Flexibility and intrinsic disorder are conserved features of hepatitis C virus E2 glycoprotein

The glycoproteins of hepatitis C virus, E1E2, are unlike any other viral fusion machinery yet described, and are the current focus of immunogen design in HCV vaccine development; thus, making E1E2 both scientifically and medically important. We used pre-existing, but fragmentary, structures to model a complete ectodomain of the major glycoprotein E2 from three strains of HCV. We then performed molecular dynamic simulations to explore the conformational landscape of E2, revealing a number of important features. Despite high sequence divergence, and subtle differences in the models, E2 from different strains behave similarly, possessing a stable core flanked by highly flexible regions, some of which perform essential functions such as receptor binding. Comparison with sequence data suggest that this consistent behaviour is conferred by a network of conserved residues that act as hinge and anchor points throughout E2. The variable regions (HVR-1, HVR-2 and VR-3) exhibit particularly high flexibility, and bioinformatic analysis suggests that HVR-1 is a putative intrinsically disordered protein region. Dynamic cross-correlation analyses demonstrate intramolecular communication and suggest that specific regions, such as HVR-1, can exert influence throughout E2. To support our computational approach we performed small-angle X-ray scattering with purified E2 ectodomain; this data was consistent with our MD experiments, suggesting a compact globular core with peripheral flexible regions. This work captures the dynamic behaviour of E2 and has direct relevance to the interaction of HCV with cell-surface receptors and neutralising antibodies.Author summary: Hepatitis C virus (HCV) is a globally important pathogen for which no vaccine is available. E2 is a protein found on the surface of HCV particles; it mediates interaction of HCV with cells and is a target for the human immune response. Current evidence suggests that antibodies targeting E2 are able to clear HCV infection, therefore, E2 is being pursued as a candidate vaccine. In this study we have built structural models of E2 from different strains of HCV and performed computational simulation to investigate how the E2 molecule moves. We have discovered that E2 possesses highly mobile regions; we propose that flexibility and disorder are defining characteristics of E2. This work provides a new perspective on E2 and will guide future studies into its basic functions and interactions with the immune system. Ultimately, our goal is to use this information to design new vaccine candidates by, for instance, locking the flexible regions of E2 such that they can be better targeted by antibodies.