Studies to Investigate the Protein-Based Molecular Recognition of the Adenine Ring James Ricky Cox, Department of Chemistry, Murray State University Understanding the recognition of biologically-important aromatic systems has implications across chemistry and the field of molecular recognition. The adenine ring is one of the most important aromatic systems in nature. An aminoglycoside antibiotic kinase, APH(3’)-IIIa, was as used as a model protein to investigate the protein-based molecular recognition of the adenine ring. A combination of kinetic, calorimetric and computational methods yielded the following outcomes: -kinetic experiments revealed that the nucleobase specificity in the adenine-binding region is determined largely by H-bonding interactions and that small aromatic compounds, structurally distinct from adenine, can also bind in the adenine-binding pocket. -calorimetric experiments revealed that the protein-based recognition of the adenine ring is governed largely by electrostatic interactions and that a cooperative network of hydrogen bonds and a pi-pi stacking interaction mediate the specificity and affinity of compounds that bind in the adenine-binding pocket. -computational and calorimetric experiments suggest that the sulfide side chain of methionine-90, in the adenine-binding pocket of APH(3’)-IIIa, can serve as a H-bond donor and help in the orientation of the adenine ring in its binding pocket.