Multi-state dimerization of the effector domain may regulate the assembly of non-structural protein 1 from the influenza A virus

Non-structural protein 1 (NS1) from the influenza A virus (IAV) is a multifunctional virulence factor with two main roles of inhibiting the host immune response and supporting viral replication. It has an RNA binding domain (RBD) and an effector domain (ED) joined by a 12-AA flexible linker. Self-assembly of NS1 has been suggested to be involved in its multiple roles during the infection cycle. The RBDs associate to form a stable dimer, whereas EDs associate more weakly, pointing to the association between EDs as a potential way to control the assembly behavior. There are two known types of ED dimers, referred to as Type-A and Type-B ED dimers. We studied the interactions between EDs by performing all-atom molecular dynamics simulations of NS1 from the H5N1 (PDB 3F5T) and H6N6 (PDB 4OPH) strains of IAV. One microsecond-long equilibrium simulations revealed that the Type-A ED dimers start in a weakly bound (open) state, which has a tendency to transition to a more strongly bound (closed) state. Compared to the two-state, Type-A ED dimer, the Type-B ED dimer binds on an opposite side of the ED. Furthermore, umbrella sampling simulations to separate the two types of ED dimers revealed that the closed state of the Type-A dimer is about twice as strong as the open state, and the Type-B dimer has stability comparable to the closed state Type-A dimer. Our results suggest that the association between EDs involves multiple states that differ in stability and kinetic accessibility, which may have implications for the dynamic control of NS1 assembly.