Structure
Volume 1, Issue 2, 15 October 1993, Pages 83-93
Journal home page for Structure

Research article
Major antigen-induced domain rearrangements in an antibody

https://doi.org/10.1016/0969-2126(93)90024-BGet rights and content

Abstract

Background: Recent structural results have shown that antibodies use an induced fit mechanism to recognize and bind their antigens. Here we present the crystallographically determined structure of an Fab directed against an HIV-1 peptide (Fab 50.1) in the unliganded state and compare it with the peptide-bound structure. We perform a detailed analysis of the components that contribute to enhanced antigen binding and recognition.

Results: Induced fit of Fab 50.1 to its peptide antigen involves a substantial rearrangement of the third complementarity determining region loop of the heavy chain (H3), as well as a large rotation of the variable heavy (VH) chain relative to the variable light (VL) chain. Analysis of other Fab structures suggests that the extent of the surface area buried at the VL-VH interface correlates with the ability to alter antibody quaternary structure by reorientation of the VL-VH domains.

Conclusion: Fab 50.1 exhibits the largest conformational changes yet observed in a single antibody. These can be attributed to the flexibility of the variable region. Comparisons of new data with previous examples lend to the general conclusion that a small VL-VH interface, due in part to a short H3 loop, permits substantial alterations to the antigen-binding pocket. This has major implications for the prediction, engineering and design of antibody-combining sites.

References (50)

  • P.H Walls et al.

    New algorithm to model protein-protein recognition based on surface complementarity

    Applications to antibody-antigen docking

    J. Mol. Biol.

    (1992)
  • C Chothia et al.

    Canonical structures for the hypervariable regions of immunoglobulins

    J. Mol. Biol.

    (1987)
  • E.A Padlan et al.

    Modeling of antibody combining sites

    Meth. Enzymol.

    (1991)
  • M.G Rossmann et al.

    A comparison of the heme binding pocket in globins and cytochrome b5

    J. Biol. Chem.

    (1975)
  • S Sheriff et al.

    Structure of myohemerythrin in the azidomet state at 1.71.3 Å resolution

    J. Mol. Biol.

    (1987)
  • T.O Fischmann et al.

    Crystallographic refinement of the three-dimensional structure of the Fab D1.3-Lysozyme complex at 2.5 Å resolution

    J. Biol. Chem.

    (1991)
  • M Marquart et al.

    Crystallographic refinement and atomic models of the intact immunoglobulin Kol and its antigen-binding fragment at 0.3 nm and 0.19 nm resolution

    J. Mol. Biol.

    (1980)
  • Y Satow et al.

    The phosphorylcholine binding immunoglobulin Fab McPC603: an X-ray diffraction study at 2.7 Å

    J. Mol. Biol.

    (1986)
  • F.A Saul et al.

    Preliminary refinement and structural analysis of the Fab fragment from human immunoglobulin New at 2.0 Å resolution

    J. Biol. Chem.

    (1978)
  • F.C Bernstein et al.

    The protein data bank: a computer-based archival file for macromolecular structures

    J. Biol. Mol.

    (1977)
  • M.L Connolly

    Depth-buffer algorithms for molecular modelling

    J. Mol. Graph.

    (1985)
  • R.L Stanfield et al.

    Crystal structures of an antibody bound to a peptide and its complex with peptide antigen at 2.8 Å

    Science

    (1990)
  • T.N Bhat et al.

    Small rearrangements in structures of Fv and Fab fragments of antibody D1.3 on antigen binding

    Nature

    (1990)
  • J.N Herron et al.

    An auto- antibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex

    Proteins

    (1991)
  • J.M Rini et al.

    Structural evidence for induced fit as a mechanism for antibody-antigen recognition

    Science

    (1992)
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    Present address: Teijin Institute for Bio-Medical Research, Teijin Limited, 4-3-2 Asahigaoka, Hino, Tokyo 191, Japan

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