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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...
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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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Protein Folding01:25

Protein Folding

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Study of Protein Dynamics via Neutron Spin Echo Spectroscopy
08:03

Study of Protein Dynamics via Neutron Spin Echo Spectroscopy

Published on: April 13, 2022

An efficient null model for conformational fluctuations in proteins.

Tim Harder1, Mikael Borg, Sandro Bottaro

  • 1The Bioinformatics Section, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.

Structure (London, England : 1993)
|May 15, 2012
PubMed
Summary
This summary is machine-generated.

TYPHON is a novel computational method for exploring protein conformational fluctuations. This efficient probabilistic approach offers insights into protein dynamics, aligning with experimental findings.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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Area of Science:

  • Computational Biology
  • Biophysics
  • Structural Biology

Background:

  • Protein dynamics are essential for biological function, catalytic activity, and disease mechanisms.
  • Molecular dynamics (MD) simulations are valuable for studying protein conformational changes but are computationally intensive, limiting their timescale.
  • Efficient computational methods are needed to probe protein conformational fluctuations.

Purpose of the Study:

  • To introduce TYPHON, a probabilistic method for exploring protein conformational space.
  • To provide a computationally efficient alternative to traditional MD simulations for studying protein dynamics.
  • To validate TYPHON's ability to capture experimentally relevant conformational fluctuations.

Main Methods:

  • TYPHON utilizes a probabilistic model of local protein structure.
  • It incorporates nonlocal interactions, such as hydrogen bonds and disulfide bridges, as restraints.
  • The method functions as a null model for conformational fluctuations under specified restraints.

Main Results:

  • TYPHON successfully explores protein conformational space.
  • The method provides information on conformational fluctuations that correlates with experimental data.
  • TYPHON demonstrates computational efficiency in probing protein dynamics.

Conclusions:

  • TYPHON offers a flexible and computationally efficient approach to study protein conformational fluctuations.
  • This method complements existing techniques for investigating protein dynamics.
  • TYPHON can yield insights into protein function, activity, and pathogenesis through conformational analysis.