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Related Concept Videos

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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

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

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.
Induced-fit Model01:13

Induced-fit Model

Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical characteristics of...

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15N CPMG Relaxation Dispersion for the Investigation of Protein Conformational Dynamics on the µs-ms Timescale
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Applications of the molecular dynamics flexible fitting method.

Leonardo G Trabuco1, Eduard Schreiner, James Gumbart

  • 1Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Journal of Structural Biology
|October 12, 2010
PubMed
Summary

Cryo-electron microscopy (cryo-EM) now provides high-resolution structures. Molecular dynamics flexible fitting (MDFF) integrates these with existing data to reveal complex molecular mechanisms and dynamics.

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Area of Science:

  • Structural biology
  • Biophysics
  • Computational biology

Background:

  • Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structure of large biomolecular complexes.
  • Recent advances in cryo-EM have significantly improved resolution, enabling routine sub-nanometer structural determination.
  • Bridging the gap between structural data and functional mechanisms requires advanced computational tools.

Purpose of the Study:

  • To present recent applications of molecular dynamics flexible fitting (MDFF) in structural biology.
  • To demonstrate how MDFF can interpret cryo-electron microscopy (cryo-EM) data for complex biomolecules.
  • To showcase the utility of MDFF in deriving atomic models and investigating molecular dynamics.

Main Methods:

  • Molecular dynamics flexible fitting (MDFF) simulations.
  • Integration of X-ray crystallography structures with cryo-electron microscopy (cryo-EM) density maps.
  • Computational modeling of large biomolecular complexes.

Main Results:

  • MDFF successfully derived atomic models for large biomolecular complexes from cryo-EM data.
  • Applications included interpreting cryo-EM data of the ribosome during translation.
  • The structure of a membrane-curvature-inducing photosynthetic complex was elucidated.

Conclusions:

  • MDFF is a valuable hybrid modeling tool for integrating structural data and revealing molecular mechanisms.
  • MDFF enables the study of biomolecular dynamics in various functional states.
  • This approach advances the understanding of complex biological systems through high-resolution structural insights.