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Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies
Open accessAbstract
Antibodies capable of neutralizing HIV-1 often target variable regions 1 and 2 (V1V2) of the HIV-1 envelope, but the mechanism of their elicitation has been unclear. Here we define the developmental pathway by which such antibodies are generated and acquire the requisite molecular characteristics for neutralization. Twelve somatically related neutralizing antibodies (CAP256-VRC26.01–12) were isolated from donor CAP256 (from the Centre for the AIDS Programme of Research in South Africa (CAPRISA)); each antibody contained the protruding tyrosine-sulphated, anionic antigen-binding loop (complementarity-determining region (CDR) H3) characteristic of this category of antibodies. Their unmutated ancestor emerged between weeks 30–38 post-infection with a 35-residue CDR H3, and neutralized the virus that superinfected this individual 15 weeks after initial infection. Improved neutralization breadth and potency occurred by week 59 with modest affinity maturation, and was preceded by extensive diversification of the virus population. HIV-1 V1V2-directed neutralizing antibodies can thus develop relatively rapidly through initial selection of B cells with a long CDR H3, and limited subsequent somatic hypermutation. These data provide important insights relevant to HIV-1 vaccine development.
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UCSF Chimera—A visualization system for exploratory research and analysis
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004) · Journal of Computational Chemistry · doi:10.1002/jcc.20084 · Cited by 45,828
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., & Kumar, S. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msr121 · Cited by 39,969
[20] Processing of X-ray diffraction data collected in oscillation mode
Otwinowski, Z., & Minor, W. (1997) · Methods in Enzymology · doi:10.1016/s0076-6879(97)76066-x · Cited by 33,475
Coot : model-building tools for molecular graphics
Emsley, P., & Cowtan, K. (2004) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444904019158 · Cited by 30,571
Clustal W and Clustal X version 2.0
Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., et al. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm404 · Cited by 28,358
The PyMOL Molecular Graphics System
DeLano, W. L. (2002) · Medical Entomology and Zoology · Cited by 18,147
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894
WebLogo: A Sequence Logo Generator: Figure 1
Crooks, G. E., Hon, G., Chandonia, J.-M., & Brenner, S. E. (2004) · Genome Research · doi:10.1101/gr.849004 · Cited by 12,386
Sequences of proteins of immunological interest
(1984) · Analytical Biochemistry · doi:10.1016/0003-2697(84)90805-4 · Cited by 3,363
HyPhy: hypothesis testing using phylogenies
Pond, S. L. K., Frost, S. D. W., & Muse, S. V. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti079 · Cited by 2,866
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Huang, J., Kang, B. H., Ishida, E., Zhou, T., Griesman, T., Sheng, Z., Wu, F., Doria-Rose, N. A., Zhang, B., McKee, K., et al. (2016) · Immunity · doi:10.1016/j.immuni.2016.10.027 · Cited by 369
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Metadata
- Authors
- Doria-Rose, N. A., Schramm, C. A., Gorman, J., Moore, P. L., Bhiman, J. N., DeKosky, B. J., Ernandes, M. J., Georgiev, I. S., Kim, H. J., Pancera, M., Staupe, R. P., Altae-Tran, H. R., Bailer, R. T., Crooks, E. T., Cupo, A., Druz, A., Garrett, N. J., Hoi, K. H., Kong, R., Louder, M. K., Longo, N. S., McKee, K., Nonyane, M., O’Dell, S., Roark, R. S., Rudicell, R. S., Schmidt, S. D., Sheward, D. J., Soto, C., Wibmer, C. K., Yang, Y., Zhang, Z., Sequencing, N. C., Mullikin, J. C., Binley, J. M., Sanders, R. W., Wilson, I. A., Moore, J. P., Ward, A. B., Georgiou, G., Williamson, C., Abdool Karim, S. S., Morris, L., Kwong, P. D., Shapiro, L., & Mascola, J. R.
- Venue
- Nature
- Published
- 2014-03-02
- Volume
- 509
- Issue
- 7498
- Pages
- 55-62
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W2010959676
- Cited by
- 709
- References
- 83
- FWCI
- 44.62
- Type
- journal article
- Language
- en
- Open access
- green
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- Doria-Rose, N. A., Schramm, C. A., Gorman, J., Moore, P. L., Bhiman, J. N., DeKosky, B. J., Ernandes, M. J., Georgiev, I. S., Kim, H. J., Pancera, M., Staupe, R. P., Altae-Tran, H. R., Bailer, R. T., Crooks, E. T., Cupo, A., Druz, A., Garrett, N. J., Hoi, K. H., Kong, R., . . . Mascola, J. R. (2014). Developmental pathway for potent V1V2-directed HIV-neutralizing antibodies. Nature. https://doi.org/10.1038/nature13036
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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