title: Aromatic-aromatic interaction: a mechanism of protein structure stabilization.
abstract: Analysis of neighboring aromatic groups in four biphenyl peptides or peptide analogs and 34 proteins reveals a specific aromatic-aromatic interaction. Aromatic pairs (less than 7 A between phenyl ring centroids) were analyzed for the frequency of pair type, their interaction geometry (separation and dihedral angle), their nonbonded interaction energy, the secondary structural locations of interacting residues, their environment, and their conservation in related molecules. The results indicate that on average about 60 percent of aromatic side chains in proteins are involved in aromatic pairs, 80 percent of which form networks of three or more interacting aromatic side chains. Phenyl ring centroids are separated by a preferential distance of between 4.5 and 7 A, and dihedral angles approaching 90 degrees are most common. Nonbonded potential energy calculations indicate that a typical aromatic-aromatic interaction has energy of between -1 and -2 kilocalories per mole. The free energy contribution of the interaction depends on the environment of the aromatic pair. Buried or partially buried pairs constitute 80 percent of the surveyed sample and contribute a free energy of between -0.6 and -1.3 kilocalories per mole to the stability of the protein's structure at physiologic temperature. Of the proteins surveyed, 80 percent of these energetically favorable interactions stabilize tertiary structure, and 20 percent stabilize quaternary structure. Conservation of the interaction in related molecules is particularly striking.
mesh_terms: D000596:Amino Acids; D000818:Animals; D005075:Biological Evolution; D002135:Calcium-Binding Proteins; D002918:Chymotrypsin / Q000037:antagonists & inhibitors; D004268:DNA-Binding Proteins; D005914:Globins; D006358:Hot Temperature; D006801:Humans; D007140:Immunoglobulin Fab Fragments; D009842:Oligopeptides; D011485:Protein Binding; D011487:Protein Conformation; D012097:Repressor Proteins; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; D014867:Water
chemical_list: D000596:Amino Acids; D002135:Calcium-Binding Proteins; D004268:DNA-Binding Proteins; D007140:Immunoglobulin Fab Fragments; D009842:Oligopeptides; D012097:Repressor Proteins; D014764:Viral Proteins; D054334:Viral Regulatory and Accessory Proteins; C016649:phage repressor proteins; D014867:Water; D005914:Globins; D002918:Chymotrypsin