Building Atomic Models of the Ion Channels Based on Low Resolution Electron Microscopy Maps and Homology Modeling

Interface studies of CVD Si3N4 grown on (11$\overline 1$) SiC single crystal substrates have been made by transmission electron microscopy (TEM). It is found that there are two orientation relationships both of which involve the same (10$\overline 1$0)Si3N4//(11$\overline 1$)SiC planar relationship. However, the orientation relationships are not perfect and rotations of 2–6° are commonly seen between both directions and planes involved. High resolution electron microscopy (HREM) of the interfaces shows that the SiC and Si3N4 are continuous up to the interface and that no intermediate phases are formed. However, due to the small rotations, the HREM images are difficult to interpret directly in terms of atomic positions. Nevertheless, possible atomic models of the interface are proposed based upon the experimental findings. These models exploit the similarities between the [SiN4] and [SiC4] tetrahedra in Si3N4 and SiC, respectively. The observed orientation relationships appear to be due to matching of tetrahedra across the interface along with adequate lattice matches.

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A new method for the construction of coarse-grained models of large biomolecules from low-resolution cryo-electron microscopy data

Physical Chemistry Chemical Physics ◽

10.1039/c9cp01370a ◽

2019 ◽

Vol 21 (19) ◽

pp. 9720-9727 ◽

Cited By ~ 2

Author(s):

Yuwei Zhang ◽

Kelin Xia ◽

Zexing Cao ◽

Frauke Gräter ◽

Fei Xia

Keyword(s):

Electron Microscopy ◽

Electron Density ◽

Rapid Development ◽

Coarse Grained ◽

Low Resolution ◽

Density Data ◽

Cryo Electron Microscopy ◽

Electron Microscopy Data ◽

Resolution Electron ◽

Microscopy Data

The rapid development of cryo-electron microscopy (cryo-EM) has led to the generation of significant low-resolution electron density data of biomolecules.

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TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits

Journal of Applied Crystallography ◽

10.1107/s1600576715010092 ◽

2015 ◽

Vol 48 (4) ◽

pp. 1314-1323 ◽

Cited By ~ 45

Author(s):

Irene Farabella ◽

Daven Vasishtan ◽

Agnel Praveen Joseph ◽

Arun Prasad Pandurangan ◽

Harpal Sahota ◽

...

Keyword(s):

Electron Microscopy ◽

Three Dimensional ◽

Dimensional Electron ◽

Low Resolution ◽

Macromolecular Assemblies ◽

Atomic Models ◽

Density Maps ◽

Consensus Scoring ◽

Ensemble Generation ◽

Modular Nature

Three-dimensional electron microscopy is currently one of the most promising techniques used to study macromolecular assemblies. Rigid and flexible fitting of atomic models into density maps is often essential to gain further insights into the assemblies they represent. Currently, tools that facilitate the assessment of fitted atomic models and maps are needed.TEMPy(template and electron microscopy comparison using Python) is a toolkit designed for this purpose. The library includes a set of methods to assess density fits in intermediate-to-low resolution maps, both globally and locally. It also provides procedures for single-fit assessment, ensemble generation of fits, clustering, and multiple and consensus scoring, as well as plots and output files for visualization purposes to help the user in analysing rigid and flexible fits. The modular nature ofTEMPyhelps the integration of scoring and assessment of fits into large pipelines, making it a tool suitable for both novice and expert structural biologists.

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Electron microscopy and diffraction studies of polyimides

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100074069 ◽

1983 ◽

Vol 41 ◽

pp. 28-29

Author(s):

O.C. de Hodgins ◽

K. R. Lawless ◽

R. Anderson

Keyword(s):

Electron Microscopy ◽

Electron Microscope ◽

Structural Features ◽

Inert Atmosphere ◽

Polyimide Films ◽

Resolution Electron ◽

The Matrix ◽

High Resolution Electron Microscope ◽

Diffraction Patterns ◽

Polymeric Samples

Commercial polyimide films have shown to be homogeneous on a scale of 5 to 200 nm. The observation of Skybond (SKB) 705 and PI5878 was carried out by using a Philips 400, 120 KeV STEM. The objective was to elucidate the structural features of the polymeric samples. The specimens were spun and cured at stepped temperatures in an inert atmosphere and cooled slowly for eight hours. TEM micrographs showed heterogeneities (or nodular structures) generally on a scale of 100 nm for PI5878 and approximately 40 nm for SKB 705, present in large volume fractions of both specimens. See Figures 1 and 2. It is possible that the nodulus observed may be associated with surface effects and the structure of the polymers be regarded as random amorphous arrays. Diffraction patterns of the matrix and the nodular areas showed different amorphous ring patterns in both materials. The specimens were viewed in both bright and dark fields using a high resolution electron microscope which provided magnifications of 100,000X or more on the photographic plates if desired.

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