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2. Trispecific broadly neutralizing HIV antibodies mediate potent SHIV protection in macaques

Author

Xu, Ling, Pegu, Amarendra, Rao, Ercole, Doria-Rose, Nicole, Beninga, Jochen, McKee, Krisha, Lord, Dana M., Wei, Ronnie R., Deng, Gejing, Louder, Mark, Schmidt, Stephen D., Mankoff, Zachary, Wu, Lan, Asokan, Mangaiarkarasi, Beil, Christian, Lange, Christian, Leuschner, Wulf Dirk, Kruip, Jochen, Sendak, Rebecca, Do Kwon, Young, Zhou, Tongqing, Chen, Xuejun, Bailer, Robert T., Wang, Keyun, Choe, Misook, Tartaglia, Lawrence J., Barouch, Dan H., OʼDell, Sijy, Todd, John-Paul, Burton, Dennis R., Roederer, Mario, Connors, Mark, Koup, Richard A., Kwong, Peter D., Yang, Zhi-yong, Mascola, John R., and Nabel, Gary J.

Published
2017
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4. Structures of HIV-1 Neutralizing Antibody 10E8 Delineate the Mechanistic Basis of Its Multi-Peak Behavior on Size-Exclusion Chromatography

Author

Do Kwon, Young, primary, Wang, Xiangchun E., additional, Bender, Michael F., additional, Yang, Rong, additional, Li, Yile, additional, McKee, Krisha, additional, Rawi, Reda, additional, O’Dell, Sijy, additional, Schneck, Nicole A., additional, Shaddeau, Andrew, additional, Zhang, Baoshan, additional, Arnold, Frank J., additional, Connors, Mark, additional, Doria-Rose, Nicole A., additional, Kwong, Peter D., additional, and Lei, Q. Paula, additional

Published
2021
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5. Structure of HIV-1 gp120 V1/V2 domain with broadly neutralizing antibody PG9

Author

McLellan, Jason S., Pancera, Marie, Carrico, Chris, Gorman, Jason, Julien, Jean-Philippe, Khayat, Reza, Louder, Robert, Pejchal, Robert, Sastry, Mallika, Dai, Kaifan, O’Dell, Sijy, Patel, Nikita, Shahzad-ul-Hussan, Syed, Yang, Yongping, Zhang, Baoshan, Zhou, Tongqing, Zhu, Jiang, Boyington, Jeffrey C., Chuang, Gwo-Yu, Diwanji, Devan, Georgiev, Ivelin, Do Kwon, Young, Lee, Doyung, Louder, Mark K., Moquin, Stephanie, Schmidt, Stephen D., Yang, Zhi-Yong, Bonsignori, Mattia, Crump, John A., Kapiga, Saidi H., Sam, Noel E., Haynes, Barton F., Burton, Dennis R., Koff, Wayne C., Walker, Laura M., Phogat, Sanjay, Wyatt, Richard, Orwenyo, Jared, Wang, Lai-Xi, Arthos, James, Bewley, Carole A., Mascola, John R., Nabel, Gary J., Schief, William R., Ward, Andrew B., Wilson, Ian A., and Kwong, Peter D.

Published
2011
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6. Multidonor Analysis Reveals Structural Elements, Genetic Determinants, and Maturation Pathway for HIV-1 Neutralization by VRC01-Class Antibodies

Author

Zhou, Tongqing, Zhu, Jiang, Wu, Xueling, Moquin, Stephanie, Zhang, Baoshan, Acharya, Priyamvada, Georgiev, Ivelin S., Altae-Tran, Han R., Chuang, Gwo-Yu, Joyce, Gordon M., Do Kwon, Young, Longo, Nancy S., Louder, Mark K., Luongo, Timothy, McKee, Krisha, Schramm, Chaim A., Skinner, Jeff, Yang, Yongping, Yang, Zhongjia, Zhang, Zhenhai, Zheng, Anqi, Bonsignori, Mattia, Haynes, Barton F., Scheid, Johannes F., Nussenzweig, Michel C., Simek, Melissa, Burton, Dennis R., Koff, Wayne C., Mullikin, James C., Connors, Mark, Shapiro, Lawrence, Nabel, Gary J., Mascola, John R., and Kwong, Peter D.

Published
2013
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7. Delineating Antibody Recognition in Polyclonal Sera from Patterns of HIV-1 Isolate Neutralization

Author

Georgiev, Ivelin S., Doria-Rose, Nicole A., Zhou, Tongqing, Do Kwon, Young, Staupe, Ryan P., Moquin, Stephanie, Chuang, Gwo-Yu, Louder, Mark K., Schmidt, Stephen D., Altae-Tran, Han R., Bailer, Robert T., McKee, Krisha, Nason, Martha, OʼDell, Sijy, Ofek, Gilad, Pancera, Marie, Srivatsan, Sanjay, Shapiro, Lawrence, Connors, Mark, Migueles, Stephen A., Morris, Lynn, Nishimura, Yoshiaki, Martin, Malcolm A., Mascola, John R., and Kwong, Peter D.

Published
2013
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9. Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env

Author

Do Kwon, Young, primary, Pancera, Marie, additional, Acharya, Priyamvada, additional, Georgiev, Ivelin S, additional, Crooks, Emma T, additional, Gorman, Jason, additional, Joyce, M Gordon, additional, Guttman, Miklos, additional, Ma, Xiaochu, additional, Narpala, Sandeep, additional, Soto, Cinque, additional, Terry, Daniel S, additional, Yang, Yongping, additional, Zhou, Tongqing, additional, Ahlsen, Goran, additional, Bailer, Robert T, additional, Chambers, Michael, additional, Chuang, Gwo-Yu, additional, Doria-Rose, Nicole A, additional, Druz, Aliaksandr, additional, Hallen, Mark A, additional, Harned, Adam, additional, Kirys, Tatsiana, additional, Louder, Mark K, additional, O'Dell, Sijy, additional, Ofek, Gilad, additional, Osawa, Keiko, additional, Prabhakaran, Madhu, additional, Sastry, Mallika, additional, Stewart-Jones, Guillaume B E, additional, Stuckey, Jonathan, additional, Thomas, Paul V, additional, Tittley, Tishina, additional, Williams, Constance, additional, Zhang, Baoshan, additional, Zhao, Hong, additional, Zhou, Zhou, additional, Donald, Bruce R, additional, Lee, Lawrence K, additional, Zolla-Pazner, Susan, additional, Baxa, Ulrich, additional, Schön, Arne, additional, Freire, Ernesto, additional, Shapiro, Lawrence, additional, Lee, Kelly K, additional, Arthos, James, additional, Munro, James B, additional, Blanchard, Scott C, additional, Mothes, Walther, additional, Binley, James M, additional, McDermott, Adrian B, additional, Mascola, John R, additional, and Kwong, Peter D, additional

Published
2015
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10. Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection

Author

Wu, Xueling, primary, Zhang, Zhenhai, additional, Schramm, Chaim A., additional, Joyce, M. Gordon, additional, Do Kwon, Young, additional, Zhou, Tongqing, additional, Sheng, Zizhang, additional, Zhang, Baoshan, additional, O’Dell, Sijy, additional, McKee, Krisha, additional, Georgiev, Ivelin S., additional, Chuang, Gwo-Yu, additional, Longo, Nancy S., additional, Lynch, Rebecca M., additional, Saunders, Kevin O., additional, Soto, Cinque, additional, Srivatsan, Sanjay, additional, Yang, Yongping, additional, Bailer, Robert T., additional, Louder, Mark K., additional, Mullikin, James C., additional, Connors, Mark, additional, Kwong, Peter D., additional, Mascola, John R., additional, Shapiro, Lawrence, additional, Benjamin, Betty, additional, Blakesley, Robert, additional, Bouffard, Gerry, additional, Brooks, Shelise, additional, Coleman, Holly, additional, Dekhtyar, Mila, additional, Gregory, Michael, additional, Guan, Xiaobin, additional, Gupta, Jyoti, additional, Han, Joel, additional, Hargrove, April, additional, Ho, Shi-ling, additional, Legaspi, Richelle, additional, Maduro, Quino, additional, Masiello, Cathy, additional, Maskeri, Baishali, additional, McDowell, Jenny, additional, Montemayor, Casandra, additional, Park, Morgan, additional, Riebow, Nancy, additional, Schandler, Karen, additional, Schmidt, Brian, additional, Sison, Christina, additional, Stantripop, Mal, additional, Thomas, James, additional, Thomas, Pam, additional, Vemulapalli, Meg, additional, and Young, Alice, additional

Published
2015
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12. Structural Basis of Immune Evasion at the Site of CD4 Attachment on HIV-1 gp120

Author

Chen, Lei, primary, Do Kwon, Young, additional, Zhou, Tongqing, additional, Wu, Xueling, additional, O’Dell, Sijy, additional, Cavacini, Lisa, additional, Hessell, Ann J., additional, Pancera, Marie, additional, Tang, Min, additional, Xu, Ling, additional, Yang, Zhi-Yong, additional, Zhang, Mei-Yun, additional, Arthos, James, additional, Burton, Dennis R., additional, Dimitrov, Dimiter S., additional, Nabel, Gary J., additional, Posner, Marshall R., additional, Sodroski, Joseph, additional, Wyatt, Richard, additional, Mascola, John R., additional, and Kwong, Peter D., additional

Published
2009
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13. Small-Molecule CD4 Mimics Interact with a Highly Conserved Pocket on HIV-1 gp120

Author

Madani, Navid, primary, Schön, Arne, additional, Princiotto, Amy M., additional, LaLonde, Judith M., additional, Courter, Joel R., additional, Soeta, Takahiro, additional, Ng, Danny, additional, Wang, Liping, additional, Brower, Evan T., additional, Xiang, Shi-Hua, additional, Do Kwon, Young, additional, Huang, Chih-chin, additional, Wyatt, Richard, additional, Kwong, Peter D., additional, Freire, Ernesto, additional, Smith, Amos B., additional, and Sodroski, Joseph, additional

Published
2008
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14. Combinatorial Optimization of a CD4-Mimetic Miniprotein and Cocrystal Structures with HIV-1 gp120 Envelope Glycoprotein

Author

Stricher, François, primary, Huang, Chih-chin, additional, Descours, Anne, additional, Duquesnoy, Sophie, additional, Combes, Olivier, additional, Decker, Julie M., additional, Do Kwon, Young, additional, Lusso, Paolo, additional, Shaw, George M., additional, Vita, Claudio, additional, Kwong, Peter D., additional, and Martin, Loïc, additional

Published
2008
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16. Human zinc fingers as building blocks in the construction of artificial transcription factors

Author

Bae, Kwang-Hee, primary, Do Kwon, Young, additional, Shin, Hyun-Chul, additional, Hwang, Moon-Sun, additional, Ryu, Eun-Hyun, additional, Park, Kyung-Soon, additional, Yang, Hyo-Young, additional, Lee, Dong-ki, additional, Lee, Yangsoon, additional, Park, Jinwoo, additional, Sun Kwon, Heung, additional, Kim, Hyun-Won, additional, Yeh, Byung-Il, additional, Lee, Hyean-Woo, additional, Hyung Sohn, Soon, additional, Yoon, Joonho, additional, Seol, Wongi, additional, and Kim, Jin-Soo, additional

Published
2003
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17. Residue-Level Prediction of HIV-1 Antibody Epitopes Based on Neutralization of Diverse Viral Strains.

Author

Gwo-Yu Chuang, Acharya, Priyamvada, Schmidt, Stephen D., Yongping Yang, Louder, Mark K., Zhou, Tongqing, Do Kwon, Young, Pancera, Marie, Bailer, Robert T., Doria-Rose, Nicole A., Nussenzweig, Michel C., Mascola, John R., Kwong, Peter D., and Georgiev, Ivelin S.

Subjects
*EPITOPES, *HIV, *IMMUNOGLOBULINS, *GENETIC mutation, *IMMUNE complexes, *VACCINES
Abstract

Delineation of antibody epitopes at the residue level is key to understanding antigen resistance mutations, designing epitopespecific probes for antibody isolation, and developing epitope-based vaccines. Ideally, epitope residues are determined in the context of the atomic-level structure of the antibody-antigen complex, though structure determination may in many cases be impractical. Here we describe an efficient computational method to predict antibody-specific HIV-1 envelope (Env) epitopes at the residue level, based on neutralization panels of diverse viral strains. The method primarily utilizes neutralization potency data over a set of diverse viral strains representing the antigen, and enhanced accuracy could be achieved by incorporating information from the unbound structure of the antigen. The method was evaluated on 19 HIV-1 Env antibodies with neutralization panels comprising 181 diverse viral strains and with available antibody-antigen complex structures. Prediction accuracy was shown to improve significantly over random selection, with an average of greater-than-8-fold enrichment of true positives at the 0.05 false-positive rate level. The method was used to prospectively predict epitope residues for two HIV-1 antibodies, 8ANC131 and 8ANC195, for which we experimentally validated the predictions. The method is inherently applicable to antigens that exhibit sequence diversity, and its accuracy was found to correlate inversely with sequence conservation of the epitope. Together the results show how knowledge inherent to a neutralization panel and unbound antigen structure can be utilized for residuelevel prediction of antibody epitopes. [ABSTRACT FROM AUTHOR]

Published
2013
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