title: [Classification and Contribution Analysis of Aromatic Clusters in Protein-Ligand Complexes].
abstract: Intermolecular interactions are key features in the stabilization or destabilization of complexes. In particular, interactions involving aromatic rings have been extensively studied both theoretically and experimentally. Studies have shown that aromatic-aromatic interactions can be categorized by ring-ring orientation into a variety of different types, such as stacking interactions and T-shaped interactions. Because these different orientations affect stabilization, analyses of such interactions, for example ab initio molecular orbital calculations, are applied to pairs of aromatic rings, both in model systems and real systems. An important series of aromatic-aromatic interactions include those between pairs of aromatic residues in proteins. These residues have been studied computationally using both a theoretical chemistry approach and a knowledge-based analys. Protein 3D structural information is essential for knowledge-based studies of aromatic-aromatic interactions in protein-ligand complexes. Some databases filter entries from the Protein Data Bank (PDB) using criteria that make them suitable for computational approaches involving specific research targets. Lanzarotti et al. have shown that aromatic clusters in which three or more aromatic residues are in close proximity to each other are found in many protein structures, expanding pairwise aromatic-aromatic interactions. Moreover, these clusters are thought to be important in terms of protein function, structural stability and ligand recognition. Here, we show that aromatic clusters, as well as individual proteins, are found in a variety of protein-ligand complexes. As such, we anticipate that these clusters might have a significant role in ligand binding and could help in efficient ligand design.
authors.affiliation: School of Pharmacy, Kitasato University.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Yamasaki
authors.forename: Jun
authors.initials: J
authors.lastname: Koseki
authors.forename: Yoshihiko
authors.initials: Y
authors.lastname: Nishibata
authors.forename: Shuichi
authors.initials: S
authors.lastname: Hirono
mesh_terms: D024322:Amino Acids, Aromatic / Q000737:chemistry*; D001665:Binding Sites; D008024:Ligands; D011485:Protein Binding; D054730:Protein Interaction Domains and Motifs; D055550:Protein Stability; D020836:Protein Structure, Quaternary; D011506:Proteins / Q000737:chemistry*
chemical_list: D024322:Amino Acids, Aromatic; D008024:Ligands; D011506:Proteins