Extended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfaces
Here, the authors analyse the distance between the body of an antibody and a protein antigen denoted as the Antibody-Framework-to-Antigen Distance (AFAD) for about 2000 non-redundant antibody-protein antigen complexes in the Protein Data Bank. They observe that antibodies with exceptionally long AFA...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2021-11-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-021-26579-z |
| _version_ | 1818837763009544192 |
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| author | Myungjin Lee Anita Changela Jason Gorman Reda Rawi Tatsiana Bylund Cara W. Chao Bob C. Lin Mark K. Louder Adam S. Olia Baoshan Zhang Nicole A. Doria-Rose Susan Zolla-Pazner Lawrence Shapiro Gwo-Yu Chuang Peter D. Kwong |
| author_facet | Myungjin Lee Anita Changela Jason Gorman Reda Rawi Tatsiana Bylund Cara W. Chao Bob C. Lin Mark K. Louder Adam S. Olia Baoshan Zhang Nicole A. Doria-Rose Susan Zolla-Pazner Lawrence Shapiro Gwo-Yu Chuang Peter D. Kwong |
| author_sort | Myungjin Lee |
| collection | DOAJ |
| description | Here, the authors analyse the distance between the body of an antibody and a protein antigen denoted as the Antibody-Framework-to-Antigen Distance (AFAD) for about 2000 non-redundant antibody-protein antigen complexes in the Protein Data Bank. They observe that antibodies with exceptionally long AFADs were all broad HIV-1-neutralizing antibodies that targeted densely glycosylated regions on the HIV-1-envelope trimer. The connection between long AFAD and dense glycan was further validated by the cryo-EM structure of antibody 2909 recognizing a glycan hole and by glycan shielding analyses based on molecular dynamics simulations. |
| first_indexed | 2024-12-19T03:27:40Z |
| format | Article |
| id | doaj.art-c6314cb8177848269383e9f05a200718 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-12-19T03:27:40Z |
| publishDate | 2021-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-c6314cb8177848269383e9f05a2007182022-12-21T20:37:33ZengNature PortfolioNature Communications2041-17232021-11-0112111010.1038/s41467-021-26579-zExtended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfacesMyungjin Lee0Anita Changela1Jason Gorman2Reda Rawi3Tatsiana Bylund4Cara W. Chao5Bob C. Lin6Mark K. Louder7Adam S. Olia8Baoshan Zhang9Nicole A. Doria-Rose10Susan Zolla-Pazner11Lawrence Shapiro12Gwo-Yu Chuang13Peter D. Kwong14Vaccine Research Center, NIAID, National Institutes of HealthVaccine Research Center, NIAID, National Institutes of HealthVaccine Research Center, NIAID, National Institutes of HealthVaccine Research Center, NIAID, National Institutes of HealthVaccine Research Center, NIAID, National Institutes of HealthVaccine Research Center, NIAID, National Institutes of HealthVaccine Research Center, NIAID, National Institutes of HealthVaccine Research Center, NIAID, National Institutes of HealthVaccine Research Center, NIAID, National Institutes of HealthVaccine Research Center, NIAID, National Institutes of HealthVaccine Research Center, NIAID, National Institutes of HealthDepartment of Medicine and Department of Microbiology, Icahn School of Medicine at Mount SinaiVaccine Research Center, NIAID, National Institutes of HealthVaccine Research Center, NIAID, National Institutes of HealthVaccine Research Center, NIAID, National Institutes of HealthHere, the authors analyse the distance between the body of an antibody and a protein antigen denoted as the Antibody-Framework-to-Antigen Distance (AFAD) for about 2000 non-redundant antibody-protein antigen complexes in the Protein Data Bank. They observe that antibodies with exceptionally long AFADs were all broad HIV-1-neutralizing antibodies that targeted densely glycosylated regions on the HIV-1-envelope trimer. The connection between long AFAD and dense glycan was further validated by the cryo-EM structure of antibody 2909 recognizing a glycan hole and by glycan shielding analyses based on molecular dynamics simulations.https://doi.org/10.1038/s41467-021-26579-z |
| spellingShingle | Myungjin Lee Anita Changela Jason Gorman Reda Rawi Tatsiana Bylund Cara W. Chao Bob C. Lin Mark K. Louder Adam S. Olia Baoshan Zhang Nicole A. Doria-Rose Susan Zolla-Pazner Lawrence Shapiro Gwo-Yu Chuang Peter D. Kwong Extended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfaces Nature Communications |
| title | Extended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfaces |
| title_full | Extended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfaces |
| title_fullStr | Extended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfaces |
| title_full_unstemmed | Extended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfaces |
| title_short | Extended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfaces |
| title_sort | extended antibody framework to antigen distance observed exclusively with broad hiv 1 neutralizing antibodies recognizing glycan dense surfaces |
| url | https://doi.org/10.1038/s41467-021-26579-z |
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