Kelly K Lee

An HIV-1 Broadly Neutralizing Antibody Overcomes Structural and Dynamic Variation through Highly Focused Epitope Targeting

Edgar A. Hodge1, Ananya Chatterjee3, Chengbo Chen1,2, Meghan McGrath1, Gajendra S. Naika1, Mint Laohajaratsang1, David Montefiori4, Vidya Mangala Prasad1,3, Kelly K. Lee1,2*

1. Department of Medicinal Chemistry, University of Washington, Seattle, WA 98195, USA.
2. Biological Physics, Structure and Design Graduate Program, University of Washington, Seattle, WA 98195, USA
3. Molecular Biophysics Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India.
4. Laboratory for AIDS Vaccine Research & Development; Department of Surgery; Duke University Medical Center, Durham, NC USA

Introduction: The HIV-1 envelope glycoprotein (Env) mediates receptor binding and membrane fusion to initiate infection of a host cell. Env is the sole target for neutralizing antibodies and is under intense immune pressures, causing it to evolve and diversify into the most highly variable part of the virus. While recent studies have reported high-resolution structures for Env, however they represent static, platonic ideals, and structural and functional implications of Env variation remain poorly understood. Indeed, under native conditions, Env dynamically flickers between antigenically and functionally distinct conformational states. Probing the impact of these dynamic traits on Env-antibody recognition is essential for understanding the underlying basis for differences in antigenic and neutralization profiles among HIV-1 isolates.

Methods: We used hydrogen/deuterium-exchange mass spectrometry (HDX-MS) and quantitative measurements of antibody binding kinetics by biolayer interferometry to investigate HIV Env structural dynamic variation and to measure the effect of epitope dynamics on antibody binding ability. Single-particle cryo-EM was also used to image the 3-dimensional structure of a broadly cross-reactive antibody that can neutralize diverse HIV-1 isolates (bnAb) in complex with two highly divergent Env variants.

Preliminary data: The existence of remarkable bnAbs against HIV-1 has been appreciated for more than a decade. Understanding how these antibodies grapple with variability in their targets across diverse viral isolates however lags, as this requires first characterizing the extent of structural and antigenic variation embodied in Env and then identifying how a bnAb overcomes that variation at a structural level. HDX-MS and BLI experiments show that variation in structural ordering and local dynamics in the V1/V2 apex of Env across a globally representative panel of HIV-1 isolates has a marked effect on antibody association rates and affinities. We also report cryo-EM structures of an apex-targeting bnAb bound to two divergent Env that exhibit different degrees of structural dynamics throughout their trimer structures. Parallel HDX-MS experiments demonstrate that this bnAb has an exquisitely focused binding footprint at the trimer apex where binding did not result in allosteric changes throughout the rest of the structure. These results demonstrate that structural dynamics are a cryptic determinant of antigenicity, and mature antibodies that have achieved breadth and potency in some cases achieve broad cross-reactivity by “threading the needle” and binding in a highly focused fashion.

Novel aspect: Structural mass spectrometry combined with cryo-EM elucidates how a bnAb overcomes antigenic variation in HIV-1, providing guidance for vaccine design.

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