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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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Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
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Published on: September 17, 2017

Protein loop closure using orientational restraints from NMR data.

Chittaranjan Tripathy1, Jianyang Zeng, Pei Zhou

  • 1Department of Computer Science, Duke University, Durham, North Carolina 27708.

Proteins
|December 14, 2011
PubMed
Summary
This summary is machine-generated.

This study introduces a new algorithm for accurately modeling protein loops using sparse residual dipolar coupling (RDC) data. The method improves protein structure determination by precisely calculating loop conformations from NMR data.

Keywords:
algorithmsinverse kinematicsloop closurenuclear magnetic resonanceprotein loopsresidual dipolar couplingssphero-conicstructural biology

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Biology

Background:

  • Protein loops are critical for protein function and specificity.
  • Accurate loop modeling is essential but challenging.
  • Existing methods lack rigorous approaches for global orientational restraints like RDC data.

Purpose of the Study:

  • To present a novel algorithm for protein loop structure determination using sparse RDC data.
  • To address limitations in current protein loop modeling techniques.
  • To enable precise calculation of loop conformations from NMR spectroscopy.

Main Methods:

  • Developed a sparse data, RDC-based algorithm.
  • Utilized the interplay between RDC-derived sphero-conics and protein kinematics.
  • Formulated loop structure determination as solving low-degree polynomial equations.
  • Employed systematic search with provable pruning strategies for completeness.

Main Results:

  • Achieved higher accuracy in loop modeling compared to traditional methods.
  • Demonstrated a three- to six-fold improvement in backbone RMSD on experimental RDC datasets.
  • Validated performance on synthetic RDC datasets for various loop lengths.
  • Successfully computed protein loop conformations consistent with sparse NMR data.

Conclusions:

  • The novel algorithm accurately determines protein loop conformations from sparse NMR data.
  • This approach enhances high-resolution protein backbone structure determination.
  • The method offers a significant improvement over existing structure determination protocols.