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Structure-based modeling of SARS-CoV-2 peptide/HLA-A02 antigens

Santrupti Nerli, View ORCID ProfileNikolaos G. Sgourakis
doi: https://doi.org/10.1101/2020.03.23.004176
Santrupti Nerli
1Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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Nikolaos G. Sgourakis
2Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA 95064, USA
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  • ORCID record for Nikolaos G. Sgourakis
  • For correspondence: nsgourak@ucsc.edu
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ABSTRACT

As a first step toward the development of diagnostic and therapeutic tools to fight the Coronavirus disease (COVID-19), we aim to characterize CD8+ T cell epitopes in the SARS-CoV-2 peptidome that can trigger adaptive immune responses. Here, we use RosettaMHC, a comparative modeling approach which leverages existing high-resolution X-ray structures from peptide/MHC complexes available in the Protein Data Bank, to derive physically realistic 3D models for high-affinity SARS-CoV-2 epitopes. We outline an application of our method to model 439 9mer and 279 10mer predicted epitopes displayed by the common allele HLA-A*02:01, and we make our models publicly available through an online database (https://rosettamhc.chemistry.ucsc.edu). As more detailed studies on antigen-specific T cell repertoires become available, RosettaMHC models of antigens from different strains and HLA alleles can be used as a basis to understand the link between peptide/HLA complex structure and surface chemistry with immunogenicity, in the context of SARS-CoV-2 infection.

Footnotes

  • https://rosettamhc.chemistry.ucsc.edu

  • https://github.com/snerligit/mhc-pep-threader

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted March 27, 2020.
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Structure-based modeling of SARS-CoV-2 peptide/HLA-A02 antigens
Santrupti Nerli, Nikolaos G. Sgourakis
bioRxiv 2020.03.23.004176; doi: https://doi.org/10.1101/2020.03.23.004176
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Structure-based modeling of SARS-CoV-2 peptide/HLA-A02 antigens
Santrupti Nerli, Nikolaos G. Sgourakis
bioRxiv 2020.03.23.004176; doi: https://doi.org/10.1101/2020.03.23.004176

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