Evaluation of non-covalent interaction between Seryl-Histidine dipeptide and cyclophilin A using NMR and molecular modeling

Seryl-Histidine dipeptide (Ser-His) has been previously reported to be capable of cleaving DNAs and carboxyl esters, as well as proteins. The protein cleavage mechanism has not been addressed yet. As an initial step of protein cleavage activity, the non-covalent binding affinity of Ser-His for proteins is a crucial prerequisite. In this work, we took cyclophilin A (CyPA) as a substrate protein, and evaluated the non-covalent interaction between CyPA and Ser-His using a combination of NMR spectroscopy and molecular modeling approach. Two independent Ser-His binding sites on CyPA were detected using 15N-1H heteronuclear single-quantum coherence (HSQC) spectra. Each binding site binds one Ser-His molecule. Dissociation constants, Kd1 and Kd2, were estimated to be 2.07 and 6.66 mmol/L, respectively, indicative of the weak non-covalent interaction between Ser-His and CyPA. Based on molecular modeling results, we suggest that both the α-amino and the side chain hydroxyl group of Ser-His are crucial for the non-covalent interaction between Ser-His and CyPA. This work sheds light on the molecular mechanism of Ser-His and its analogues cleaving proteins.