Molecular Bases and Specificity behind the Activation of the Immune System OAS/RNAse L Pathway by Viral RNA

Abstract

The first line of defense against invading pathogens usually relies on innate immune systems. In this context, the recognition of exogenous RNA structures is primordial to fight, notably, against RNA viruses. One of the most efficient immune response pathways is based on the sensing of RNA double helical motifs by the oligoadenylate synthase (OAS) proteins, which in turn triggers the activity of RNase L and, thus, cleaves cellular and viral RNA. In this contribution, by using long-range molecular dynamics simulations, complemented with enhanced sampling techniques, we elucidate the structural features leading to the activation of OAS by interaction with a model double-strand RNA oligomer mimicking a viral RNA. We characterize the allosteric regulation induced by the nucleic acid leading to the population of the active form of the protein. Furthermore, we also identify the free energy profile connected to the active vs. inactive conformational transitions in the presence and absence of RNA. Finally, the role of two RNA mutations, identified as able to downregulate OAS activation, in shaping the protein/nucleic acid interface and the conformational landscape of OAS is also analyzed.

Keywords: RNA viruses; free energy profiles; innate immune system; molecular dynamics; oligoadenylate synthase.

Figure 1

Representative snapshot showing the structure of the human OAS1 protein (in cyan) interacting with model RNA double strand (in purple). In the inlay, there is a zoomed-in element of the active site showing the Mg₂⁴⁺ cluster complexed by aspartate ligands.

Figure 2

Superposition of representative snapshots issued from the MD simulation between the HOLO (cyan) and the APO1 (panel (A) in purple) and APO2 (panel (B) in red). A zoomed-in section of the region mostly affected by the conformational changes is also provided.

Figure 3

(A) Superposition of the HOLO (cyan) and APO2 (red) structures highlighting the position of the residues E223, K66, and R195 in the two structures. (B) Time evolution of the distances between the residues E233, R195, and K66 in HOLO (cyan), APO1 (purple), and APO2 (red).

Figure 4

Potential of mean force for active/inactive transition in HOLO (cyan) and APO2 (red) systems obtained from umbrella sampling-enhanced MD simulations. Note that the inactive conformation ΔRMSD = −2.7 Å, i.e., the minimum free energy for the APO system, corresponds to the APO2 conformation.

Figure 5

(A) The interaction interface between OAS1 and the model double-strand RNA model. The protein interfacial basic residues (lysine red and arginine orange) are highlighted in van der Waals representation. (B) A representation of the hydrophobicity of the OAS1 protein interacting with the RNA. The protein is rendered in surface representation. Residues colored in green are hydrophobic, in red are hydrophilic, and in white are amphiphilic.

Figure 6

Representative structure of the HOLO17 ((A), magenta) and HOLO18 ((B), orange) mutants in complex with OAS1 and superposed to the original HOLO structure (in cyan).