scholarly journals Three-dimensional structural dynamics and fluctuations of DNA-nanogold conjugates by individual-particle electron tomography

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Lei Zhang ◽  
Dongsheng Lei ◽  
Jessica M. Smith ◽  
Meng Zhang ◽  
Huimin Tong ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Individual Particle

scholarly journals Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Dongsheng Lei ◽  
Alexander E. Marras ◽  
Jianfang Liu ◽  
Chao-Min Huang ◽  
Lifeng Zhou ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Dna Origami ◽  
Individual Particle

scholarly journals 3D Structural Fluctuation of IgG1 Antibody Revealed by Individual Particle Electron Tomography

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Xing Zhang ◽  
Lei Zhang ◽  
Huimin Tong ◽  
Bo Peng ◽  
Matthew J. Rames ◽  
...  
Keyword(s):  
Protein Dynamics ◽  
Electron Tomography ◽  
3D Structure ◽  
Three Dimensional ◽  
Individual Particle ◽  
Single Particle Reconstruction ◽  
X Ray Crystallography ◽  
Igg1 Antibody ◽  
Structural Fluctuation ◽  
Dynamics Simulations

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 negatively-stained ET images, we obtained 120 ab-initio 3D density maps at an intermediate resolution (~1–3 nm) from 120 individual IgG1 antibody particles. Using these maps as a constraint, we derived 120 conformations of the antibody via structural flexible docking of the crystal structure to these maps by targeted molecular dynamics simulations. Statistical analysis of the various conformations disclosed the antibody 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 protein dynamics and functions.

scholarly journals Three Dimensional Dynamics and Fluctuations of DNA-Nanogold Dimers by Individual-Particle Electron Tomography

2016 ◽  
Vol 110 (3) ◽  
pp. 184a
Author(s):  
Lei Zhang ◽  
Dongsheng Lei ◽  
Jessica M. Smith ◽  
Huimin Tong ◽  
Xing Zhang ◽  
...  
Keyword(s):  
Electron Tomography ◽  
Three Dimensional ◽  
Individual Particle

scholarly journals 3D Images of Neuronal Adhesion Molecule Contactin-2 Reveal an Unanticipated Two-State Architecture

2018 ◽  
Author(s):  
Z. Lu ◽  
D. Lei ◽  
S. Seshadrinathan ◽  
A. Szwed ◽  
J. Liu ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Single Molecule ◽  
Adhesion Molecule ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Extracellular Domain ◽  
Imaging Method ◽  
Contact Points ◽  
Neural Adhesion Molecule ◽  
Terminal Domains

ABSTRACTContactins (CNTNs) are important cell adhesion molecules that mediate neuronal and axoglial contacts, and lesions in these molecules are linked to neuropsychiatric disorders. The extracellular domain of CNTNs contains six Ig domains and four FNIII domains. Crystal structures have shown that Ig1-Ig4 forms a horseshoe-shaped headpiece, in which the N-terminal domains might fold back on the C-terminal domains to form molecular super-U shaped architecture. The arrangement of these domains has been controversial, which may due to the structural dynamics and conformation heterogeneity of the protein. Here, we used a single-molecule 3D imaging method, individual-particle electron tomography (IPET), to study the extracellular domain of CNTN2 that forms monomers with a broad spectrum of conformations, and obtained 60 three-dimensional (3D) reconstructions. In addition to the known horseshoe-shaped headpiece, ~75% headpieces unexpectedly adopt an open (elongated) or a semi-open conformations contributed to our understanding about structural dynamics. The ectodomains formed curve but not double-back in any uniform way, with an averaged molecular dimension of ~255 Å. The first-time demonstration of the dynamic nature and conformational preferences of the full-length CNTN2 ectodomain suggest that the headpiece exists in equilibrium in the ‘closed’ or ‘not-closed’ states. The important architecture may provide a structural platform for protein partners to influence this balance regulating the function of CNTN2. Encoding the ability of this neural adhesion molecule to form both homomers with itself, as well as recruit different protein partner to neuronal and axoglial contact points play the key role in mediating cell-cell interactions.

Practical electron tomography

1995 ◽  
Vol 53 ◽  
pp. 742-743
Author(s):  
C.L. Woodcock
Keyword(s):  
Electron Tomography ◽  
Tomographic Reconstruction ◽  
Three Dimensional ◽  
3D Shape ◽  
Computational Resources ◽  
Shape Of Particles

Despite the potential of the technique, electron tomography has yet to be widely used by biologists. This is in part related to the rather daunting list of equipment and expertise that are required. Thanks to continuing advances in theory and instrumentation, tomography is now more feasible for the non-specialist. One barrier that has essentially disappeared is the expense of computational resources. In view of this progress, it is time to give more attention to practical issues that need to be considered when embarking on a tomographic project. The following recommendations and comments are derived from experience gained during two long-term collaborative projects.Tomographic reconstruction results in a three dimensional description of an individual EM specimen, most commonly a section, and is therefore applicable to problems in which ultrastructural details within the thickness of the specimen are obscured in single micrographs. Information that can be recovered using tomography includes the 3D shape of particles, and the arrangement and dispostion of overlapping fibrous and membranous structures.

Three-Dimensional reconstruction of isolated centrosomes by automated electron tomography

1994 ◽  
Vol 52 ◽  
pp. 310-311
Author(s):  
M.B. Braunfeld ◽  
M. Moritz ◽  
B.M. Alberts ◽  
J.W. Sedat ◽  
D.A. Agard
Keyword(s):  
Electron Tomography ◽  
Three Dimensional ◽  
Vital Role ◽  
Complex Nature ◽  
Animal Cells ◽  
Microtubule Organizing Center ◽  
Nucleation Sites ◽  
Dimensional Reconstruction ◽  
Organizing Center ◽  
Resolution Model

In animal cells, the centrosome functions as the primary microtubule organizing center (MTOC). As such the centrosome plays a vital role in determining a cell's shape, migration, and perhaps most importantly, its division. Despite the obvious importance of this organelle little is known about centrosomal regulation, duplication, or how it nucleates microtubules. Furthermore, no high resolution model for centrosomal structure exists.We have used automated electron tomography, and reconstruction techniques in an attempt to better understand the complex nature of the centrosome. Additionally we hope to identify nucleation sites for microtubule growth.Centrosomes were isolated from early Drosophila embryos. Briefly, after large organelles and debris from homogenized embryos were pelleted, the resulting supernatant was separated on a sucrose velocity gradient. Fractions were collected and assayed for centrosome-mediated microtubule -nucleating activity by incubating with fluorescently-labeled tubulin subunits. The resulting microtubule asters were then spun onto coverslips and viewed by fluorescence microscopy.

Three-Dimensional Nanoparticle Distribution and Local Curvature of Heterogeneous Catalysts Revealed by Electron Tomography

2007 ◽  
Vol 111 (31) ◽  
pp. 11501-11505 ◽  
Author(s):  
Edmund P. W. Ward ◽  
Timothy J. V. Yates ◽  
José-Jesús Fernández ◽  
David E. W. Vaughan ◽  
Paul A. Midgley
Keyword(s):  
Heterogeneous Catalysts ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Local Curvature ◽  
Nanoparticle Distribution

scholarly journals Capturing Enveloped Viruses on Affinity Grids for Downstream Cryo-Electron Microscopy Applications

2013 ◽  
Vol 20 (1) ◽  
pp. 164-174 ◽  
Author(s):  
Gabriella Kiss ◽  
Xuemin Chen ◽  
Melinda A. Brindley ◽  
Patricia Campbell ◽  
Claudio L. Afonso ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Measles Virus ◽  
Influenza A ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Nitrilotriacetic Acid ◽  
Dimensional Structure ◽  
Enveloped Viruses ◽  
Cryo Electron Microscopy ◽  
Human Immunodeficiency Virus Virus

AbstractElectron microscopy (EM), cryo-electron microscopy (cryo-EM), and cryo-electron tomography (cryo-ET) are essential techniques used for characterizing basic virus morphology and determining the three-dimensional structure of viruses. Enveloped viruses, which contain an outer lipoprotein coat, constitute the largest group of pathogenic viruses to humans. The purification of enveloped viruses from cell culture presents certain challenges. Specifically, the inclusion of host-membrane-derived vesicles, the complete destruction of the viruses, and the disruption of the internal architecture of individual virus particles. Here, we present a strategy for capturing enveloped viruses on affinity grids (AG) for use in both conventional EM and cryo-EM/ET applications. We examined the utility of AG for the selective capture of human immunodeficiency virus virus-like particles, influenza A, and measles virus. We applied nickel-nitrilotriacetic acid lipid layers in combination with molecular adaptors to selectively adhere the viruses to the AG surface. This further development of the AG method may prove essential for the gentle and selective purification of enveloped viruses directly onto EM grids for ultrastructural analyses.

The Prospect of Three-Dimensional Induction Mapping Inside Magnetic Nanostructures by Combining Electron Holography with Electron Tomography

2004 ◽  
Vol 10 (S02) ◽  
pp. 1010-1011 ◽  
Author(s):  
Rafal E Dunin-Borkowski ◽  
Takeshi Kasama
Keyword(s):  
Electron Tomography ◽  
Three Dimensional ◽  
Magnetic Nanostructures ◽  
Electron Holography

Extended abstract of a paper presented at Microscopy and Microanalysis 2004 in Savannah, Georgia, USA, August 1–5, 2004.

scholarly journals High-resolution three-dimensional probes of biomaterials and their interfaces

2012 ◽  
Vol 370 (1963) ◽  
pp. 1337-1351 ◽  
Author(s):  
Kathryn Grandfield ◽  
Anders Palmquist ◽  
Håkan Engqvist
Keyword(s):  
High Resolution ◽  
Electron Tomography ◽  
Three Dimensional ◽  
Controlled Drug Release ◽  
Biological Tissues ◽  
Dimensional Structure ◽  
Bone Interface ◽  
Biomaterial Interfaces ◽  
Titania Coating

Interfacial relationships between biomaterials and tissues strongly influence the success of implant materials and their long-term functionality. Owing to the inhomogeneity of biological tissues at an interface, in particular bone tissue, two-dimensional images often lack detail on the interfacial morphological complexity. Furthermore, the increasing use of nanotechnology in the design and production of biomaterials demands characterization techniques on a similar length scale. Electron tomography (ET) can meet these challenges by enabling high-resolution three-dimensional imaging of biomaterial interfaces. In this article, we review the fundamentals of ET and highlight its recent applications in probing the three-dimensional structure of bioceramics and their interfaces, with particular focus on the hydroxyapatite–bone interface, titanium dioxide–bone interface and a mesoporous titania coating for controlled drug release.

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