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Related Concept Videos

¹H NMR: Pople Notation01:09

¹H NMR: Pople Notation

2.9K
The Pople nomenclature system classifies spin systems based on the difference between their chemical shifts. Coupled spins are denoted by capital letters with subscripts indicating the number of equivalent nuclei. When the coupled nuclei have well-separated chemical shifts, they are assigned letters that are far apart in the alphabet, such as A and X. When the difference in chemical shifts is small, coupled nuclei are named using adjacent letters of the alphabet (AB, MN, or XY).
A proton...
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2D NMR: Overview of Homonuclear Correlation Techniques01:16

2D NMR: Overview of Homonuclear Correlation Techniques

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Homonuclear correlation spectroscopy (COSY) is a powerful technique used in Nuclear Magnetic Resonance (NMR) spectroscopy to study the correlations between nuclei of the same type within a molecule. It provides information about scalar couplings between adjacent nuclei, which helps determine connectivity and structural information. There are several COSY variants, each with its unique strengths and experimental parameters.
COSY90 is the standard two-dimensional (2D) COSY experiment that...
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¹H NMR: Complex Splitting01:13

¹H NMR: Complex Splitting

2.2K
A proton M that is coupled to a proton X results in doublet signals for M. However, NMR-active nuclei can be simultaneously coupled to more than one nonequivalent nucleus. When M is coupled to a second proton A, such as in styrene oxide, each peak in the doublet is split into another doublet.
Splitting diagrams or splitting tree diagrams are routinely used to depict such complex couplings. While drawing splitting diagrams, the splitting with the larger coupling constant is usually applied...
2.2K
¹H NMR: Interpreting Distorted and Overlapping Signals01:02

¹H NMR: Interpreting Distorted and Overlapping Signals

1.8K
Spin systems where the difference in chemical shifts of the coupled nuclei is greater than ten times J are called first-order spin systems. These nuclei are weakly coupled, and their chemical shifts and coupling constant can generally be estimated from the well-separated signals in the spectrum.
As Δν decreases and the signals move closer, the doublets appear increasingly distorted. The intensities of the inner lines increase at the cost of those of the outer lines as the signals are...
1.8K
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

1.4K
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...
1.4K
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

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

1.8K
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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Systematic solution to homo-oligomeric structures determined by NMR.

Jeffrey W Martin1, Pei Zhou, Bruce R Donald

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

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PubMed
Summary

Determining protein structure using nuclear magnetic resonance (NMR) can fail for homo-oligomeric proteins due to ambiguous constraints. This study reveals multiple possible folds, challenging the assumption that NMR convergence equals the global minimum structure.

Keywords:
distance restraintnuclear magnetic resonance spectroscopyprotein homo-oligomerssimulated annealingstructure determination

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Biophysics

Background:

  • Nuclear magnetic resonance (NMR) spectroscopy is a key technique for protein structure determination.
  • Simulated annealing is commonly used to find a converged protein fold based on distance constraints, such as those from nuclear Overhauser effects (NOEs).
  • Good convergence in NMR structure determination is often assumed to represent the global minimum energy conformation.

Purpose of the Study:

  • To investigate the reliability of NMR-based protein structure determination for homo-oligomeric proteins.
  • To evaluate the impact of ambiguous constraints on conformational search in NMR.
  • To address the fundamental limitations in determining global folds for homo-oligomeric proteins.

Main Methods:

  • Utilized simulated annealing for conformational search in NMR structure determination.
  • Employed distance constraints derived from nuclear Overhauser effects (NOEs), paramagnetic relaxation enhancement, and cysteine crosslinking.
  • Systematically evaluated conformational solutions satisfying NMR constraints for a trimeric membrane protein (DAGK).

Main Results:

  • Demonstrated that the criterion of convergence equaling the global minimum breaks down for homo-oligomeric proteins with ambiguous NMR constraints.
  • Identified 9 distinct folds for the trimeric membrane protein DAGK that satisfy the NMR constraints.
  • The identified folds included previously reported NMR and crystal structures.

Conclusions:

  • Ambiguous distance constraints from NMR experiments on homo-oligomeric proteins fundamentally limit global fold determination.
  • The assumption that NMR convergence guarantees the global minimum is invalid in such cases.
  • Developed a systematic method for the exhaustive enumeration of all NMR constraint-satisfying solutions for homo-oligomeric proteins.