Mechanism of the Activation of Ribosome Rescue Factor ArfB

Messenger RNAs (mRNAs) which lack a stop codon result in ribosomes stalled at the 3’ end of mRNA. Alternative ribosome-rescue factor B (ArfB) rescues by tRNA-peptide hydrolysis and thus releasing peptide. ArfB consists an N-terminal domain with GGQ motif required for hydrolysis, C-terminal acts as sensor empty mRNA entry channel, linker connecting domains. binds to ribosomal A site regardless length truncated However, only gets activated when forms specific interactions channel. Here, I use explicit-solvent all-atom molecular dynamics simulations ribosome-ArfB complex investigate how conformation results distant domain. Simulations were carried out wild-type ArfB, cut linker, mutations highly conserved residues (K103A, R105A). In alpha helix (residues 80-99), directly connects stabilizes CCA tail tRNA hydrolysis-competent conformation. contrast, cutting well shift consequently different attached From these observations, suggest that placement channel determines position linker. The positioning restricts helix, turn peptidyl-tRNA