Download MendeleyExtended antibody-framework-to-antigen distance observed exclusively with broad HIV-1-neutralizing antibodies recognizing glycan-dense surfaces.
Lee, M., Changela, A., Gorman, J., Rawi, R., Bylund, T., Chao, C.W., Lin, B.C., Louder, M.K., Olia, A.S., Zhang, B., Doria-Rose, N.A., Zolla-Pazner, S., Shapiro, L., Chuang, G.Y., Kwong, P.D.(2021) Nat Commun 12: 6470-6470
- PubMed: 34753907
- DOI: https://doi.org/10.1038/s41467-021-26579-z
- Primary Citation of Related Structures:
7LY9 - PubMed Abstract:
Antibody-Framework-to-Antigen Distance (AFAD) - the distance between the body of an antibody and a protein antigen - is an important parameter governing antibody recognition. Here, we quantify AFAD for ~2,000 non-redundant antibody-protein-antigen complexes in the Protein Data Bank. AFADs showed a gaussian distribution with mean of 16.3 Å and standard deviation (σ) of 2.4 Å. Notably, antibody-antigen complexes with extended AFADs (>3σ) were exclusively human immunodeficiency virus-type 1 (HIV-1)-neutralizing antibodies. High correlation (R 2 = 0.8110) was observed between AFADs and glycan coverage, as assessed by molecular dynamics simulations of the HIV-1-envelope trimer. Especially long AFADs were observed for antibodies targeting the glycosylated trimer apex, and we tested the impact of introducing an apex-glycan hole (N160K); the cryo-EM structure of the glycan hole-targeting HIV-1-neutralizing antibody 2909 in complex with an N160K-envelope trimer revealed a substantially shorter AFAD. Overall, extended AFADs exclusively recognized densely glycosylated surfaces, with the introduction of a glycan hole enabling closer recognition.
Organizational Affiliation:
Vaccine Research Center, NIAID, National Institutes of Health, Bethesda, MD, 20892, USA.
