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Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
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Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
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Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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Optimized Negative Staining: a High-throughput Protocol for Examining Small and Asymmetric Protein Structure by Electron Microscopy
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Variability of Protein Structure Models from Electron Microscopy.

Lyman Monroe1, Genki Terashi2, Daisuke Kihara3

  • 1Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.

Structure (London, England : 1993)
|March 7, 2017
PubMed
Summary
This summary is machine-generated.

Electron microscopy (EM) structure models vary in quality. Refinement analysis shows model accuracy depends on EM map resolution, indicating caution is needed when interpreting EM data.

Keywords:
EMDBcomputational modellingcryo-EMelectron microscopymodel refinementprotein structure modellingprotein tertiary structurestructure biologystructure optimization

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Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • Electron microscopy (EM) is increasingly used to determine biomolecular structures.
  • The quality and reliability of structure models derived from EM maps vary significantly.
  • Assessing the information content within EM maps is crucial for accurate structural modeling.

Purpose of the Study:

  • To evaluate the extent to which biomolecular structure models are supported by the information present in electron microscopy maps.
  • To quantify the relationship between EM map resolution and the accuracy of derived structure models.
  • To provide a method for estimating structural deviations based on map resolution.

Main Methods:

  • Utilized two computational structure refinement methods.
  • Analyzed a dataset of 49 EM maps with associated structure models.
  • Correlated the degree of structure modification and model disagreement with global and local map resolutions.

Main Results:

  • The extent of structure modification during refinement decreased as EM map resolution improved.
  • Disagreement between models generated by different refinement methods was inversely proportional to map resolution.
  • Developed a quantitative estimation of structural deviations for specific map resolutions.

Conclusions:

  • The discrepancy between deposited EM maps and refined models stems from inherent limitations in the structural information content of EM maps.
  • EM map resolution is a critical factor determining the reliability of associated structure models.
  • Users should exercise caution when interpreting and utilizing structural annotations derived from EM data for downstream applications.