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Combating HIV with Novel Antibody Architectures


Galimidi, Rachel P. (2016) Combating HIV with Novel Antibody Architectures. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/Z9QC01FR.


More than 30 years has passed since the discovery of Human Immunodeficiency Virus (HIV) yet it remains one of the most important current threats to global public health. HIV is a T-lymphotrophic retrovirus that is the causative agent of Acquired Immune Deficiency Syndrome, and despite decades of research, there remains no cure. Vaccines are most effective when they are able to induce broadly neutralizing antibodies at concentrations capable of blocking viral infection. Notwithstanding all of the effort, a successful vaccine that is capable of inducing complete protection from the immune system has yet to be found. In this thesis, the first chapter provides a history of the discovery of HIV, the origins of the virus, description of the HIV genome, focusing primarily on the envelope glycoprotein, a trimeric spike on the surface of the HIV virion necessary for viral fusion and the sole epitope for broadly neutralizing antibodies. Lastly, the first chapter reviews an overview of the antiviral immune response specifically the role of humoral immune branch and broadly neutralizing antibodies, as well as their limitations in protection against HIV. Antibodies developed during HIV-1 infection lose efficacy as the viral spike mutates. In addition to structural features of HIV’s envelope spike that facilitate antibody evasion, we proposed that the low-density and limited lateral mobility of HIV spikes impedes bivalent binding by antibodies. The resulting predominantly monovalent binding minimizes avidity and thereby high affinity binding and potent neutralization, thus expanding the range of HIV mutations permitting antibody evasion. The work described in subsequent chapters attempts to overcome HIV’s evasion strategy of low spike density through the design of novel antibody architectures.

We postulated that anti-HIV-1 spike antibodies primarily bind monovalently because HIV’s low spike density impedes bivalent binding through inter-spike crosslinking, and the spike trimer structure prohibits bivalent binding through intra-spike crosslinking. Monovalent binding reduces avidity and neutralization potency, thus expanding the range of mutations permitting antibody evasion. To test this idea, we engineered antibody-based molecules capable of bivalent binding through intra-spike crosslinking. We used DNA as a “molecular ruler” to measure intra-epitope distances on virion-bound spikes and to construct intra-spike crosslinking molecules. Optimal bivalent reagents exhibited up to 2.5 orders of magnitude of increased potency (>100-fold average increases across a virus panel) and identified conformational states of virion-bound spikes. The demonstration that intra-spike crosslinking lowers the concentration of antibodies required for neutralization supports the hypothesis that low spike densities facilitate antibody evasion and the use of molecules capable of intra-spike crosslinking for therapy or passive protection. These results shed light on dynamic spike conformations and are relevant to therapeutic interventions.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:HIV ; Antibody ; Engineering
Degree Grantor:California Institute of Technology
Division:Biology and Biological Engineering
Major Option:Immunology
Awards:Milton and Francis Clauser Doctoral Prize, 2016. Demetriades-Tsafka-Kokkalis Prize in Biotechnology or Related Fields, 2016. Lawrence L. and Audrey W. Ferguson Prize, 2016.
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Bjorkman, Pamela J. (advisor)
  • Baltimore, David L. (co-advisor)
Thesis Committee:
  • Mazmanian, Sarkis K. (chair)
  • Clemons, William M.
  • Rothenberg, Ellen V.
  • Zack, Jerome
Defense Date:5 February 2016
Non-Caltech Author Email:rachelgalimidi (AT)
Funding AgencyGrant Number
NIH Director's Pioneer AwardUNSPECIFIED
Record Number:CaltechTHESIS:06082016-141626444
Persistent URL:
Related URLs:
URLURL TypeDescription adapted for ch. 2 adapted for ch. 2 adapted for ch. 2 adapted for ch. 3 adapted for ch. 4 adapted for Appendix B
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:9864
Deposited By: Rachel Galimidi
Deposited On:16 Jun 2016 20:40
Last Modified:08 Nov 2023 00:16

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