Hypothesis Aromatic-aromatic interactions in structures of proteins and protein-DNA complexes: a study based on orientation and distance

Abstract: Interactions between the aromatic amino acid residues have a significant influence on the protein structures and protein-DNA complexes. These interactions individually provide little stability to the structure; however, together they contribute significantly to the conformational stability of the protein structure. In this study, we focus on the four aromatic amino acid residues and their interactions with one another and their individual interactions with the four nucleotide bases. These are analyzed in order to determine the extent to which their orientation and the number of interactions contribute to the protein and protein-DNA complex structures. Background: Aromatic compounds are unsaturated cyclic and planar molecules that contain an aromatic ring. They possess additional stability as a result of the arrangement of the π -electrons situated above and below the plane of the aromatic ring. These electrons give rise to what is known as a π-electron cloud over the ring. Aromaticity is a chemical property associated with such cyclic and planar compounds and is attributed to these π-electrons which are free to cycle around the circular arrangements of atoms found in the aromatic moieties. It can be considered as a manifestation of cyclic delocalization and resonance which is found in planar ring systems such as benzene [1, 2]. The flat face of an aromatic ring has a partial negative charge owing to these π electrons. Out of the 20 amino acids found in protein structures, four are aromatic. They are phenylalanine, tyrosine, tryptophan and histidine [3]. The interactions that take place between the sidechains of the aromatic amino acid residues are referred to as aromatic-aromatic interactions. Formally, aromatic-aromatic interactions are defined as pairs of interacting aromatic residues which satisfy the following criteria: (i) the centers of th