Structural Diversity in Antibody Interactions with HIV-1 Env Immunogens

Thesis (Ph.D.)--University of Washington, 2013

Due to the impressive diversity of human immunodeficiency virus type 1 (HIV-1), control of the HIV-1 pandemic will likely depend on the design of a vaccine that can elicit broadly neutralizing antibodies (bNAbs) that can prevent transmission of diverse HIV-1 isolates. Although bNAbs have been observed in HIV-infected individuals, we are currently unable to elicit them through vaccination. The difficulty associated with eliciting broadly reactive antibodies is rooted in the exceptional sequence, structural, and conformational diversity of the HIV-1 Envelope glycoprotein (Env), the sole target of neutralizing antibodies. In addition, we have an incomplete understanding of the factors that govern Env-antibody interactions, and we are poorly equipped to rationally manipulate these interactions in order to obtain desired antibody specificities through vaccination. This thesis explores structural heterogeneity in purified soluble Env immunogens and the antibodies that recognize them, in order to understand how structural diversity - generated through post-translational modifications or conformational flexibility - impacts Env-antibody interactions. First, I measured soluble Env ectodomain immunogen binding to the antibodies PG9 and PG16, which were reported to preferentially recognize the native Env trimer. I tested the impact of glycosylation, proteolysis, and oligomerization state on exposure of the PG9/PG16 epitope and demonstrated that PG9/PG16 are less specific for the native trimer than previously reported. Next, I used small angle x-ray scattering (SAXS) and hydrogen-deuterium exchange with mass spectrometry (HDX-MS) to characterize the solution structure and conformational dynamics of soluble monomeric gp120 Env proteins from four diverse HIV-1 isolates. This work showed that while the overall subunit morphology is similar among diverse gp120 proteins, there are distinct differences in conformational dynamics. I observed that more dynamic gp120 proteins were poorly recognized by conformation-dependent antibodies. Finally, to examine the potential influence of antibody conformational dynamics on Env recognition, I measured changes in antibody paratope stability over the course of affinity maturation for the bNAbs VRC03 and VRC26, which target the CD4-binding site and a V2-quaternary epitope, respectively. I observed that paratope stability does not increase uniformly or linearly over the course of affinity maturation for either antibody, although germline antibodies were relatively more dynamic than mature antibodies. Altogether, this work provides useful insight into the structural heterogeneity of purified Env immunogens and the role of conformational dynamics in modifying Env-antibody interactions. These data suggest that targeted stabilization may facilitate rational manipulation of Env-antibody interactions during vaccination.