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Chakraborty K, Durani V, Miranda E, Citron M, Liang X, Schleif W, Joyce J, Varadarajan R. Design of immunogens that present the crown of the HIV-1 V3 loop in a conformation competent to generate 447-52D-like antibodies. Biochem J 2006; 399:483-91. [PMID: 16827663 PMCID: PMC1615908 DOI: 10.1042/bj20060588] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
gp120 is a subunit of the envelope glycoprotein of HIV-1. The third variable loop region of gp120 (V3 loop) contains multiple immunodominant epitopes and is also functionally important for deciding cell-tropism of the virus. 447-52D is a monoclonal antibody that recognizes the conserved tip of the V3 loop in a beta-turn conformation. This antibody has previously been shown to neutralize diverse strains of the virus. In an attempt to generate an immunogen competent to generate 447-52D-like antibodies, the known epitope of 447-52D was inserted at three different surface loop locations in the small, stable protein Escherichia coli Trx (thioredoxin). At one of the three locations (between residues 74 and 75), the insertion was tolerated, the resulting protein was stable and soluble, and bound 447-52D with an affinity similar to that of intact gp120. Upon immunization, the V3 peptide-inserted Trx scaffold was able to generate anti-V3 antibodies that could compete out 447-52D binding to gp120. Epitope mapping studies demonstrated that these anti-V3 antibodies recognized the same epitope as 447-52D. Although the 447-52D-type antibodies were estimated to be present at concentrations of 50-400 microg/ml of serum, these were not able to effect neutralization of strains like JRFL and BAL but could neutralize the sensitive MN strain. The data suggest that because of the low accessibility of the V3 loop on primary isolates such as JRFL, it will be difficult to elicit a V3-specific, 447-52D-like antibody response to effectively neutralize such isolates.
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Affiliation(s)
- Kausik Chakraborty
- *Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | - Venuka Durani
- *Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
| | | | - Michael Citron
- †Merck Research Laboratories, West Point, PA 19486, U.S.A
| | - Xiaoping Liang
- †Merck Research Laboratories, West Point, PA 19486, U.S.A
| | | | - Joseph G. Joyce
- *Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
- †Merck Research Laboratories, West Point, PA 19486, U.S.A
- Correspondence may be addressed to either of the authors (email or )
| | - Raghavan Varadarajan
- *Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
- †Merck Research Laboratories, West Point, PA 19486, U.S.A
- ‡Chemical Biology Unit, Jawaharlal Center for Advanced Scientific Research, Jakkur, P.O., Bangalore 560 004, India
- Correspondence may be addressed to either of the authors (email or )
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Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger SP, Stewart S, Surko P, Way S, Wilson S, Sette A. The design and implementation of the immune epitope database and analysis resource. Immunogenetics 2005; 57:326-36. [PMID: 15895191 PMCID: PMC4780685 DOI: 10.1007/s00251-005-0803-5] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2004] [Revised: 04/22/2005] [Indexed: 01/13/2023]
Abstract
Epitopes are defined as parts of antigens interacting with receptors of the immune system. Knowledge about their intrinsic structure and how they affect the immune response is required to continue development of techniques that detect, monitor, and fight diseases. Their scientific importance is reflected in the vast amount of epitope-related information gathered, ranging from interactions between epitopes and major histocompatibility complex molecules determined by X-ray crystallography to clinical studies analyzing correlates of protection for epitope based vaccines. Our goal is to provide a central resource capable of capturing this information, allowing users to access and connect realms of knowledge that are currently separated and difficult to access. Here, we portray a new initiative, "The Immune Epitope Database and Analysis Resource." We describe how we plan to capture, structure, and store this information, what query interfaces we will make available to the public, and what additional predictive and analytical tools we will provide.
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Affiliation(s)
- Bjoern Peters
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
| | - John Sidney
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
| | - Phil Bourne
- San Diego Supercomputer Center, P.O.Box 85608 San Diego, CA, 92186-5608, USA
| | - Huynh-Hoa Bui
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
| | - Soeren Buus
- University of Copenhagen, Panum Building 18.3.22, Bleadamsvei 3, 220 Copenhagen, Denmark
| | - Grace Doh
- SH Grace Consulting, A-402 Hannam Riverhill, 390 Hannam-dong, Youngsan-ku, Seoul, 140-210, South Korea
| | - Ward Fleri
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
| | - Mitch Kronenberg
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
| | - Ralph Kubo
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
| | - Ole Lund
- BioCentrum-DTU, Technical University of Denmark, Building 208, Lyngby, 2800, Denmark
| | - David Nemazee
- Department of Immunology, The Scripps Research Institute, 10550 North Torrey Pines Road, IMM-29, La Jolla, CA, 92037, USA
| | | | - Muthu Sathiamurthy
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
| | - Stephen P. Schoenberger
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
| | - Scott Stewart
- Science Applications International Corporation, 9455 Towne Center Drive, MS-W2, San Diego, CA, 92121, USA
| | - Pamela Surko
- Science Applications International Corporation, 9455 Towne Center Drive, MS-W2, San Diego, CA, 92121, USA
| | - Scott Way
- Science Applications International Corporation, 9455 Towne Center Drive, MS-W2, San Diego, CA, 92121, USA
| | - Steve Wilson
- La Jolla Institute of Allergy and Immunology, 3030 Bunker Hill Street, Suite 326, San Diego, CA, 92109, USA
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