Do antibody CDR loops change conformation upon binding?
Antibodies have increasingly been developed as drugs with over 100 now licensed in the US or EU. During development, it is often necessary to increase or reduce the affinity of an antibody and rational attempts to do so rely on having a structure of the antibody-antigen complex often obtained by mod...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Taylor & Francis Group
2024-12-01
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| Series: | mAbs |
| Subjects: | |
| Online Access: | https://www.tandfonline.com/doi/10.1080/19420862.2024.2322533 |
| _version_ | 1826846320173776896 |
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| author | Chu’nan Liu Lilian M. Denzler Oliver E.C. Hood Andrew C.R. Martin |
| author_facet | Chu’nan Liu Lilian M. Denzler Oliver E.C. Hood Andrew C.R. Martin |
| author_sort | Chu’nan Liu |
| collection | DOAJ |
| description | Antibodies have increasingly been developed as drugs with over 100 now licensed in the US or EU. During development, it is often necessary to increase or reduce the affinity of an antibody and rational attempts to do so rely on having a structure of the antibody-antigen complex often obtained by modeling. The antigen-binding site consists primarily of six loops known as complementarity-determining regions (CDRs), and an open question has been whether these loops change their conformation when they bind to an antigen. Existing surveys of antibody-antigen complex structures have only examined CDR conformational change in case studies or small-scale surveys. With an increasing number of antibodies where both free and complexed structures have been deposited in the Protein Data Bank, a large-scale survey of CDR conformational change during binding is now possible. To this end, we built a dataset, AbAgDb, that currently includes 177 antibodies with high-quality CDRs, each of which has at least one bound and one unbound structure. We analyzed the conformational change of the Cα backbone of each CDR upon binding and found that, in most cases, the CDRs (other than CDR-H3) show minimal movement, while 70.6% and 87% of CDR-H3s showed global Cα RMSD ≤ 1.0Å and ≤ 2.0Å, respectively. We also compared bound CDR conformations with the conformational space of unbound CDRs and found most of the bound conformations are included in the unbound conformational space. In future, our results will contribute to developing insights into antibodies and new methods for modeling and docking. |
| first_indexed | 2024-04-25T00:11:48Z |
| format | Article |
| id | doaj.art-ea0ff2b1ed564d10a991b78706b3b6b9 |
| institution | Directory Open Access Journal |
| issn | 1942-0862 1942-0870 |
| language | English |
| last_indexed | 2025-02-16T15:00:24Z |
| publishDate | 2024-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | mAbs |
| spelling | doaj.art-ea0ff2b1ed564d10a991b78706b3b6b92025-01-31T04:19:38ZengTaylor & Francis GroupmAbs1942-08621942-08702024-12-0116110.1080/19420862.2024.2322533Do antibody CDR loops change conformation upon binding?Chu’nan Liu0Lilian M. Denzler1Oliver E.C. Hood2Andrew C.R. Martin3Structural and Molecular Biology, Division of Biosciences, University College London, London, UKStructural and Molecular Biology, Division of Biosciences, University College London, London, UKStructural and Molecular Biology, Division of Biosciences, University College London, London, UKStructural and Molecular Biology, Division of Biosciences, University College London, London, UKAntibodies have increasingly been developed as drugs with over 100 now licensed in the US or EU. During development, it is often necessary to increase or reduce the affinity of an antibody and rational attempts to do so rely on having a structure of the antibody-antigen complex often obtained by modeling. The antigen-binding site consists primarily of six loops known as complementarity-determining regions (CDRs), and an open question has been whether these loops change their conformation when they bind to an antigen. Existing surveys of antibody-antigen complex structures have only examined CDR conformational change in case studies or small-scale surveys. With an increasing number of antibodies where both free and complexed structures have been deposited in the Protein Data Bank, a large-scale survey of CDR conformational change during binding is now possible. To this end, we built a dataset, AbAgDb, that currently includes 177 antibodies with high-quality CDRs, each of which has at least one bound and one unbound structure. We analyzed the conformational change of the Cα backbone of each CDR upon binding and found that, in most cases, the CDRs (other than CDR-H3) show minimal movement, while 70.6% and 87% of CDR-H3s showed global Cα RMSD ≤ 1.0Å and ≤ 2.0Å, respectively. We also compared bound CDR conformations with the conformational space of unbound CDRs and found most of the bound conformations are included in the unbound conformational space. In future, our results will contribute to developing insights into antibodies and new methods for modeling and docking.https://www.tandfonline.com/doi/10.1080/19420862.2024.2322533antibodiesantibody structurecomplementarity determining regionsCDRsCDR flexibilityantibody binding |
| spellingShingle | Chu’nan Liu Lilian M. Denzler Oliver E.C. Hood Andrew C.R. Martin Do antibody CDR loops change conformation upon binding? mAbs antibodies antibody structure complementarity determining regions CDRs CDR flexibility antibody binding |
| title | Do antibody CDR loops change conformation upon binding? |
| title_full | Do antibody CDR loops change conformation upon binding? |
| title_fullStr | Do antibody CDR loops change conformation upon binding? |
| title_full_unstemmed | Do antibody CDR loops change conformation upon binding? |
| title_short | Do antibody CDR loops change conformation upon binding? |
| title_sort | do antibody cdr loops change conformation upon binding |
| topic | antibodies antibody structure complementarity determining regions CDRs CDR flexibility antibody binding |
| url | https://www.tandfonline.com/doi/10.1080/19420862.2024.2322533 |
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