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Related Concept Videos

Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.
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Related Experiment Video

Updated: May 31, 2026

Ubiquitin Chain Analysis by Parallel Reaction Monitoring
08:33

Ubiquitin Chain Analysis by Parallel Reaction Monitoring

Published on: June 17, 2020

Mapping the hydration dynamics of ubiquitin.

Nathaniel V Nucci1, Maxim S Pometun, A Joshua Wand

  • 1Graduate Group in Biochemistry & Molecular Biophysics and Department of Biochemistry & Biophysics, University of Pennsylvania, 422 Curie Boulevard, Philadelphia, Pennsylvania 19104-6059, United States.

Journal of the American Chemical Society
|July 19, 2011
PubMed
Summary

Investigating protein hydration dynamics using solution NMR spectroscopy reveals distinct water molecule behaviors. This study quantifies protein-water interactions, uncovering hydration clustering and long-lived water at recognition sites.

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Area of Science:

  • Biophysics
  • Structural Biology
  • Biochemistry

Background:

  • Characterizing atomic-level water-protein interactions is challenging.
  • Solution Nuclear Magnetic Resonance (NMR) spectroscopy offers potential for studying protein hydration dynamics but suffers from artifacts.
  • Previous methods enabled quantification of protein surface-water interactions using nuclear Overhauser effects.

Purpose of the Study:

  • To extend NMR methods for detailed analysis of protein hydration dynamics.
  • To investigate dipolar interactions between hydration water and protein carbon-bound hydrogens.
  • To map hydration dynamics across the protein surface.

Main Methods:

  • Encapsulating proteins in reverse micelle particles to control water dynamics.
  • Utilizing low viscosity liquid propane to manipulate molecular reorientation times.
  • Acquiring rotating frame nuclear Overhauser effects (ROPE) using (1)H bonded to (13)C signals.
  • Measuring T(1ρ) relaxation time constants.

Main Results:

  • High-quality ROPE data were obtained by lengthening relaxation times.
  • Hydration dynamics were mapped across the majority of the protein surface, including interactions with nitrogen-bound hydrogens.
  • A broad spectrum of hydration dynamics was observed, with clustering evident on the molecular surface.
  • Regions with long-lived hydration water correlate with protein-binding sites.

Conclusions:

  • The extended NMR approach provides detailed insights into protein hydration dynamics.
  • Observed hydration clustering and long-lived water at interaction sites suggest evolutionary optimization of solvent entropy in binding.
  • This method advances the understanding of water's role in protein function and molecular recognition.