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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.
Abstract:
The backbone dynamics of the channel-forming peptide antibiotic zervamicin IIB (Zrv-IIB) in methanol were studied by 15N nuclear magnetic resonance relaxation measurements at 11.7, 14.1 and 18.8 T magnetic fields. The anisotropic overall rotation of the peptide was characterized based on 15N relaxation data and by hydrodynamic calculations. 'Model-free' analysis of the relaxation data showed that the peptide is fairly rigid on a sub-nanosecond time-scale. The residues from the polar side of Zrv-IIB helix are involved in micro-millisecond time-scale conformational exchange. The conformational exchange observed might indicate intramolecular processes or specific intermolecular interactions of potential relevance to Zrv-IIB ion channel formation.
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.