Date of Award

Spring 2020

Document Type

Restricted Thesis

Terms of Use

© 2020 Naomi S. Bronkema. All rights reserved. Access to this work is restricted to users within the Swarthmore College network and may only be used for non-commercial, educational, and research purposes. Sharing with users outside of the Swarthmore College network is expressly prohibited. For all other uses, including reproduction and distribution, please contact the copyright holder.

Degree Name

Bachelor of Arts


Chemistry & Biochemistry Department

First Advisor

Daniela Fera


The HIV-1 envelope (Env) glycoprotein is the sole HIV-1 surface protein recognized by the humoral antibody response. A current goal of vaccine design is to elicit broadly neutralizing antibodies (bNAbs) against many variants of the HIV-1 Env. Because bNAbs take a long time to develop and have properties that prevent their elicitation, a design strategy involves triggering the development ofbNAb precursors by vaccination, followed by vaccine boosts to drive an antibody lineage to breadth. Here we describe the structural analysis of an early intermediate (IA4) of the DH270.6 bNAb lineage, a lineage that recognizes the Env V3-loop glycan supersite which includes the N332 glycan and whose bNAb was isolated from blood samples of an HIV-1 infected individual using a Man₉-V3 glycopeptide. 2D class averages obtained from negative stain electron microscopy (NSEM) experiments confirm that IA4 binds stoichiometrically to the Env trimer, but most of the population of complexes is not fully saturated with IA4. A high resolution cryo-EM structure will elucidate the contacts made by this bNAb precursor and comparing them to those made by the bNAb will contribute to our knowledge of how one family of bNAbs was able to evolve to broadly neutralize Env. We also describe a crystal structure of an antibody, termed DH717.1, isolated from rhesus macaques immunized with the HIV-1 Env Man₉-V3 glycopeptide. DH717.1 did not incorporate any of the V3 loop into its recognition epitope but recognized α1 → 2 mannose glycan moieties. This structure provides initial information on the immunization potential of the lone V3 loop glycopeptide to produce bNAbs.