CHARACTERIZING THE STRUCTURE AND DYNAMICS OF ADAPTIVE IMMUNE PROTEINS TO INFORM IMMUNOTHERAPY DESIGN

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Degree type
PhD
Graduate group
Biochemistry and Molecular Biophysics
Discipline
Biochemistry, Biophysics, and Structural Biology
Immunology and Infectious Disease
Biochemistry, Biophysics, and Structural Biology
Subject
IL-2
interleukin-2
major histocompatability complex
MHC
Nuclear Magnetic Resonance
T cell receptor
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Copyright date
01/01/2025
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Author
Woodward, Claire
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Abstract

Human interleukin-2 (IL-2) is a crucial cytokine for T cell regulation, with therapeutic potential in cancer and autoimmune diseases. However, IL-2's pleiotropic effects across different immune cell types often lead to toxicity and limited efficacy. The first study in this thesis presents a detailed characterization of IL-2 dynamics compared to two engineered IL-2 mutants, “superkines” S15 and S1, which exhibit biased signaling towards effector T cells. Using NMR spectroscopy and molecular dynamics simulations, we demonstrate significant variations in core dynamic landscapes across the three variants. Furthermore, we rationally design a mutation (L56A) in the S1 core network, which partially reverts its dynamics, receptor binding affinity, and T cell signaling behavior. Our results suggest that modulating IL-2 dynamics is an untapped approach for designing immunotherapies with improved immune cell selectivity profiles.The intrinsic instability and inconsistent T cell receptor binding mode of the class I major histocompatibility complex (MHC-I) are fundamental challenges that hinder development of therapeutics. The second study leverages the positive allosteric coupling between the peptide and β2m subunits of MHC-I by engineering a disulfide bond bridging conserved epitopes across the HC/β2m interface to generate stable, peptide-receptive molecules. Using solution NMR, we demonstrate that the disulfide bond induces long-range conformational and dynamical changes in the α2-1 helix., indicating that the interchain disulfide bond stabilizes MHC-I molecules in an open conformation to promote peptide exchange. In the third study, we demonstrate the application of a designed MHC-I design, SMART A02:01, for solution mapping of the A6c134 TCR docking footprint using NMR spectroscopy. We establish that the use of our engineered construct recapitulates the native conformation of the MHC-I peptide binding groove and accurately detects the critical binding sites on SMART A02:01 that engage A6c134. Our approach allows for high-resolution mapping of TCR/MHC-I interactions, alleviating the need for complete structure elucidation, and may be paired with computational modeling approaches for structure-guided optimization and clinical development. Taken together, solution NMR techniques provide high-resolution insights into protein structure and conformational dynamics. Furthermore, these efforts highlight the application of NMR analyses to inform rational protein design and guide the development of diagnostics and therapeutics.

Advisor
Sgourakis, Nikolaos, G
Date of degree
2025
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