Understanding RNA Chaperone Activity of ProQ Protein

RNA-binding proteins (RBPs) are crucial in recognizing and binding small RNAs that modulate gene expression. RBPs often act as RNA chaperones, facilitating the sRNA-mRNA duplex formation. One of the most studied sRNA chaperones is Hfq, the post-transcriptional gene regulator in bacteria. Recently, a new RNA-chaperone protein, ProQ, has been discovered, which binds to a novel sRNA RaiZ, derived from the 3'-end of mRNA encoding ribosome-inactivating protein, and promotes its base pairing with the ribosome binding site of hupA mRNA, leading to the repression of HU-α protein synthesis. Despite these studies, the RNA-binding mechanism in ProQ has not been well explored in detail to date. In this work, we studied the binding of raiZ RNA to ProQ using atomistic long time scale molecular dynamics and the exploratory variant of on-the-fly probability-based enhanced sampling (OPES_E) simulations. The raiZ RNA binds to ProQ's concave surface, mostly decorated with polar and positively charged residues like arginine and lysine, exerting electrostatic stabilization to the RNA. In-silico mutations of these crucial residues lead to a significant loss of the intermolecular interactions, resulting in the detachment of the RNA from the protein. The free energy surface obtained from the OPES_E simulation helps identify stable raiZ-bound ProQ structures as well as intermediate states. The pertinent atomistic insights into the protein-RNA interactions and deciphering the binding mechanism of the raiZ RNA to ProQ enrich our knowledge about ProQ and its RNA chaperone activity.