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Related Concept Videos

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...
Spin–Spin Coupling Constant: Overview01:08

Spin–Spin Coupling Constant: Overview

In bromoethane, the three methyl protons are coupled to the two methylene protons that are three bonds away. In accordance with the n+1 rule, the signal from the methyl protons is split into three peaks with 1:2:1 relative intensities. The methylene protons appear as a quartet, with the relative intensities of 1:3:3:1.
Qualitatively, any spin plus-half nucleus polarizes the spins of its electrons to the minus-half state. Consequently, the paired electron in the hydrogen–carbon bond must have a...
Spin–Spin Coupling: Two-Bond Coupling (Geminal Coupling)01:20

Spin–Spin Coupling: Two-Bond Coupling (Geminal Coupling)

Two NMR-active nuclei bonded to a central atom can be involved in geminal or two-bond coupling. Geminal coupling is commonly seen between diastereotopic protons in chiral molecules and unsymmetrical alkenes, among others.
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¹H NMR of Labile Protons: Temporal Resolution01:10

¹H NMR of Labile Protons: Temporal Resolution

Protons bonded to heteroatoms such as nitrogen and oxygen exhibit a range of chemical shift values. This is due to the varying degree of hydrogen bonding between the proton and the heteroatom in other molecules. The extent of hydrogen bonding affects the electron density around the proton, thereby giving different chemical shift values for the protons in the proton NMR spectrum.
The –OH proton in alcohols typically appears in the range of δ 2 to 5 ppm but can vary depending on the specific...
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Atomic Nuclei: Types of Nuclear Relaxation

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NMR Spectroscopy: Spin–Spin Coupling

The spin state of an NMR-active nucleus can have a slight effect on its immediate electronic environment. This effect propagates through the intervening bonds and affects the electronic environments of NMR-active nuclei up to three bonds away; occasionally, even farther. This phenomenon is called spin–spin coupling or J-coupling. Coupling interactions are mutual and result in small changes in the absorption frequencies of both nuclei involved. While nuclei of the same element are involved in...

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Related Experiment Video

Updated: May 7, 2026

Site Directed Spin Labeling and EPR Spectroscopic Studies of Pentameric Ligand-Gated Ion Channels
11:19

Site Directed Spin Labeling and EPR Spectroscopic Studies of Pentameric Ligand-Gated Ion Channels

Published on: July 4, 2016

RosettaEPR: rotamer library for spin label structure and dynamics.

Nathan S Alexander1, Richard A Stein, Hanane A Koteiche

  • 1Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, United States of America ; Department of Chemistry, Vanderbilt University, Nashville, Tennessee, United States of America.

Plos One
|September 17, 2013
PubMed
Summary

This study introduces a rotamer library for methanethiosulfonate spin labels (MTSSL) into Rosetta software, improving protein structure modeling. The enhanced RosettaEPR tool accurately predicts spin label positions and distances, aiding structural biology research.

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Area of Science:

  • Structural Biology
  • Computational Biology
  • Biophysics

Background:

  • Measuring distances between protein-bound spin labels is crucial in structural biology.
  • A key limitation is the unknown orientation of spin labels relative to the protein backbone.

Purpose of the Study:

  • To develop and validate a computational method for predicting spin label conformations and distances.
  • To integrate a methanethiosulfonate spin label (MTSSL) rotamer library into the Rosetta protein modeling software.

Main Methods:

  • Developed MTSSL rotamer library from crystal structures and molecular dynamics simulations.
  • Integrated the library into Rosetta, creating RosettaEPR.
  • Validated RosettaEPR against experimental data for T4 lysozyme and membrane proteins LeuT and MsbA.

Main Results:

  • Rosetta accurately recovers spin label conformations, achieving 99.8% accuracy for core sites and 53% for surface sites.
  • Predicts distances between two spin labels with a mean error of 4.4 Å.
  • Predicts the flexibility (width of distance distribution) with a mean error of 1.3 Å.

Conclusions:

  • RosettaEPR provides accurate full-atom modeling of MTSSL spin labels.
  • The method enhances protein structure determination using EPR distance measurements.
  • Makes advanced spin label modeling accessible to the scientific community.