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NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins
09:25

NMR 15N Relaxation Experiments for the Investigation of Picosecond to Nanoseconds Structural Dynamics of Proteins

Published on: November 1, 2024

Backbone dynamics of the channel-forming antibiotic zervamicin IIB studied by 15N NMR relaxation

D M Korzhnev1, E V Bocharov, A V Zhuravlyova

  • 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, 117997 Moscow, Russia.

FEBS Letters
|April 27, 2001
PubMed

Insights

Zervamicin IIB (Zrv-IIB) peptide dynamics in methanol reveal a rigid structure on short timescales. Conformational exchange on the micro-millisecond scale suggests interactions crucial for its ion channel formation.

Area of Science:

  • Biophysics
  • Structural Biology
  • Biochemistry

Background:

  • Zervamicin IIB (Zrv-IIB) is a channel-forming peptide antibiotic.
  • Understanding its dynamics is key to elucidating its function.
  • Previous studies have explored its structure, but dynamics require further investigation.

Purpose of the Study:

  • To investigate the backbone dynamics of Zrv-IIB in methanol.
  • To characterize the overall rotation of the peptide.
  • To identify time-scales of conformational flexibility and their relevance to channel formation.

Main Methods:

  • 15N nuclear magnetic resonance (NMR) relaxation measurements at multiple magnetic fields (11.7, 14.1, and 18.8 T).
  • Hydrodynamic calculations to characterize peptide rotation.
  • 'Model-free' analysis of NMR relaxation data.

Main Results:

  • The peptide exhibits a rigid structure on the sub-nanosecond timescale.
  • Residues on the polar side of the Zrv-IIB helix undergo conformational exchange on the micro-millisecond timescale.
  • Anisotropic overall rotation of the peptide was successfully characterized.

Conclusions:

  • Zrv-IIB is largely rigid at fast timescales, with flexibility emerging at slower timescales.
  • Micro-millisecond conformational exchange may be linked to intramolecular processes or intermolecular interactions.
  • These dynamics are potentially significant for the ion channel formation mechanism of Zrv-IIB.

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