Aromatic-aromatic interactions in proteins: beyond the dimer

ESTEBAN LANZAROTTI; ROLF BIEKOVSKY; DARIO A ESTRIN; MARCELO A MARTI; ADRIAN G TURJANSKI

JOURNAL OF CHEMICAL INFORMATION AND MODELING

AMER CHEMICAL SOC

Lugar: Washington; Año: 2011 p. 1623 - 1633

1549-9596

 Aromatic residues are key widespread elements of protein structures and have beenshown to be important for structure stability, folding, proteinÀprotein recognition, and ligand binding.The interactions of pairs of aromatic residues (aromatic dimers) have been extensively studied inprotein structures. Isolated aromatic molecules tend to form higher order clusters, like trimers,tetramers, and pentamers, that adopt particular well-defined structures. Taking this into account, wehave surveyed protein structures deposited in the Protein Data Bank in order to find clusters ofaromatic residues in proteins larger than dimers and characterized them. Our results show that largerclusters are found in one of every two unique proteins crystallized so far, that the clusters are builtadopting the same trimer motifs found for benzene clusters in vacuum, and that they are clearlynonlocal brining primary structure distant sites together. We extensively analyze the trimers andtetramers conformations and found two main cluster types: a symmetric cluster and an extendedladder. Finally, using calmodulin as a test case, we show aromatic clsuters possible role in folding andproteinÀprotein interactions. All together, our study highlights the relevance of aromatic clustersbeyond the dimer in protein function, stability, and ligand recognition.