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Related Concept Videos

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
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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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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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At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
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Related Experiment Video

Updated: Jul 24, 2025

Using Tomoauto: A Protocol for High-throughput Automated Cryo-electron Tomography
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MDTOMO method for continuous conformational variability analysis in cryo electron subtomograms based on molecular

Rémi Vuillemot1,2, Isabelle Rouiller2,3, Slavica Jonić4

  • 1IMPMC-UMR 7590 CNRS, Sorbonne Université, Muséum National d'Histoire Naturelle, CC 115, 4 Place Jussieu, 75005, Paris, France.

Scientific Reports
|June 30, 2023
PubMed
Summary

MDTOMO analyzes continuous conformational variability in cryo-electron tomography (cryo-ET) data using molecular dynamics (MD) simulations. This method reveals atomic-scale models and free-energy landscapes, offering a more complete view of molecular complex dynamics.

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Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • Cryo-electron tomography (cryo-ET) visualizes macromolecular complexes in native environments.
  • Subtomogram averaging (STA) reveals 3D structures but is limited by small complex numbers, hindering comprehensive conformational analysis.
  • Current methods struggle to capture the full conformational landscape of molecular complexes.

Purpose of the Study:

  • To introduce MDTOMO, a novel method for analyzing continuous conformational variability in cryo-ET data.
  • To generate atomic-scale models and free-energy landscapes from cryo-ET subtomograms.
  • To overcome limitations of discrete classification in revealing complete conformational heterogeneity.

Main Methods:

  • MDTOMO integrates cryo-ET subtomograms with Molecular Dynamics (MD) simulations.
  • The method analyzes continuous conformational changes within molecular complexes.
  • It models the free-energy landscape associated with observed conformations.

Main Results:

  • MDTOMO successfully generated atomic-scale models of conformational variability.
  • The method elucidated free-energy landscapes from cryo-ET data.
  • Performance was validated on synthetic ABC exporter and in situ SARS-CoV-2 spike datasets.

Conclusions:

  • MDTOMO provides a powerful approach to analyze dynamic properties of molecular complexes.
  • This method enhances understanding of biological functions through in situ structural data.
  • MDTOMO has potential applications in structure-based drug discovery.