Reconstruction of 3D Structures of MET Antibodies From Electron Microscopy 2D Class Averages

PLoS One. 2017 Apr 13;12(4):e0175758. doi: 10.1371/journal.pone.0175758. eCollection 2017.

Abstract

Dynamics of three MET antibody constructs (IgG1, IgG2, and IgG4) and the IgG4-MET antigen complex was investigated by creating their atomic models with an integrative experimental and computational approach. In particular, we used two-dimensional (2D) Electron Microscopy (EM) images, image class averaging, homology modeling, Rapidly exploring Random Tree (RRT) structure sampling, and fitting of models to images, to find the relative orientations of antibody domains that are consistent with the EM images. We revealed that the conformational preferences of the constructs depend on the extent of the hinge flexibility. We also quantified how the MET antigen impacts on the conformational dynamics of IgG4. These observations allow to create testable hypothesis to investigate MET biology. Our protocol may also help describe structural diversity of other antigen systems at approximately 5 Å precision, as quantified by Root-Mean-Square Deviation (RMSD) among good-scoring models.

MeSH terms

  • Animals
  • Crystallography, X-Ray
  • Imaging, Three-Dimensional / methods
  • Immunoglobulin G / chemistry*
  • Immunoglobulin G / metabolism*
  • Mice
  • Microscopy, Electron / methods
  • Models, Molecular
  • Protein Conformation
  • Proto-Oncogene Proteins c-met / chemistry
  • Proto-Oncogene Proteins c-met / immunology*
  • Structural Homology, Protein

Substances

  • Immunoglobulin G
  • Proto-Oncogene Proteins c-met