Sialic Acid Induced Conformational Ensemble Shifts in the Hemagglutinin-Neuraminidase Protein of the Newcastle Disease Virus

Abstract

Newcastle disease virus (NDV) belongs to the family of enveloped paramyxoviruses that cause many diseases in humans and farm animals. NDV is of serious concern to poultry, and infects over 200 species of birds. To gain entry into host cells, NDV uses a concerted action of two of its membrane proteins: the Hemagglutinin-Neuraminidase (HN) protein, and the fusion protein (F). HN binds to sialic acids expressed on the host surface, and this binding causes HN to activate F, which, in turn, mediates NDV-host membrane fusion. However, the mechanism of long-distance (> 2 nm) allosteric coupling between HN's sialic acid (receptor) binding domains (RBDs) and F-activating domain (FAD) is unknown. Understanding this signaling process has been challenging because HN belongs to the category of proteins like GPCRs and PDZ domains where receptor-induced structural changes are of the order of thermal fluctuations. To gain insight, we carry out multiple all-atom molecular dynamics simulations of HN in its monomer/dimeric forms as well as in its apo and sialic acid bound states. We consider also both optical isomers of sialic acid — the α-anomer that is expressed on host surfaces and the β-anomer that is preferred over the α-anomer in solution, but which does not induce HN to activate F. We find that while the two anomers induce similar RBD-RBD reorientations, they produce strikingly different conformational ensemble shifts within individual RBDs, suggesting that allosteric signaling must involve the RBD-FAD interface. Further analysis yields a cluster of residues proximal to both RBD-FAD and RBD-RBD interfaces whose conformational ensembles are shifted by α-sialic acid. Together, these results suggest that allosteric coupling between RBD and FAD involves a complex pathway comprising of multiple inter-domain interfaces.