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). doi: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). doi:10.1038/ncomms11083

Zhuoyang Lu, M.V.V.V. Sekhar Reddy, et al., Molecular Architecture of Contactin-associated Protein-like 2 (CNTNAP2) and its Interaction with Contactin 2 (CNTN2), Journal of Biological Chemistry, (2016), 291(46):24133-24147

Yadong Yu, Yu-Lin Kuang, et al. Polyhedral 3D Structure of Human Plasma Very-Low-Density Lipoproteins by Individual Particle Cryo-Electron Tomography, Journal of Lipid Research, (2016), 57(10):1879-1888

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). doi:10.1038/s41467-018-03018-0

Jianfang Liu, Anurag Misra, et al., Structural Plasticity of Neurexin 1α: Implications for its Role as Synaptic Organizer, J. Mol. Biolo., (2018), 430(21):4325-4343, DOI: 10.1016/j.jmb.2018.08.026

Jacob White Jay, Brinkley Ann Bray et al., IgG Antibody 3D Structures and Dynamics, Antibodies, (2018), 7(2), 18, DOI: 10.3390/antib7020018

D. Lei, Yadong Yu, et al., Single-Molecule 3D Imaging of Human Plasma Intermediate-Density Lipoproteins Reveals a Polyhedral Structure, Dongsheng BBA Molecular and Cell Biology of Lipids, (2019), 1864(3):260-270

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). doi:10.1038/s41598-019-44978-7

Meng Zhang, César Díaz-Celis, et al., Molecular Organization of the Early Stages of Nucleosome Phase Separation Visualized by Cryo-Electron Tomography, Molecular Cell, (2022), 18;82(16):3000-3014.e9; DOI: 10.1016/j.molcel.2022.06.032

Hubert Lee, Nicolas Chofflet, et al., Designer molecules of the synaptic organizer MDGA1 reveal 3D conformational control of biological function, J. Bio. Chem., (2023), 299(4):104586, Doi: 10.1016/j.jbc.2023.104586

Ewan K.S. McRae, Helena Østergaard Rasmussen, et al., Structure, folding and flexibility of co-transcriptional RNA origami, Nature Nanotechnology, (2023), 18(7):808-817. doi: 10.1038/s41565-023-01321-6

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-Nanogold 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);