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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.
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Crystal field theory (CFT) is applicable to molecules in geometries other than octahedral. In octahedral complexes, the lobes of the dx2−y2 and dz2 orbitals point directly at the ligands. For tetrahedral complexes, the d orbitals remain in place, but with only four ligands located between the axes. None of the orbitals points directly at the tetrahedral ligands. However, the dx2−y2 and dz2 orbitals (along the Cartesian axes) overlap with the ligands less than the dxy,...
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In an NMR sample, precise measurement of the absolute absorption frequencies of nuclei is difficult. A standard internal reference compound is added, and the frequency difference between the reference signal and sample signals is measured.
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Crystal Field Theory
To explain the observed behavior of transition metal complexes (such as colors), a model involving electrostatic interactions between the electrons from the ligands and the electrons in the unhybridized d orbitals of the central metal atom has been developed. This electrostatic model is crystal field theory (CFT). It helps to understand, interpret, and predict the colors, magnetic behavior, and some structures of coordination compounds of transition metals.
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NMR Spectroscopy: Chemical Shift Overview01:15

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The position of the absorption signal of a sample is reported relative to the position of the signal of tetramethylsilane (TMS), which is added as an internal reference while recording spectra. The difference between the absorption frequencies of the sample and TMS (in Hz) is divided by the spectrometer operating frequency (in MHz) to obtain a dimensionless quantity called the chemical shift. It is reported on the δ (delta) scale and expressed in parts per million.
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Structural Isomerism02:34

Structural Isomerism

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Isomerism in Complexes
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Related Experiment Video

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A protocol for the refinement of NMR structures using simultaneously pseudocontact shift restraints from multiple

Davide Sala1, Andrea Giachetti1, Claudio Luchinat2,3

  • 1Magnetic Resonance Center (CERM), University of Florence, Via Luigi Sacconi 6, 50019, Sesto Fiorentino, Italy.

Journal of Biomolecular NMR
|October 25, 2016
PubMed
Summary

This study introduces an enhanced computational method for protein structure determination using paramagnetic metal ions. The new protocol refines protein structures with multiple pseudocontact shift datasets, improving geometric quality for deposition.

Keywords:
Lanthanide ionMetalloproteinProtein structurePseudocontact shiftStructure refinement

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Area of Science:

  • Structural Biology
  • Biophysics
  • Computational Chemistry

Background:

  • Paramagnetic metal ions induce measurable effects on protein NMR spectra, such as pseudocontact shifts (PCSs).
  • Anisotropic magnetic susceptibility of metal ions, like lanthanide(III) ions, generates PCSs, which are valuable restraints for determining the solution structures of metal-binding proteins.
  • Lanthanide(III) ions can be used to induce PCSs in diamagnetic proteins, often by replacing native calcium(II) ions, enabling the generation of protein structure ensembles from multiple PCS datasets.

Purpose of the Study:

  • To extend the capabilities of the AMBER molecular dynamics (MD) package to handle multiple pseudocontact shift (PCS) datasets for protein structure refinement.
  • To tune an existing NMR structure refinement protocol to achieve consistent convergence using PCS restraints.
  • To enable the energetic refinement of protein structure ensembles (bundles) generated using multiple PCS datasets, leading to geometrically suitable structures for deposition in the Protein Data Bank (PDB).

Main Methods:

  • Extension of the PCS module within the AMBER MD package to accommodate multiple PCS datasets.
  • Tuning of a previously established protocol for NMR structure refinement to effectively incorporate PCS restraints.
  • Utilizing restrained molecular dynamics (rMD) simulations in explicit solvent for energetic refinement of protein structures.

Main Results:

  • The developed protocol successfully refines protein structures using multiple PCS datasets, yielding improved geometric quality.
  • Test calculations with real experimental data demonstrate that the new implementation produces structures suitable for PDB deposition.
  • Initial protein structures generated with traditional restraints can also be effectively refined using both traditional and PCS restraints simultaneously.

Conclusions:

  • The extended AMBER package and refined protocol provide a robust method for protein structure determination using multiple PCS datasets.
  • This approach significantly improves the geometric quality of protein structures derived from NMR data, facilitating PDB deposition.
  • The method is versatile, allowing for the refinement of structures using a combination of traditional and PCS restraints.