Interactions of Aromatic Residues in Amyloids: A Survey of Protein Data Bank Crystallographic Data

Aromatic-aromatic interactions have long been considered important in the self assembly of amyloids. In spite of their importance, aromatic amino acids are not detected in every amyloid. In the present study, the occurrence and geometry of these interactions were analyzed for the amyloid structures found in the Protein Data Bank. The data confirm that aromatic amino acids are not crucial for amyloid fibril formation. In fact, aromatic-aliphatic interactions are more frequent than the aromatic-aromatic interactions. Aromatic-aliphatic interactions are present in higher numbers of structures and in certain amyloid sequences they are more frequent than aromatic-aromatic interactions. An analysis of aromatic/aromatic interactions shows different interaction geometries in intrasheet and intersheet contacts; the intrasheet aromatic-aromatic interactions are mostly parallel and displaced, while intersheet interactions are not parallel. Thus, among the aromatic-aromatic interactions there are important edge-to-face attractions in addition to parallel stacking ones.