The DOI matches its Crossref record; 68 of the 68 references it cites were found in a registry or an index.
Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus
Open accessAbstract
Current human immunodeficiency virus-1 (HIV-1) vaccines elicit strain-specific neutralizing antibodies. However, cross-reactive neutralizing antibodies arise in approximately 20% of HIV-1-infected individuals, and details of their generation could provide a blueprint for effective vaccination. Here we report the isolation, evolution and structure of a broadly neutralizing antibody from an African donor followed from the time of infection. The mature antibody, CH103, neutralized approximately 55% of HIV-1 isolates, and its co-crystal structure with the HIV-1 envelope protein gp120 revealed a new loop-based mechanism of CD4-binding-site recognition. Virus and antibody gene sequencing revealed concomitant virus evolution and antibody maturation. Notably, the unmutated common ancestor of the CH103 lineage avidly bound the transmitted/founder HIV-1 envelope glycoprotein, and evolution of antibody neutralization breadth was preceded by extensive viral diversification in and near the CH103 epitope. These data determine the viral and antibody evolution leading to induction of a lineage of HIV-1 broadly neutralizing antibodies, and provide insights into strategies to elicit similar antibodies by vaccination.
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[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
Phaser crystallographic software
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007) · Journal of Applied Crystallography · doi:10.1107/s0021889807021206 · Cited by 20,612
The CCP4 suite: programs for protein crystallography
Collaborative Computational Project, N. 4. (1994) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444994003112 · Cited by 17,270
Feinleib, M., & Zar, J. H. (1975) · Journal of the American Statistical Association · doi:10.2307/2285423 · Cited by 12,680
Inference of Macromolecular Assemblies from Crystalline State
Krissinel, E., & Henrick, K. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.05.022 · Cited by 9,984
PHENIX : building new software for automated crystallographic structure determination
Adams, P. D., Grosse-Kunstleve, R. W., Hung, L.-W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K., & Terwilliger, T. C. (2002) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444902016657 · Cited by 4,361
MolProbity: all-atom contacts and structure validation for proteins and nucleic acids
Davis, I. W., Leaver-Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., Murray, L. W., Arendall, W. B., Snoeyink, J., Richardson, J. S., et al. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm216 · Cited by 3,896
Sequences of proteins of immunological interest
(1984) · Analytical Biochemistry · doi:10.1016/0003-2697(84)90805-4 · Cited by 3,363
Cited by
Human neutralizing antibodies elicited by SARS-CoV-2 infection
Ju, B., Zhang, Q., Ge, J., Wang, R., Sun, J., Ge, X., Yu, J., Shan, S., Zhou, B., Song, S., et al. (2020) · Nature · doi:10.1038/s41586-020-2380-z · Cited by 1,667
Self-citationDevelopmental pathway for potent V1V2-directed HIV-neutralizing antibodies
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., et al. (2014) · Nature · doi:10.1038/nature13036 · Cited by 709
Self-citationThe promise and challenge of high-throughput sequencing of the antibody repertoire
Georgiou, G., Ippolito, G. C., Beausang, J., Busse, C. E., Wardemann, H., & Quake, S. R. (2014) · Nature Biotechnology · doi:10.1038/nbt.2782 · Cited by 652
Peptide-based synthetic vaccines
Skwarczynski, M., & Toth, I. (2016) · Chemical Science · doi:10.1039/c5sc03892h · Cited by 596
Reverse vaccinology 2.0: Human immunology instructs vaccine antigen design
Rappuoli, R., Bottomley, M. J., D’Oro, U., Finco, O., & De Gregorio, E. (2016) · Journal of Experimental Medicine · doi:10.1084/jem.20151960 · Cited by 435
Metadata
- Authors
- Liao, H.-X., Lynch, R., Zhou, T., Gao, F., Alam, S. M., Boyd, S. D., Fire, A. Z., Roskin, K. M., Schramm, C. A., Zhang, Z., Zhu, J., Shapiro, L., Program, N. C. S., Becker, J., Benjamin, B., Blakesley, R., Bouffard, G., Brooks, S., Coleman, H., Dekhtyar, M., Gregory, M., Guan, X., Gupta, J., Han, J., Hargrove, A., Ho, S.-L., Johnson, T., Legaspi, R., Lovett, S., Maduro, Q., Masiello, C., Maskeri, B., McDowell, J., Montemayor, C., Mullikin, J., Park, M., Riebow, N., Schandler, K., Schmidt, B., Sison, C., Stantripop, M., Thomas, J., Thomas, P., Vemulapalli, M., Young, A., Mullikin, J. C., Gnanakaran, S., Hraber, P., Wiehe, K., Kelsoe, G., Yang, G., Xia, S.-M., Montefiori, D. C., Parks, R., Lloyd, K. E., Scearce, R. M., Soderberg, K. A., Cohen, M., Kamanga, G., Louder, M. K., Tran, L. M., Chen, Y., Cai, F., Chen, S., Moquin, S., Du, X., Joyce, M. G., Srivatsan, S., Zhang, B., Zheng, A., Shaw, G. M., Hahn, B. H., Kepler, T. B., Korber, B. T. M., Kwong, P. D., Mascola, J. R., & Haynes, B. F.
- Venue
- Nature
- Published
- 2013-04-03
- Volume
- 496
- Issue
- 7446
- Pages
- 469-476
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W1978398372
- Cited by
- 988
- References
- 68
- FWCI
- 52.25
- Type
- journal article
- Language
- en
- Open access
- green
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- Liao, H.-X., Lynch, R., Zhou, T., Gao, F., Alam, S. M., Boyd, S. D., Fire, A. Z., Roskin, K. M., Schramm, C. A., Zhang, Z., Zhu, J., Shapiro, L., Program, N. C. S., Becker, J., Benjamin, B., Blakesley, R., Bouffard, G., Brooks, S., Coleman, H., . . . Haynes, B. F. (2013). Co-evolution of a broadly neutralizing HIV-1 antibody and founder virus. Nature. https://doi.org/10.1038/nature12053
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