Double-Stranded RNA Binding Domain (dsRBD) of PKR Shows Variable Dynamics in the Presence of Bacteriophage Pf1: An NMR Insight and its Possible Implications

The human Protein Kinase R (PKR) is one of the important and critical components of the innate immune response against viral infection. It regulates distinct cellular functions and controls the fate of an RNA molecule in the cell. PKR dephosphorylation is characterised by inhibitory interactions between the kinase domain and the RNA binding domains (RBDs), but the complete structural details and dynamics of the latent state and its activation are not yet clear. Several studies on the activation of double stranded RNA binding domain (dsRBD) of Protein Kinase R (dsRBD-PKR) have been attempted during the last few decades. In order to further investigate on its activation mechanism, we have analysed the backbone [H-N]-dynamics and chemical shift perturbation studies of dsRBD-PKR in the presence of bacteriophage Pf1. Pf1 is known to orient the protein in the presence of external magnetic field and, can be further used to get useful information about the protein properties such as the different dynamic behaviour in multidomain proteins like dsRBD-PKR. These NMR based results improve our basic understanding of the domain flexibilities of dsRBD-PKR where some secondary structural regions of dsRBM1 (dsRNA binding motif 1) show a different behaviour than the one from dsRBM2 (dsRNA binding motif 2) these observations further lead to a better understanding of PKR mechanism where dsRBM1 has more affinity towards RNA as compared to dsRBM2.