West Nile virus (WNV), a mosquito-borne flavivirus, causes a febrile illness that can progress to fatal encephalitis. During infection, icosahedral WNV enters cells through receptor-mediated endocytosis and undergoes endosomal membrane fusion catalyzed by envelope glycoprotein (E) rearrangement of domain III (DIII) and exposure of the fusion loop. Antibodies, the majority of which are against E, are critical for clearance of WNV.

To understand the essential protective function of the humoral response to WNV we studied WNV E alone and with neutralizing Fabs. WNV E adopts the common flavivirus three-domain architecture though it lacks the dimer partner seen in other flavivirus E protein structures. Within the crystal lattice each WNV E fusion loop is buried at the DI-DIII interface of another perpendicular E. E proteins could use this fusion loop pocket as a pivot, allowing virion conformational transitions while minimizing hydrophobic residue exposure.

Virologic studies have demonstrated two critical WNV E protein epitopes. Herein are the crystal structures of two neutralizing Fabs, E16 and E53, bound to DIII and the fusion loop, respectively. E16, highly effective against in vitro and in vivo WNV infection, binds an epitope that is conserved within WNV but divergent among flaviviruses. E16 inhibits infection primarily at a step after cellular attachment, potentially by blocking E conformational changes. The fusion loop, to which the plurality of WNV specific antibodies are directed, is highly conserved among flaviviruses in contrast to the DIII epitope. E53-like fusion loop antibodies block cellular attachment, allow antibody dependent enhancement even at neutralizing concentrations and are less effective at neutralization in vivo and in vitro. Additionally, initial cryo-electron microscopy studies suggest that while E16 binds two-thirds of the available epitopes on WNV, E53 binds only one-third. These findings suggest that optimally designed vaccines would direct immune responses toward the strongly neutralizing DIII epitope and away from the fusion loop epitope.

Additionally, this dissertation examines the basis for recognition of many of divergent ligands with a broad range of affinities by costimulatory immunoreceptor NKG2D. Computational and binding studies demonstrate electrostatics are important to develop high affinity binding to the unusually promiscuous NKG2D.