Hepatitis a virus proteinase 3C binding to viral RNA: Correlation with substrate binding and enzyme dimerization

Proteinase 3C of hepatitis A virus (HAV) plays a key role in the viral life cycle by generating mature viral proteins from the precursor polyprotein. In addition to its proteolytic activity, 3C binds to viral RNA, and thus influences viral genome replication. In order to investigate the interplay between proteolytic activity and RNA binding at the molecular level, we subjected HAV 3C and three variants carrying mutations of the cysteine residues [C24S (Cys-24 → Ser), C172A and C24S/C172A] to proteolysis assays with peptide substrates, and to surface plasmon resonance binding studies with peptides and viral RNA. We report that the enzyme readily forms dimers via disulphide bridges involving Cys-24. Dissociation constants (K_D) for peptides were in the millimolar range. The binding kinetics for the peptides were characterized by k_on and k_off values of the order of 10² M^-1 · s^-1 and 10^-2 to 10^-1 s^-1 respectively. In contrast, 3C binding to immobilized viral RNA, representing the structure of the 5′-terminal domain, followed fast binding kinetics with k_on and k_off values beyond the limits of the kinetic resolution of the technique. The affinity of viral RNA depended strongly on the dimerization status of 3C. Whereas monomeric 3C bound to the viral RNA with a K_D in the millimolar range, dimeric 3C had a significantly increased binding affinity with K_D values in the micromolar range. A model of the 3C dimer suggests that spatial proximity of the presumed RNA-binding motifs KFRDI is possible. 3C binding to RNA was also promoted in the presence of substrate peptides, indicating co-operativity between RNA binding and protease activity. The data imply that the dual functions of 3C are mutually dependent, and regulate protein and RNA synthesis during the viral life cycle.