TY - JOUR
T1 - Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages
AU - Chen, Qi
AU - Vieth, Michal
AU - Timm, David E.
AU - Humblet, Christine
AU - Schneidman-Duhovny, Dina
AU - Chemmama, Ilan E.
AU - Sali, Andrej
AU - Zeng, Wei
AU - Lu, Jirong
AU - Liu, Ling
N1 - Publisher Copyright:
© 2017 Chen et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
PY - 2017/4
Y1 - 2017/4
N2 - 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 goodscoring models.
AB - 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 goodscoring models.
UR - http://www.scopus.com/inward/record.url?scp=85017552446&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0175758
DO - 10.1371/journal.pone.0175758
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C2 - 28406969
AN - SCOPUS:85017552446
SN - 1932-6203
VL - 12
JO - PLoS ONE
JF - PLoS ONE
IS - 4
M1 - e0175758
ER -