301
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Olivieri DN, von Haeften B, Sánchez-Espinel C, Faro J, Gambón-Deza F. Genomic V exons from whole genome shotgun data in reptiles. Immunogenetics 2014; 66:479-92. [DOI: 10.1007/s00251-014-0784-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 05/23/2014] [Indexed: 10/25/2022]
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302
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Krawczyk K, Liu X, Baker T, Shi J, Deane CM. Improving B-cell epitope prediction and its application to global antibody-antigen docking. Bioinformatics 2014; 30:2288-94. [PMID: 24753488 PMCID: PMC4207425 DOI: 10.1093/bioinformatics/btu190] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Motivation: Antibodies are currently the most important class of biopharmaceuticals. Development of such antibody-based drugs depends on costly and time-consuming screening campaigns. Computational techniques such as antibody–antigen docking hold the potential to facilitate the screening process by rapidly providing a list of initial poses that approximate the native complex. Results: We have developed a new method to identify the epitope region on the antigen, given the structures of the antibody and the antigen—EpiPred. The method combines conformational matching of the antibody–antigen structures and a specific antibody–antigen score. We have tested the method on both a large non-redundant set of antibody–antigen complexes and on homology models of the antibodies and/or the unbound antigen structure. On a non-redundant test set, our epitope prediction method achieves 44% recall at 14% precision against 23% recall at 14% precision for a background random distribution. We use our epitope predictions to rescore the global docking results of two rigid-body docking algorithms: ZDOCK and ClusPro. In both cases including our epitope, prediction increases the number of near-native poses found among the top decoys. Availability and implementation: Our software is available from http://www.stats.ox.ac.uk/research/proteins/resources. Contact:deane@stats.ox.ac.uk Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Konrad Krawczyk
- Department of Statistics, Oxford University, OX1 3TG, Oxford, UCB Pharma, SL1 3WE Slough, UK and Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiaofeng Liu
- Department of Statistics, Oxford University, OX1 3TG, Oxford, UCB Pharma, SL1 3WE Slough, UK and Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Terry Baker
- Department of Statistics, Oxford University, OX1 3TG, Oxford, UCB Pharma, SL1 3WE Slough, UK and Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jiye Shi
- Department of Statistics, Oxford University, OX1 3TG, Oxford, UCB Pharma, SL1 3WE Slough, UK and Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, ChinaDepartment of Statistics, Oxford University, OX1 3TG, Oxford, UCB Pharma, SL1 3WE Slough, UK and Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Charlotte M Deane
- Department of Statistics, Oxford University, OX1 3TG, Oxford, UCB Pharma, SL1 3WE Slough, UK and Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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303
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Using a combined computational-experimental approach to predict antibody-specific B cell epitopes. Structure 2014; 22:646-57. [PMID: 24631463 DOI: 10.1016/j.str.2014.02.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Revised: 01/23/2014] [Accepted: 02/01/2014] [Indexed: 11/22/2022]
Abstract
Antibody epitope mapping is crucial for understanding B cell-mediated immunity and required for characterizing therapeutic antibodies. In contrast to T cell epitope mapping, no computational tools are in widespread use for prediction of B cell epitopes. Here, we show that, utilizing the sequence of an antibody, it is possible to identify discontinuous epitopes on its cognate antigen. The predictions are based on residue-pairing preferences and other interface characteristics. We combined these antibody-specific predictions with results of cross-blocking experiments that identify groups of antibodies with overlapping epitopes to improve the predictions. We validate the high performance of this approach by mapping the epitopes of a set of antibodies against the previously uncharacterized D8 antigen, using complementary techniques to reduce method-specific biases (X-ray crystallography, peptide ELISA, deuterium exchange, and site-directed mutagenesis). These results suggest that antibody-specific computational predictions and simple cross-blocking experiments allow for accurate prediction of residues in conformational B cell epitopes.
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304
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Sundling C, Zhang Z, Phad GE, Sheng Z, Wang Y, Mascola JR, Li Y, Wyatt RT, Shapiro L, Karlsson Hedestam GB. Single-cell and deep sequencing of IgG-switched macaque B cells reveal a diverse Ig repertoire following immunization. THE JOURNAL OF IMMUNOLOGY 2014; 192:3637-44. [PMID: 24623130 DOI: 10.4049/jimmunol.1303334] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The nonhuman primate model is important for preclinical evaluation of prophylactic and therapeutic intervention strategies. The recent description of the rhesus macaque germline Ig loci and establishment of a database of germline gene segments offer improved opportunities to delineate Ig gene usage in the overall B cell repertoire as well as in response to vaccination. We applied 454-pyrosequencing and single-cell RT-PCR of bulk and sorted memory B cells, respectively, to investigate IGHV gene segment expression in rhesus macaques. The two methods gave remarkably concordant results and identified groups of gene segments that are frequently or rarely used. We further examined the VH repertoire of Ag-specific memory B cells induced by immunization with recombinant HIV-1 envelope glycoproteins, an important vaccine component. We demonstrate that HIV-1 envelope glycoprotein immunization activates a highly polyclonal response composed of most of the expressed VH gene segments, illustrating the considerable genetic diversity of responding B cells following vaccination.
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Affiliation(s)
- Christopher Sundling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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305
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Almagro JC, Gilliland GL, Breden F, Scott JK, Sok D, Pauthner M, Reichert JM, Helguera G, Andrabi R, Mabry R, Bléry M, Voss JE, Laurén J, Abuqayyas L, Barghorn S, Ben-Jacob E, Crowe JE, Huston JS, Johnston SA, Krauland E, Lund-Johansen F, Marasco WA, Parren PWHI, Xu KY. Antibody engineering and therapeutics, The Annual Meeting of the Antibody Society: December 8-12, 2013, Huntington Beach, CA. MAbs 2014; 6:577-618. [PMID: 24589717 PMCID: PMC4011904 DOI: 10.4161/mabs.28421] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The 24th Antibody Engineering & Therapeutics meeting brought together a broad range of participants who were updated on the latest advances in antibody research and development. Organized by IBC Life Sciences, the gathering is the annual meeting of The Antibody Society, which serves as the scientific sponsor. Preconference workshops on 3D modeling and delineation of clonal lineages were featured, and the conference included sessions on a wide variety of topics relevant to researchers, including systems biology; antibody deep sequencing and repertoires; the effects of antibody gene variation and usage on antibody response; directed evolution; knowledge-based design; antibodies in a complex environment; polyreactive antibodies and polyspecificity; the interface between antibody therapy and cellular immunity in cancer; antibodies in cardiometabolic medicine; antibody pharmacokinetics, distribution and off-target toxicity; optimizing antibody formats for immunotherapy; polyclonals, oligoclonals and bispecifics; antibody discovery platforms; and antibody-drug conjugates.
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Affiliation(s)
| | | | | | | | - Devin Sok
- The Scripps Research Institute; La Jolla, CA USA
| | | | | | - Gustavo Helguera
- CONICET; Laboratorio Biotecnología Farmacéutica; Instituto de Biología y Medicina Experimental, IBYME; Ciudad Autónoma de Buenos Aires, Argentina
| | | | | | | | - James E Voss
- The Scripps Research Institute; La Jolla, CA USA
| | - Juha Laurén
- Regeneron Pharmaceuticals, Inc.; Tarrytown, NY USA
| | | | | | | | - James E Crowe
- Vanderbilt University Medical Center, Nashville, TN, USA
| | | | | | | | | | | | | | - Kai Y Xu
- University of Maryland; Baltimore, MD USA
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