic clusters and the surrounding residues, we performed ab initio density functional calculations. To generate the model structures for our calculations, we analyzed aromatic clusters in 201 protein-ligand complexes data of PDBbind-CN(http://www.pdbbind.org.cn/) and picked up the aromatic clusters and the surrounding residues existing within 7Å in the protein-ligand complexes.