Periodic Reporting for period 4 - EditMHC (How MHC-I editing complexes shape the hierarchical immune response)
Reporting period: 2023-07-01 to 2024-12-31
The immune system constantly patrols our bodies, monitoring cells for signs of infection or abnormality. A key mechanism of this surveillance involves Major Histocompatibility Complex (MHC) molecules, which display small protein fragments—called peptides or antigens—on the cell surface. These peptides originate from within the cell and reflect its internal state. When immune cells detect foreign or unusual peptides, such as those from viruses or mutated proteins, they launch a targeted response to eliminate the affected cell and protect the body.
To enable this process, cells rely on a specialized system that operates within the endoplasmic reticulum (ER). This machinery not only transports antigenic peptides into the ER but also ensures that only those peptides capable of tightly binding to MHC molecules are selected and loaded. Central to this system is a large protein assembly known as the peptide-loading complex (PLC). The PLC’s transporter component moves peptides into the ER, while its chaperone and editing modules assist in the precise loading of these peptides onto MHC molecules. Until a suitable peptide is bound, MHC molecules remain unstable and are safeguarded by chaperone proteins. Once fully assembled, these MHC-peptide complexes exit the ER and present their peptide cargo at the cell surface, where they can be scanned by the immune system. Because of its pivotal role in immune detection, the PLC is a frequent target of viral evasion strategies. Viruses such as herpesviruses and poxviruses have evolved proteins that disrupt or block PLC function to avoid immune recognition and destruction.
This project has substantially advanced our understanding of these mechanisms by elucidating how different protein modules within the PLC interact to enable effective immune responses. These insights lay the groundwork for improved vaccine strategies and the development of new therapies for infectious diseases, cancer, autoimmune conditions, and transplant rejection.
To enable this process, cells rely on a specialized system that operates within the endoplasmic reticulum (ER). This machinery not only transports antigenic peptides into the ER but also ensures that only those peptides capable of tightly binding to MHC molecules are selected and loaded. Central to this system is a large protein assembly known as the peptide-loading complex (PLC). The PLC’s transporter component moves peptides into the ER, while its chaperone and editing modules assist in the precise loading of these peptides onto MHC molecules. Until a suitable peptide is bound, MHC molecules remain unstable and are safeguarded by chaperone proteins. Once fully assembled, these MHC-peptide complexes exit the ER and present their peptide cargo at the cell surface, where they can be scanned by the immune system. Because of its pivotal role in immune detection, the PLC is a frequent target of viral evasion strategies. Viruses such as herpesviruses and poxviruses have evolved proteins that disrupt or block PLC function to avoid immune recognition and destruction.
This project has substantially advanced our understanding of these mechanisms by elucidating how different protein modules within the PLC interact to enable effective immune responses. These insights lay the groundwork for improved vaccine strategies and the development of new therapies for infectious diseases, cancer, autoimmune conditions, and transplant rejection.
This project delivers a rich and cohesive narrative on the molecular foundations of antigen processing and presentation, with far-reaching implications for immunology, virology, and therapeutic development. The studies collectively detail how antigenic peptides are translocated, selected, and presented by MHC I molecules, and how this process is regulated, hijacked, or modulated.
Key findings include the full structural cycle of ATP-binding cassette (ABC) transporters involved in peptide translocation, revealing that ATP binding alone can drive conformational changes necessary for substrate movement. This insight revises longstanding models of ATP-coupled transport and highlights a unidirectional power stroke mechanism. In the context of the immune system, this mechanistic knowledge informs how the ABC transporter associated with antigen processing (TAP) fuels antigen import into the ER.
Parallel structural and functional studies on the peptide-loading complex (PLC) uncovered the critical role of chaperones like tapasin, TAPBPR, and ERp57 in stabilizing and editing MHC I-peptide interactions. Several publications resolved high-resolution structures of various PLC subcomplexes, elucidating how these components work in concert to ensure that only high-affinity peptides are presented at the cell surface. Importantly, the studies also demonstrated the dynamic interplay between peptide selection and N-linked glycan processing, tightly linking MHC I quality control to ER homeostasis.
Viral immune evasion was another focal point. Structural and functional studies showed how herpesviral proteins (e.g. ICP47 and US6) arrest the PLC in specific conformational states or block MHC I trafficking altogether. These mechanisms help viruses evade cytotoxic T cell detection. Tools such as semisynthetic, light-controllable inhibitors of the PLC were developed to probe and potentially exploit these evasion strategies therapeutically.
On the technological front, the use of synthetic biology platforms, cryo-EM, and super-resolution imaging enabled the precise visualization of molecular complexes and their spatiotemporal organization in living cells. These approaches also paved the way for quantitative measurements of peptide transport and editing, making it possible to dissect the energetic landscape of antigen processing with unprecedented precision.
The exploitation and dissemination of these results have been robust. Findings have laid a structural and mechanistic foundation for rational vaccine design and immunotherapies targeting cancer and infectious diseases. In particular, insights into TCR-peptide-MHC I interactions provide a molecular blueprint for developing T cell-based therapies. Several tools and methods, including macrocyclic peptide inhibitors and synthetic PLC regulators, are readily adaptable for academic and translational research.
Dissemination has occurred through high-impact publications in Nature, Cell, Nature Communications, eLife, and PNAS, as well as in key review articles in Annu Rev Biochem and Annu Rev Biophys that summarize and contextualize the findings for broader audiences in structural biology, immunology, and virology. Data and structural models have been made publicly available in repositories such as the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB), further enhancing accessibility and reuse. Additionally, insights from these works have been presented at major international conferences and integrated into educational and collaborative research networks, facilitating continued knowledge exchange across disciplines.
Key findings include the full structural cycle of ATP-binding cassette (ABC) transporters involved in peptide translocation, revealing that ATP binding alone can drive conformational changes necessary for substrate movement. This insight revises longstanding models of ATP-coupled transport and highlights a unidirectional power stroke mechanism. In the context of the immune system, this mechanistic knowledge informs how the ABC transporter associated with antigen processing (TAP) fuels antigen import into the ER.
Parallel structural and functional studies on the peptide-loading complex (PLC) uncovered the critical role of chaperones like tapasin, TAPBPR, and ERp57 in stabilizing and editing MHC I-peptide interactions. Several publications resolved high-resolution structures of various PLC subcomplexes, elucidating how these components work in concert to ensure that only high-affinity peptides are presented at the cell surface. Importantly, the studies also demonstrated the dynamic interplay between peptide selection and N-linked glycan processing, tightly linking MHC I quality control to ER homeostasis.
Viral immune evasion was another focal point. Structural and functional studies showed how herpesviral proteins (e.g. ICP47 and US6) arrest the PLC in specific conformational states or block MHC I trafficking altogether. These mechanisms help viruses evade cytotoxic T cell detection. Tools such as semisynthetic, light-controllable inhibitors of the PLC were developed to probe and potentially exploit these evasion strategies therapeutically.
On the technological front, the use of synthetic biology platforms, cryo-EM, and super-resolution imaging enabled the precise visualization of molecular complexes and their spatiotemporal organization in living cells. These approaches also paved the way for quantitative measurements of peptide transport and editing, making it possible to dissect the energetic landscape of antigen processing with unprecedented precision.
The exploitation and dissemination of these results have been robust. Findings have laid a structural and mechanistic foundation for rational vaccine design and immunotherapies targeting cancer and infectious diseases. In particular, insights into TCR-peptide-MHC I interactions provide a molecular blueprint for developing T cell-based therapies. Several tools and methods, including macrocyclic peptide inhibitors and synthetic PLC regulators, are readily adaptable for academic and translational research.
Dissemination has occurred through high-impact publications in Nature, Cell, Nature Communications, eLife, and PNAS, as well as in key review articles in Annu Rev Biochem and Annu Rev Biophys that summarize and contextualize the findings for broader audiences in structural biology, immunology, and virology. Data and structural models have been made publicly available in repositories such as the Protein Data Bank (PDB) and Electron Microscopy Data Bank (EMDB), further enhancing accessibility and reuse. Additionally, insights from these works have been presented at major international conferences and integrated into educational and collaborative research networks, facilitating continued knowledge exchange across disciplines.
This project substantially advances the understanding of antigen processing at the molecular level, surpassing prior knowledge in several key ways. It provides the first complete structural snapshots of ABC transporters during the peptide translocation cycle, overturning established models by demonstrating that ATP binding—not hydrolysis—is sufficient to drive substrate transport in some contexts. High-resolution cryo-EM structures of the peptide-loading complex (PLC) and its viral-inhibited states uncover the dynamic interactions between MHC I, chaperones, and viral immune evasion proteins, revealing previously uncharacterized mechanisms of quality control and antigen editing. The discovery of an allosteric coupling between glycan processing and peptide selection, as well as the structural basis of viral interference with antigen presentation, represents a major conceptual leap. Novel chemical biology tools, including light-controlled PLC inhibitors and synthetic transport systems, offer entirely new ways to study and manipulate antigen processing.