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Related Concept Videos

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.
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Conservation of Protein Domains Over Different Proteins02:26

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

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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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Updated: Jun 19, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

A method to explore protein side chain conformational variability using experimental data.

Jane R Allison1, Wilfred F van Gunsteren

  • 1Laboratory of Physical Chemistry, Swiss Federal Institute of Technology ETH, 8093 Zurich, Switzerland.

Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry
|November 3, 2009
PubMed
Summary
This summary is machine-generated.

Molecular dynamics simulations with local-elevation (LE) biasing improve conformational sampling for biomolecules. This method enhances the accuracy of protein structural analysis using experimental data, overcoming limitations of traditional simulations.

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

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

Published on: July 25, 2013

Related Experiment Videos

Last Updated: Jun 19, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

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

Published on: July 25, 2013

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • Experimentally measured biomolecular properties represent averages, limiting detailed conformational analysis.
  • Nuclear Magnetic Resonance (NMR) coupling constants ((3)J-coupling) exhibit complex, nonlinear relationships with dihedral angles.
  • Traditional molecular dynamics (MD) simulations face challenges with limited sampling and force field dependency.

Purpose of the Study:

  • To evaluate the uncertainty in theoretically predicted dihedral angle values from experimental NMR data.
  • To develop an MD-based method for detecting experimental data inconsistencies and identifying conformational averaging or force field deficiencies.
  • To demonstrate the efficacy of local-elevation (LE) biased MD for generating accurate biomolecular ensembles.

Main Methods:

  • Utilized time-averaging with local-elevation (LE) biasing for enhanced conformational searching in MD simulations.
  • Applied the method to side chain (3)J-coupling values of the FK506 binding protein (FKBP).
  • Developed a novel MD-based technique to analyze experimental data quality and simulation parameter accuracy.

Main Results:

  • Investigated and quantified the uncertainty in theoretical dihedral angle predictions.
  • Successfully identified degrees of freedom exhibiting conformational averaging and potential force field parameter issues.
  • Demonstrated that LE-biased MD simulations yield ensembles that best fit experimental (3)J-coupling data on average.

Conclusions:

  • Local-elevation biased molecular dynamics is a powerful tool for overcoming sampling limitations in biomolecular simulations.
  • The proposed MD-based technique effectively detects inconsistencies in experimental NMR data.
  • LE-biased MD provides superior ensembles for accurately representing biomolecular conformation in solution.