Fig. 4: Allosteric regulation of ExoN activity and excision of bemnifosbuvir and sofosbuvir.
From: Mechanism of SARS-CoV-2 resistance to nucleotide analog-based antivirals
a Detailed interactions between SARS-CoV-2 ExoN and RNA 3′-end BMP. Metal coordination bonds and hydrogen bonds are shown as gray dashed lines. Hydrophobic interactions are shown as green dashed lines. Mg2+ ions, green spheres. +1BP, Mg2+ ion, and nsp14 residues are superimposed with their cryo-EM densities. b Detailed interactions between SARS-CoV-2 ExoN and RNA 3′-end SMP. Metal coordination bonds and hydrogen bonds are shown as gray dashed lines. Hydrophobic interactions are shown as green dashed lines. Mg2+ ions, green spheres. +1SP, Mg2+ ion, and nsp14 residues are superimposed with their cryo-EM densities. c Superimposition of nsp14 P140–L149 loop and α4-α5 loop between ExoN•T20P14-B and ExoN•standard RNA (PDB 7N0C) complexes. The displacement of the P140–L149 loop upon the binding of T20P14-B RNA is indicated. d Bridging interactions between the nsp14 P140–L149 loop and α4-α5 loop in the ExoN•standard RNA complex structure. Hydrogen bonds are shown as gray dashed lines. e Loss of bridging interactions between the nsp14 P140–L149 loop and α4-α5 loop in the ExoN•T20P14-B complex structure. Nsp14 residues are superimposed with their cryo-EM densities. An important role of the nsp14 P140–L149 loop in the excision of f 3′-end BMP and g 3′-end SMP by ExoN. Exonucleolytic digestion of T20P14-B or T20P14-S RNA by WT or mutant forms of ExoN was stopped at indicated time points, and RNA products were resolved by denaturing PAGE and visualized by FAM imaging. The percentage of substrate RNA remaining at each time point was quantified using Bio-Rad Image Lab from three independent experiments and is shown as mean ± SEM. Rate constant (k) values are determined using the One-phase decay model in GraphPad Prism. Statistical analyses were performed using the two-sided extra sum-of-squares F test. P values for the comparisons of decay rate constants between WT and each mutant are indicated. Source data are provided as a Source Data file.
