Related Experiment Video
Updated: Jul 11, 2026

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
Published on: September 17, 2017
Structure determination by restrained molecular dynamics using NMR pseudocontact shifts as experimentally determined
1Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA.
Abstract:
The structure of a DNA octamer d(TTGGCCAA)(2) complexed to chromomycin-A(3) and a single divalent cobalt ion has been solved by using the pseudocontact shifts due to the unpaired electrons on the cobalt. A protocol was developed and critically evaluated for using the pseudocontact shifts in structure determination. The pseudocontact shifts were input as experimental restraints in molecular dynamics simulations with or without NOE constraints. Both the magnitude and orientation of the susceptibility anisotropy tensor required for the shift calculations were determined during the simulations by iterative refinement. The pseudocontact shifts could be used to define the structure to a very high precision and accuracy compared with a corresponding NOE-determined structure. Convergence was obtained from different starting structures and tensors. A structure determination using both NOE's and pseudocontact shifts revealed a general agreement between the two data sets. However, some evidence for a discrepancy between NOE's and pseudocontact shifts was observed in the backbone and terminal base pairs of the DNA. Violations in shift or NOE restraints remaining in the final structures were examined and may be a reflection of motional averaging of the constraints and evidence for flexibility. This work demonstrates that pseudocontact shifts are a powerful tool for NMR structure determination.
More Related Videos
Related Concept Videos
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR
¹H NMR: Interpreting Distorted and Overlapping Signals
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 slanted or...
Chemical Shift: Internal References and Solvent Effects
The internal reference compound generally used in NMR spectroscopy is tetramethylsilane (TMS). TMS is preferred because it is chemically inert, soluble in NMR solvents, and easily removable. Also, the highly shielded methyl protons in TMS yield an intense...
NMR Spectroscopy: Chemical Shift Overview
For instance, the proton...
¹³C NMR: Distortionless Enhancement by Polarization Transfer (DEPT)

