UNRAVELING THE MOLECULAR BASIS OF MHC-I ANTIGEN PROOFREADING BY THE CHAPERONE TAPBPR

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Degree type
Doctor of Philosophy (PhD)
Graduate group
Biochemistry and Molecular Biophysics
Discipline
Immunology and Infectious Disease
Biochemistry, Biophysics, and Structural Biology
Biochemistry, Biophysics, and Structural Biology
Subject
antigen processing and presentation
human leukocyte antigen
MHC-I
peptide exchange
proofreading
TAPBPR
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2024
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Author
Sun, Yi
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Abstract

Class I major histocompatibility complex proteins play a pivotal role in adaptive immunity by displaying epitopic peptides to CD8+ T cells. Dedicated molecular chaperones of MHC-I, tapasin and TAP-binding protein-related (TAPBPR), promote the selection of immunogenic antigens from a large pool of intracellular peptides. These chaperones stabilize nascent MHC-I, allowing the loading of the peptides to the empty peptide binding groove, the exchange of low-to-moderate affinity for high-affinity peptides (editing), and the momentary capture and release of peptides from a large peptide pool (proofreading). Interactions of the chaperoned MHC-I molecules with incoming peptides are transient in nature, and as a result, the precise antigen proofreading mechanism remains elusive. Therefore, this thesis work aims to understand the peptide proofreading mechanism of MHC-I by capturing and examining the biologically relevant MHC-I/TAPBPR peptide proofreading complex. Here, I demonstrate and characterize the direct interactions between TAPBPR and a repertoire of human MHC-I allotypes, revealing the polymorphic residues on the MHC-I/TAPBPR interacting surfaces can be engineered for altered chaperone recognition. Using deep mutational scanning of TAPBPR expressed at the plasma membrane, several gain-of-function TAPBPR mutants were identified that could significantly enhance the peptide exchange function of multiple disease-relevant MHC-I allotypes. I also adapt a structure-guided approach to engineering conformationally stable MHC-I molecules, named “open MHC-I,” by introducing a disulfide bond bridging conserved sites across the polymorphic MHC-I heavy chain and invariable light chain β2m interface (G120C and H31C). I show that the interchain disulfide bond increases the thermostability of molecules loaded with low- and moderate-affinity peptide cargos. Finally, we leverage one of the engineered high-fidelity TAPBPR variants, TAPBPRHiFi, containing three mutations (S104F, K211L, and R270Q) at the MHC-I binding site and conformationally stabilized open MHC-I to determine the solution structure of the human antigen proofreading complex of MHC-I/TAPBPR bound to a peptide decoy by cryogenic electron microscopy at an average resolution of 3.0 Å. Antigen proofreading is mediated by transient interactions formed between the nascent peptide binding groove with the N-terminal P2/P3 peptide anchors. Altogether, this work has important ramifications for understanding the selection of immunogenic epitopes for T cell screening and vaccine design applications.

Advisor
Sgourakis, Nikolaos, G.
Date of degree
2024
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