Aromatic interactions at atom-to-atom contact and just beyond: a case study of protein interactions of NAD⁺/NADP⁺

We probed aromatic-protein interactions based on specificity of enrichment of protein residues across a contact-based cutoff. Thus, 155 protein-NAD(+)/NADP(+) complexes were analyzed for enrichments within 10Å of centroids of aromatic groups of the ligand when the residues were contacted and not contacted with the aromatic ligand. Specifically, neutral-adenine and cationic-nicotinamide groups of the oxidized coenzymes evoked interest to know whether the contrast of charge or the shared aromaticity will manifest in the enrichments across the cutoff. We found that when in contact, the enrichments are highly specific for nicotinamide and adenine-aromatic structures, and thus possibly complex in the basis, but when not in contact, they are generic for charge and aromaticity of the structures, and thus possibly specific in the basis. The order of enrichments over the contacted residues is Tyr>Cys>Thr>His>Asn>Ser>Met>Ile>Phe against nicotinamide-π(+) structure and Asp>Ile>Thr>His>Arg>Tyr>Gly>Val against adenine-π structure, while the order over the non-contacted residues is Trp>Gly>His>Asn>Cys>Met>Tyr>Ser>Thr>Phe against nicotinamide-π(+) structure and Asn>Thr>Ser>Gly>Cys>His>Val against adenine-π structure. Neutral Trp, His, Tyr, and Phe, but not cationic Arg, are thus the non-contacted residues enriched specifically against nicotinamide-π(+) structure, while Asn, Gly, Thr, Ser, and Cys are the non-contacted residues enriched generically against both the nicotinamide-π(+) and adenine-π aromatic structures. By analyzing the enriched groups in their geometric specificities, we found that, the enrichments against nicotinamide cation manifest the specificity expected of cation-π interaction and against nicotinamide- and adenine-aromatic groups manifest the specificity expected of dipole-π interaction. The cutoff-based method is proven valuable in probing protein-ligand interactions in the physics involved.