2015Zhang IPET

Citation

Zhang, X., Zhang, L., Tong, H. et al. 3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography. Sci Rep 5, 9803 (2015). https://doi.org/10.1038/srep09803

Zhang, L., Lei, D., Smith, J. et al. Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography. Nat Commun 7, 11083 (2016). https://doi.org/10.1038/ncomms11083

Lei, D., Marras, A.E., Liu, J. et al. Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography. Nat Commun 9, 592 (2018). https://doi.org/10.1038/s41467-018-03018-0

Lei, D., Liu, J., Liu, H. et al. Single-Molecule 3D Images of “Hole-Hole” IgG1 Homodimers by Individual-Particle Electron Tomography. Sci Rep 9, 8864 (2019). https://doi.org/10.1038/s41598-019-44978-7

Abstract

Commonly used methods for determining protein structure, including X-ray crystallography and single-particle reconstruction, often provide a single and unique three-dimensional (3D) structure. However, in these methods, the protein dynamics and flexibility/fluctuation remain mostly unknown. Here, we utilized advances in electron tomography (ET) to study the antibody flexibility and fluctuation through structural determination of individual antibody particles rather than averaging multiple antibody particles together. Through individual-particle electron tomography (IPET) 3D reconstruction from optimized negatively-stained (OpNS) ET images, 14 3D map of 84-bp double-stranded DNA with two 5-nm nanogold particles from OpNS images, 129 density maps of DNA origami Bennett linkage mechanisms from cryo-positive staining (cryo-PS) and 60 hole-hole IgG1 homodimers from OpNS images. Using these maps as a constraint, we derived conformations from each density map via structural flexible docking of the structure model into each of density maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the molecular 3D conformational flexibility through the distribution of its domain distances and orientations. This blueprint approach, if extended to other flexible proteins, may serve as a useful methodology towards understanding macromolecular dynamics and functions.

Keywords

Protein dynamics, single-molecule 3D structure

Links

https://www.nature.com/articles/srep09803 (Video about IgG1 dynamics: https://www.youtube.com/watch?v=pW1gskXrp7M); https://www.nature.com/articles/s41467-018-03018-0 (Video about DNA origami dynamics: https://www.youtube.com/watch?v=2Cjaxv9-btU); https://www.nature.com/articles/ncomms11083 (Video about DNA origami dynamics: https://www.youtube.com/watch?v=lQrbmg9ry90); https://www.nature.com/articles/s41598-019-44978-7 (Video about IgG1 homodimers: https://www.youtube.com/watch?v=nO5lMpppg9Y&feature=youtu.be);