Toward high-resolution homology modeling of antibody Fv regions and application to antibody–antigen docking

Authors

  • Arvind Sivasubramanian,

    1. Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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    • Arvind Sivasubramanian and Aroop Sircar contributed equally to this work.

    • Current address: Adimab, Inc., 16 Cavendish Ct., Lebanon, New Hampshire 03766.

  • Aroop Sircar,

    1. Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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    • Arvind Sivasubramanian and Aroop Sircar contributed equally to this work.

  • Sidhartha Chaudhury,

    1. Program in Molecular and Computational Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
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  • Jeffrey J. Gray

    Corresponding author
    1. Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
    2. Program in Molecular and Computational Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218
    3. Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, 401 N Broadway, Baltimore, Maryland 21231
    • Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218
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Abstract

High-resolution homology models are useful in structure-based protein engineering applications, especially when a crystallographic structure is unavailable. Here, we report the development and implementation of RosettaAntibody, a protocol for homology modeling of antibody variable regions. The protocol combines comparative modeling of canonical complementarity determining region (CDR) loop conformations and de novo loop modeling of CDR H3 conformation with simultaneous optimization of VL-VH rigid-body orientation and CDR backbone and side-chain conformations. The protocol was tested on a benchmark of 54 antibody crystal structures. The median root mean square deviation (rmsd) of the antigen binding pocket comprised of all the CDR residues was 1.5 Å with 80% of the targets having an rmsd lower than 2.0 Å. The median backbone heavy atom global rmsd of the CDR H3 loop prediction was 1.6, 1.9, 2.4, 3.1, and 6.0 Å for very short (4–6 residues), short (7–9), medium (10–11), long (12–14) and very long (17–22) loops, respectively. When the set of ten top-scoring antibody homology models are used in local ensemble docking to antigen, a moderate-to-high accuracy docking prediction was achieved in seven of fifteen targets. This success in computational docking with high-resolution homology models is encouraging, but challenges still remain in modeling antibody structures for sequences with long H3 loops. This first large-scale antibody–antigen docking study using homology models reveals the level of “functional accuracy” of these structural models toward protein engineering applications. Proteins 2009; 74:497–514. © 2008 Wiley-Liss, Inc.

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