Relating structure to thermodynamics: The crystal structures and binding affinity of eight OppA-peptide complexes

The oligopeptide-binding protein OppA provides a useful model system for st udying the physical chemistry underlying noncovalent interactions since it binds a variety of readily synthesized ligands. We have studied the binding of eight closely related tripeptides of the type Lysine-X-Lysine, where X is an abnormal amino acid, by isothermal titration calorimetry (ITC) and X- ray crystallography. The tripeptides fall into three series of ligands, whi ch have been designed to examine the effects of small changes to the centra l side chain. Three ligands have a primary amine as the second side chain, two have a straight alkane chain, and three have ring systems. The results have revealed a definite preference for the binding of hydrophobic residues over the positively charged side chains, the latter binding only weakly du e to unfavorable enthalpic effects. Within the series of positively charged groups, a point of lowest affinity has been identified and this is propose d to arise from unfavorable electrostatic interactions in the pocket, inclu ding the disruption of a key salt bridge. Marked entropy-enthalpy compensat ion is found across the series, and some of the difficulties in designing t ightly binding ligands have been highlighted.