Structural characterization and AlphaFold modeling of human T cell receptor recognition of NRAS cancer neoantigens
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Abstract
T cell receptors (TCRs) that recognize cancer neoantigens are important for anticancer immune responses and immunotherapy. Understanding the structural basis of TCR recognition of neoantigens provides insights into their exquisite specificity and can enable design of optimized TCRs. We determined crystal structures of a human TCR in complex with NRAS Q61K and Q61R neoantigen peptides and HLA-A1 major histocompatibility complex (MHC), revealing the molecular underpinnings for dual recognition and specificity versus wild-type NRAS peptide. We then used multiple versions of AlphaFold to model the corresponding complex structures, given the challenge of immune recognition for such methods. One implementation of AlphaFold2 (TCRmodel2) with additional sampling was able to generate accurate models of the complexes, while AlphaFold3 also showed strong performance, although success was lower for other complexes. This study provides insights into TCR recognition of a shared cancer neoantigen as well as the utility and practical considerations for using AlphaFold to model TCR-peptide-MHC complexes.
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- Authors
- Wu, D., Yin, R., Chen, G., Ribeiro-Filho, H. V., Cheung, M., Robbins, P. F., Mariuzza, R. A., & Pierce, B. G.
- Affiliations
- First Affiliated Hospital of University of South China (CN)
- Institute for Bioscience and Biotechnology Research (US)
- W. M. Keck Laboratory for Structural Biology, University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA.
- National Cancer Institute (US)
- Corresponding author
- Pierce, Brian G.
- ORCID
- Venue
- Science Advances
- Published
- 2024-11-22
- Volume
- 10
- Issue
- 47
- Pages
- eadq6150-eadq6150
- ISSN
- 2375-2548 (ISSN-L)
- PMC
- PMC11584006
- OpenAlex
- W4404627616
- Cited by
- 27
- References
- 57
- Citations by year
- 2026: 14 · 2025: 12 · 2024: 1
- FWCI
- 3.66
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Science Advances (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by-nd)
- Funders
- University of Chicago
- National Institutes of Health
- National Institute of General Medical Sciences (R35GM144083)
- National Institute of Allergy and Infectious Diseases (R01AI129893)
- Argonne National Laboratory
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
- Health Sciences › Medicine › Oncology › Cancer Immunotherapy and Biomarkers
- Keywords
- T cell receptor, neoantigens, NRAS Q61K, NRAS Q61R, TCR-peptide-MHC complex, HLA-A1, AlphaFold3, AlphaFold2, TCR engineering
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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