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Ma J, Ayres CM, Brambley CA, Chandran SS, Rosales TJ, Corcelli SA, Kovrigin EL, Klebanoff CA, Baker BM. Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity. RESEARCH SQUARE 2024:rs.3.rs-4457195. [PMID: 38854019 PMCID: PMC11160895 DOI: 10.21203/rs.3.rs-4457195/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The inherent cross-reactivity of the T cell receptor (TCR) is balanced by high specificity, which often manifests in confounding ways not easily interpretable from static structures. We show here that TCR discrimination between an HLA-A*03:01 (HLA-A3)-restricted public neoantigen derived from mutant PIK3CA and its wild-type (WT) counterpart emerges from motions within the HLA binding groove that vary with the identity of the peptide's first primary anchor. The motions form a dynamic gate that in the complex with the WT peptide impedes a large conformational change required for TCR binding. The more rigid neoantigen is insusceptible to this limiting dynamic, and with the gate open, is able to transit its central tryptophan residue underneath the peptide backbone to the contralateral side of the HLA-A3 peptide binding groove, facilitating TCR binding. Our findings reveal a novel mechanism driving TCR specificity for a cancer neoantigen that is rooted in the dynamic and allosteric nature of peptide/MHC-I complexes, with implications for resolving long-standing and often confounding questions about the determinants of T cell specificity.
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Affiliation(s)
- Jiaqi Ma
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Chad A Brambley
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Smita S Chandran
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
- Center for Cell Engineering, MSKCC, New York, NY, USA
| | - Tatiana J Rosales
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
| | - Steven A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Evgenii L Kovrigin
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Christopher A Klebanoff
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center (MSKCC), New York, NY, USA
- Center for Cell Engineering, MSKCC, New York, NY, USA
- Weill Cornell Medical College, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, New York, NY, USA
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
- Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN, USA
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Ayres CM, Corcelli SA, Baker BM. The Energetic Landscape of Catch Bonds in TCR Interfaces. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:325-332. [PMID: 37459192 PMCID: PMC10361606 DOI: 10.4049/jimmunol.2300121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/14/2023] [Indexed: 07/20/2023]
Abstract
Recognition of peptide/MHC complexes by αβ TCRs has traditionally been viewed through the lens of conventional receptor-ligand theory. Recent work, however, has shown that TCR recognition and T cell signaling can be profoundly influenced and tuned by mechanical forces. One outcome of applied force is the catch bond, where TCR dissociation rates decrease (half-lives increase) when limited force is applied. Although catch bond behavior is believed to be widespread in biology, its counterintuitive nature coupled with the difficulties of describing mechanisms at the structural level have resulted in considerable mystique. In this review, we demonstrate that viewing catch bonds through the lens of energy landscapes, barriers, and the ensuing reaction rates can help demystify catch bonding and provide a foundation on which atomic-level TCR catch bond mechanisms can be built.
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Affiliation(s)
- Cory M Ayres
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
- The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN
| | - Steve A Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
| | - Brian M Baker
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN
- The Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN
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Petrova GV, Naumov YN, Naumova EN, Gorski J. Role of cross-reactivity in cellular immune targeting of influenza A M1 58-66 variant peptide epitopes. Front Immunol 2022; 13:956103. [PMID: 36211433 PMCID: PMC9539824 DOI: 10.3389/fimmu.2022.956103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 09/02/2022] [Indexed: 11/30/2022] Open
Abstract
The immunologic significance of cross-reactivity of TCR recognition of peptide:MHC complexes is still poorly understood. We have described TCR cross-reactivity in a system involving polyclonal CD8 T cell recognition of the well characterized influenza viral M158-66 epitope. While M158-66 is generally conserved between influenza A isolates, error-prone transcription generates stable variant RNA during infection which could act as novel epitopes. If packaged and viable, variant genomic RNA generates an influenza quasispecies. The stable RNA variants would generate a new transmissible epitope that can select a specific repertoire, which itself should have cross-reactive properties. We tested two candidate peptides in which Thr65 is changed to Ala (A65) or Ser (S65) using recall responses to identify responding T cell clonotypes. Both peptides generated large polyclonal T cell repertoires of their own with repertoire characteristics and cross-reactivity patterns like that observed for the M158-66 repertoire. Both substitutions could be present in viral genomes or mRNA at sufficient frequency during an infection to drive immunity. Peptides from the resulting protein would be a target for CD8 cells irrespective of virus viability or transmissibility. These data support the hypothesis that cross-reactivity is important for immunity against RNA virus infections.
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Affiliation(s)
- Galina V. Petrova
- The Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, United States
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI, United States
| | | | - Elena N. Naumova
- Division of Nutrition Epidemiology and Data Science, Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, United States
| | - Jack Gorski
- The Blood Research Institute, Versiti Wisconsin, Milwaukee, WI, United States
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