Structure and membrane interactions of the antibiotic peptide dermadistinctin k by solution and oriented 15N and 31P solid-state NMR spectroscopy
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H TOCSY | 2.0mM dermadistinctin k; trifluoroethanol; H2O 60%, D2O 40% | trifluoroethanol; H2O 60%, D2O 40% | 7.0 | ambient | 293.15 | ||
| 2 | 2D 1H-1H NOESY | 2.0mM dermadistinctin k; trifluoroethanol; H2O 60%, D2O 40% | trifluoroethanol; H2O 60%, D2O 40% | 7.0 | ambient | 293.15 | ||
| 3 | 2D 1H-13C HSQC | 2.0mM dermadistinctin k; trifluoroethanol; H2O 60%, D2O 40% | trifluoroethanol; H2O 60%, D2O 40% | 7.0 | ambient | 293.15 | ||
| 4 | 2D 1H-15N HSQC | 2.0mM dermadistinctin k; trifluoroethanol; H2O 60%, D2O 40% | trifluoroethanol; H2O 60%, D2O 40% | 7.0 | ambient | 293.15 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE DRX | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | NOE intensities were converted into semi-quantitative distances restrains. The upper limits of the distances thus obtained were 2.8, 3.4 and 5.0A; (for strong, medium, and weak NOEs, respectively). Structure calculations were performed using the Xplor-NIH software, version 2.17.0 . Starting with the extended structure, 500 structures were generated using a simulated annealing protocol. This was followed by 20000 steps of simulated annealing at 1000 K and a subsequent decrease in tempera ure in 15000 steps in the first slow-cool annealing stage. | XwinNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 500 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | XwinNMR | Bruker Biospin | |
| 2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 3 | data analysis | NMRView | 5.0.4 | Johnson, One Moon Scientific |
| 4 | chemical shift assignment | NMRView | 5.0.4 | Johnson, One Moon Scientific |
| 5 | structure solution | X-PLOR NIH | 2.17.0 | Schwieters, Kuszewski, Tjandra and Clore |
| 6 | geometry optimization | X-PLOR NIH | 2.17.0 | Schwieters, Kuszewski, Tjandra and Clore |
| 7 | data analysis | MOLMOL | 2K.2 | Koradi, Billeter and Wuthrich |
| 8 | data analysis | Procheck | 3.5.4 | Laskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Th |
| 9 | refinement | X-PLOR NIH | 2.17.0 | Schwieters, Kuszewski, Tjandra and Clore |
