Computational Screening of the Human TF-Glycome Provides a Structural Definition for the Specificity of Anti-Tumor Antibody JAA-F11

• Type of Material: Article
• Authors: Matthew B. Tessier, University of Georgia; Oliver Grant, National University of Ireland; Jamie Heimburg-Molinaro, SUNY Buffalo; David Smith, Emory University; Snehal Jadey, SUNY Buffalo; Andrew M. Gulick, SUNY Buffalo; John Glushka, University of Georgia; Susan L. Deutscher, University of Missouri; Kate Rittenhouse-Olson, SUNY Buffalo; Robert J. Woods, University of Georgia
• Language: English
• Date: 2013-01-24
• Publisher: Public Library of Science
• Publication Version: Final Published Version
• Copyright Statement: © 2013 Tessier et al.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1371/journal.pone.0054874
• Title of Journal or Parent Work: PLoS ONE
• ISSN: 1932-6203
• Volume: 8
• Issue: 1
• Start Page: e54874
• End Page: e54874
• Grant/Funding Information: RJW would like to thank the National Institutes for Health (GM085448 to DFS, GM062116, GM094919 (EUREKA), www.nih.gov) as well as the Science Foundation of Ireland (08/IN.1/B2070, www.sfi.ie) and the European Research Development Fund for support.; Diffraction data were collected at the Cornell High Energy Synchrotron Source (CHESS), which is supported by the National Science Foundation under award DMR 0225180 (www.nsf.gov) and the National Institutes of Health (RR001646).; KRO would like to acknowledge the Department of Defense (CDMRP #W81XWH-04-1-0342, www.defense.gov) for support.
• Keywords: CONFORMATION; Multidisciplinary Sciences; GLYCOBIOLOGY; CANCER; LIGAND; MONOCLONAL-ANTIBODY; THOMSEN-FRIEDENREICH; CARBOHYDRATE ANTIGEN; MULTIDISCIPLINARY SCIENCES; Science & Technology; GLYCAN-BINDING-PROTEINS; MICROARRAY; Science & Technology - Other Topics; FORCE-FIELD
• Research Categories: Chemistry, Biochemistry; Health Sciences, Immunology

Abstract

Recombinant antibodies are of profound clinical significance; yet, anti-carbohydrate antibodies are prone to undesirable cross-reactivity with structurally related-glycans. Here we introduce a new technology called Computational Carbohydrate Grafting (CCG), which enables a virtual library of glycans to be assessed for protein binding specificity, and employ it to define the scope and structural origin of the binding specificity of antibody JAA-F11 for glycans containing the Thomsen-Friedenreich (TF) human tumor antigen. A virtual library of the entire human glycome (GLibrary-3D) was constructed, from which 1,182 TF-containing human glycans were identified and assessed for their ability to fit into the antibody combining site. The glycans were categorized into putative binders, or non-binders, on the basis of steric clashes with the antibody surface. The analysis employed a structure of the immune complex, generated by docking the TF-disaccharide (Galβ1-3GalNAcα) into a crystal structure of the JAA-F11 antigen binding fragment, which was shown to be consistent with saturation transfer difference (STD) NMR data. The specificities predicted by CCG were fully consistent with data from experimental glycan array screening, and confirmed that the antibody is selective for the TF-antigen and certain extended core-2 type mucins. Additionally, the CCG analysis identified a limited number of related putative binding motifs, and provided a structural basis for interpreting the specificity. CCG can be utilized to facilitate clinical applications through the determination of the three-dimensional interaction of glycans with proteins, thus augmenting drug and vaccine development techniques that seek to optimize the specificity and affinity of neutralizing proteins, which target glycans associated with diseases including cancer and HIV.