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Related Concept Videos

Cryo-electron Microscopy01:28

Cryo-electron Microscopy

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Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...
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Electronic Structure of Atoms02:28

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An atom comprises protons and neutrons, which are contained inside the dense, central core called the nucleus, with electrons present around the nucleus. Taking into account the wave–particle duality of electrons and the uncertainty in position around the nucleus, quantum mechanics provides a more accurate model for the atomic structure. It describes atomic orbitals as the regions around the nucleus where electrons of discrete energy exist, characterized by four quantum...
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Electron Orbital Model01:18

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Orbitals are the areas outside of the atomic nucleus where electrons are most likely to reside. They are characterized by different energy levels, shapes, and three-dimensional orientations. The location of electrons is described most generally by a shell or principal energy level, then by a subshell within each shell, and finally, by individual orbitals found within the subshells.
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Overview of Electron Microscopy01:25

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The wavelengths of visible light ultimately limit the maximum theoretical resolution of images created by light microscopes. Most light microscopes can only magnify 1000X, and a few can magnify up to 1500X. Electrons, like electromagnetic radiation, can behave like waves, but with wavelengths of 0.005 nm, they produce significantly greater resolution up to 0.05 nm as compared to 500 nm for visible light. An electron microscope (EM) can create a sharp image that is magnified up to 2,000,000X.
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Scanning Electron Microscopy01:07

Scanning Electron Microscopy

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A scanning electron microscope (SEM) is used to study the surface features of a sample by using an electron beam that scans the sample surface in a two-dimensional manner. Typically, areas between ~1 centimeter to 5 micrometers in width can be imaged. SEM can be used to image bacteria, viruses, tissues as well as larger samples like insects. Conventional SEM gives a magnification ranging from 20X to 30,000X and spatial resolution of 50 to 100 nanometers.
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Transmission Electron Microscopy01:15

Transmission Electron Microscopy

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In 1931, physicist Ernst Ruska—building on the idea that magnetic fields can direct an electron beam just as lenses can direct a beam of light in an optical microscope—developed the first prototype of the electron microscope. This development led to the development of the field of electron microscopy. In the transmission electron microscope (TEM), electrons are produced by a hot tungsten element and accelerated by a potential difference in an electron gun, which gives them up to 400...
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Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling.

Massimiliano Bonomi1, Samuel Hanot2, Charles H Greenberg3

  • 1Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK.

Structure (London, England : 1993)
|November 6, 2018
PubMed
Summary

A new Bayesian scoring function improves integrative structural modeling by accurately ranking models using cryo-electron microscopy (cryo-EM) data and other experimental information. This method enhances the reliability of determining complex biological structures.

Keywords:
Gaussian mixture modelbayesian inferencecross-linking mass spectrometrycryo-electron microscopydata weighingintegrative structural modelingmacromolecular complexesstructural biology

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Cryo-electron microscopy (cryo-EM) is vital for determining complex biological structures.
  • Accurate integrative structural modeling is challenged by data errors and correlations in cryo-EM.
  • Objective weighing of cryo-EM data against other information sources remains difficult.

Purpose of the Study:

  • To develop a robust Bayesian scoring function for integrative structural modeling.
  • To accurately rank alternative structural models using cryo-EM density maps and complementary data.
  • To overcome limitations in current cryo-EM data integration methods.

Main Methods:

  • Introduction of a Bayesian scoring function for model ranking.
  • Benchmarking accuracy using known protein complex structures.
  • Application to GroEL/GroES, RNA polymerase II, and exosome complexes.

Main Results:

  • The Bayesian scoring function efficiently and accurately ranks structural models.
  • Demonstrated effectiveness in determining structures of challenging biological complexes.
  • Successful integration of cryo-EM data with other experimental and prior information.

Conclusions:

  • The developed Bayesian scoring function significantly advances integrative structural modeling.
  • Enables more reliable determination of macromolecular structures by combining diverse data.
  • The open-source implementation facilitates broader application in structural biology research.