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.
Highlights
Aromatic compounds are unsaturated cyclic and planar molecules that contain an aromatic ring
Aromatic-aromatic interactions are defined as pairs of interacting aromatic residues which satisfy the following criteria: (i) the centers of the aromatic rings of the two interacting residues are separated by a distance between 4.5 Å to 7 Å, (ii) the dihedral angle must fall between 30 ̊ to 90 ̊ and (iii) free energies of formation when such interactions take place should be between -0.6 and -1.3 kcal/mole [4]
The maximum number of specific interactions is found to be between 6.5Å to 7.0Å and for non-specific, it is observed between 7.0Å to 7.5Å (Table 3)
Summary
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. 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. The interactions between the aromatic residues within a protein and in protein and DNA complexes are integral part for the proper functioning of the protein molecule This in turn influences various biological processes that take place within an organism in which the protein is involved [5]
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