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¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

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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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Updated: Jun 17, 2025

Ubiquitin Chain Analysis by Parallel Reaction Monitoring

Ubiquitin Chain Analysis by Parallel Reaction Monitoring

Published on: June 17, 2020

Ubiquitin's Conformational Heterogeneity as Discerned by Nuclear Magnetic Resonance Spectroscopy.

David Beriashvili¹, Gert E Folkers¹, Marc Baldus¹

¹NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padaulaan 8, 3584 CH, Utrecht, The Netherlands.

Chembiochem : a European Journal of Chemical Biology

|August 14, 2024

Summary

Nuclear magnetic resonance (NMR) spectroscopy reveals ubiquitin's (Ub) dynamic motions. Research highlights Ub's conformational plasticity and calls for studies in biologically relevant environments.

Keywords:

Conformational heterogeneity NMR Post-translational modifications Protein dynamics in-cell NMR

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Last Updated: Jun 17, 2025

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Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

Area of Science:

Biophysics
Structural Biology
Molecular Biology

Background:

Visualizing protein molecular motions is crucial in biophysics.
Nuclear magnetic resonance (NMR) spectroscopy is a primary technique for this.
Ubiquitin (Ub) is a key regulatory protein whose motions are extensively studied by NMR.

Purpose of the Study:

To review 35 years of NMR research on ubiquitin's conformational plasticity.
To compare ubiquitin dynamics data obtained in vitro, ex vivo, and in vivo.
To emphasize the need for studying ubiquitin in biologically relevant contexts.

Main Methods:

Utilizing nuclear magnetic resonance (NMR) spectroscopy data.
Analyzing atomic-resolution structural and dynamic information.
Comparing findings across different experimental conditions (in vitro, ex vivo, in vivo).

Main Results:

NMR has provided atomic-resolution insights into ubiquitin's conformational plasticity.
Differences exist in observed dynamics depending on the experimental setting.
Current data predominantly comes from in vitro studies.

Conclusions:

Ubiquitin exhibits significant conformational plasticity.
In vitro, ex vivo, and in vivo conditions yield distinct dynamic profiles.
Further investigation of ubiquitin dynamics in biologically relevant backgrounds is essential.