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Deciphering cross-species reactivity of LAMP-1 antibodies using deep mutational epitope mapping and AlphaFold
Delineating the precise regions on an antigen that are targeted by antibodies has become a key step for the development of antibody therapeutics. X-ray crystallography and cryogenic electron microscopy are considered the gold standard for providing precise information about these binding sites at at...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Taylor & Francis
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9980635/ https://www.ncbi.nlm.nih.gov/pubmed/36797224 http://dx.doi.org/10.1080/19420862.2023.2175311 |
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author | Pruvost, Tiphanie Mathieu, Magali Dubois, Steven Maillère, Bernard Vigne, Emmanuelle Nozach, Hervé |
author_facet | Pruvost, Tiphanie Mathieu, Magali Dubois, Steven Maillère, Bernard Vigne, Emmanuelle Nozach, Hervé |
author_sort | Pruvost, Tiphanie |
collection | PubMed |
description | Delineating the precise regions on an antigen that are targeted by antibodies has become a key step for the development of antibody therapeutics. X-ray crystallography and cryogenic electron microscopy are considered the gold standard for providing precise information about these binding sites at atomic resolution. However, they are labor-intensive and a successful outcome is not guaranteed. We used deep mutational scanning (DMS) of the human LAMP-1 antigen displayed on yeast surface and leveraged next-generation sequencing to observe the effect of individual mutants on the binding of two LAMP-1 antibodies and to determine their functional epitopes on LAMP-1. Fine-tuned epitope mapping by DMS approaches is augmented by knowledge of experimental antigen structure. As human LAMP-1 structure has not yet been solved, we used the AlphaFold predicted structure of the full-length protein to combine with DMS data and ultimately finely map antibody epitopes. The accuracy of this method was confirmed by comparing the results to the co-crystal structure of one of the two antibodies with a LAMP-1 luminal domain. Finally, we used AlphaFold models of non-human LAMP-1 to understand the lack of mAb cross-reactivity. While both epitopes in the murine form exhibit multiple mutations in comparison to human LAMP-1, only one and two mutations in the Macaca form suffice to hinder the recognition by mAb B and A, respectively. Altogether, this study promotes a new application of AlphaFold to speed up precision mapping of antibody–antigen interactions and consequently accelerate antibody engineering for optimization. |
format | Online Article Text |
id | pubmed-9980635 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Taylor & Francis |
record_format | MEDLINE/PubMed |
spelling | pubmed-99806352023-03-03 Deciphering cross-species reactivity of LAMP-1 antibodies using deep mutational epitope mapping and AlphaFold Pruvost, Tiphanie Mathieu, Magali Dubois, Steven Maillère, Bernard Vigne, Emmanuelle Nozach, Hervé MAbs Report Delineating the precise regions on an antigen that are targeted by antibodies has become a key step for the development of antibody therapeutics. X-ray crystallography and cryogenic electron microscopy are considered the gold standard for providing precise information about these binding sites at atomic resolution. However, they are labor-intensive and a successful outcome is not guaranteed. We used deep mutational scanning (DMS) of the human LAMP-1 antigen displayed on yeast surface and leveraged next-generation sequencing to observe the effect of individual mutants on the binding of two LAMP-1 antibodies and to determine their functional epitopes on LAMP-1. Fine-tuned epitope mapping by DMS approaches is augmented by knowledge of experimental antigen structure. As human LAMP-1 structure has not yet been solved, we used the AlphaFold predicted structure of the full-length protein to combine with DMS data and ultimately finely map antibody epitopes. The accuracy of this method was confirmed by comparing the results to the co-crystal structure of one of the two antibodies with a LAMP-1 luminal domain. Finally, we used AlphaFold models of non-human LAMP-1 to understand the lack of mAb cross-reactivity. While both epitopes in the murine form exhibit multiple mutations in comparison to human LAMP-1, only one and two mutations in the Macaca form suffice to hinder the recognition by mAb B and A, respectively. Altogether, this study promotes a new application of AlphaFold to speed up precision mapping of antibody–antigen interactions and consequently accelerate antibody engineering for optimization. Taylor & Francis 2023-02-16 /pmc/articles/PMC9980635/ /pubmed/36797224 http://dx.doi.org/10.1080/19420862.2023.2175311 Text en © 2023 The Author(s). Published with license by Taylor & Francis Group, LLC. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/ (https://creativecommons.org/licenses/by-nc/4.0/) ), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Report Pruvost, Tiphanie Mathieu, Magali Dubois, Steven Maillère, Bernard Vigne, Emmanuelle Nozach, Hervé Deciphering cross-species reactivity of LAMP-1 antibodies using deep mutational epitope mapping and AlphaFold |
title | Deciphering cross-species reactivity of LAMP-1 antibodies using deep mutational epitope mapping and AlphaFold |
title_full | Deciphering cross-species reactivity of LAMP-1 antibodies using deep mutational epitope mapping and AlphaFold |
title_fullStr | Deciphering cross-species reactivity of LAMP-1 antibodies using deep mutational epitope mapping and AlphaFold |
title_full_unstemmed | Deciphering cross-species reactivity of LAMP-1 antibodies using deep mutational epitope mapping and AlphaFold |
title_short | Deciphering cross-species reactivity of LAMP-1 antibodies using deep mutational epitope mapping and AlphaFold |
title_sort | deciphering cross-species reactivity of lamp-1 antibodies using deep mutational epitope mapping and alphafold |
topic | Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9980635/ https://www.ncbi.nlm.nih.gov/pubmed/36797224 http://dx.doi.org/10.1080/19420862.2023.2175311 |
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