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Protein Organization01:24

Protein Organization

8.4K
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.
The primary structure of a protein is its amino acid sequence....
8.4K
NMR Spectrometers: Resolution and Error Correction01:14

NMR Spectrometers: Resolution and Error Correction

935
When magnetic nuclei in a sample achieve resonance and undergo relaxation, the signal detected in NMR is an approximately exponential free induction decay. Fourier transform of an exponential decay yields a Lorentzian peak in the frequency domain. Lorentzian peaks in an NMR spectrum are defined by their amplitude, full width at half maximum, and position, where the peak width is governed by the spin-spin relaxation time alone. In real experiments, however, the applied magnetic field is rendered...
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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

1.1K
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: Nov 25, 2025

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

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A method for validating the accuracy of NMR protein structures.

Nicholas J Fowler1, Adnan Sljoka2,3, Mike P Williamson4

  • 1Dept of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.

Nature Communications
|December 19, 2020
PubMed
Summary
This summary is machine-generated.

We developed a new method to assess NMR protein structure accuracy by comparing the random coil index (RCI) to rigidity predictions. This approach offers a valuable addition to existing accuracy measures for structural biology.

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Chemistry

Background:

  • Nuclear Magnetic Resonance (NMR) spectroscopy is crucial for determining protein structures.
  • Assessing the accuracy of NMR-derived protein structures is essential for reliable biological interpretation.
  • Existing methods for accuracy assessment have limitations.

Purpose of the Study:

  • To present a novel method for measuring the accuracy of NMR protein structures.
  • To compare the performance of the new method against conventional accuracy predictors.
  • To evaluate the accuracy of NMR structures relative to crystal structures.

Main Methods:

  • The method compares the random coil index (RCI) against local rigidity predicted by mathematical rigidity theory (FIRST).
  • It utilizes a correlation score for secondary structure assessment and an RMSD score for overall rigidity.
  • Performance was evaluated using explicitly solvent-refined structures, decoy structures, and standard accuracy metrics.

Main Results:

  • Explicitly solvent-refined structures showed higher accuracy than unrefined ones.
  • Restraint violations and RMSD were found to be poor indicators of NMR structure accuracy.
  • NMR structures exhibit accurate secondary structures but are generally too flexible overall compared to crystal structures, which can be too rigid in loops.

Conclusions:

  • The presented method is a useful addition to existing measures for assessing NMR protein structure accuracy.
  • The findings highlight differences in flexibility between NMR and crystal protein structures.
  • The study provides insights into the relative strengths and weaknesses of different accuracy assessment techniques.