2015Zhang IPET - Revision history

Garygangren: /* Citation */

2023-08-24T18:59:48Z

Citation

← Older revision		Revision as of 18:59, 24 August 2023
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	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		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		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		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 ==		== Abstract ==

Garygangren: /* Links */

2020-06-30T14:51:24Z

Links

← Older revision		Revision as of 14:51, 30 June 2020
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	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/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/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);		https://www.nature.com/articles/s41598-019-44978-7 (Video about IgG1 homodimers: https://www.youtube.com/watch?v=nO5lMpppg9Y&feature=youtu.be);

Garygangren: /* Links */

2020-06-30T14:50:27Z

Links

← Older revision		Revision as of 14:50, 30 June 2020
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	== Links ==		== Links ==
	https://www.nature.com/articles/srep09803 (Video about IgG1 dynamics: https://www.youtube.com/watch?v=pW1gskXrp7M);		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/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/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);		https://www.nature.com/articles/s41598-019-44978-7 (Video about IgG1 homodimers: https://www.youtube.com/watch?v=nO5lMpppg9Y&feature=youtu.be);

Garygangren: /* Citation */

2020-06-30T14:49:56Z

Citation

← Older revision		Revision as of 14:49, 30 June 2020
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	== Citation ==		== 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, 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). ~~https~~:~~//doi.org/~~10.1038/ncomms11083		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

	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., 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

	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		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

	== Abstract ==		== Abstract ==

Garygangren: /* Keywords */

2020-06-30T13:48:10Z

Keywords

← Older revision		Revision as of 13:48, 30 June 2020
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	== Keywords ==		== Keywords ==
			Protein dynamics, single-molecule 3D structure

	== Links ==		== Links ==

Garygangren: /* Links */

2020-06-30T13:45:50Z

Links

← Older revision		Revision as of 13:45, 30 June 2020
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	== Links ==		== Links ==
	https://www.nature.com/articles/srep09803		https://www.nature.com/articles/srep09803 (Video about IgG1 dynamics: https://www.youtube.com/watch?v=pW1gskXrp7M);
	https://www.~~nature~~.com/~~articles/ncomms11083~~		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/s41467-018-03018-0		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		https://www.nature.com/articles/s41598-019-44978-7 (Video about IgG1 homodimers: https://www.youtube.com/watch?v=nO5lMpppg9Y&feature=youtu.be);

	== Related software ==		== Related software ==

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2020-06-29T21:39:49Z

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== 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 ==

== Links ==
https://www.nature.com/articles/srep09803
https://www.nature.com/articles/ncomms11083
https://www.nature.com/articles/s41467-018-03018-0
https://www.nature.com/articles/s41598-019-44978-7

== Related software ==

== Related methods ==

== Comments ==