Structure and membrane interactions of the antibiotic peptide dermadistinctin K by multidimensional 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 | 2.0 mM dd k, 400 mM [U-2H] DPCd38 | 400mM DPCd38/H2O | 6.0 | ambient | 318 | ||
| 2 | 2D 1H-1H NOESY | 2.0 mM dd k, 400 mM [U-2H] DPCd38 | 400mM DPCd38/H2O | 6.0 | ambient | 318 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE III | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | NOE INTENSITIES WERE CONVERTED INTO SEMI-QUANTITATIVE DISTANCE RESTRAINS. THE UPPER LIMITS OF THE DISTANCES RESTRAINS THUS OBTAINED WERE 2.8, 3.4 AND 5.0 A (STRONG, MEDIUM, AND WEAK NOES RESPECTIVELY). STRUCTURE CALCULATIONS WERE PERFORMED USING THE XPLOR-NIH SOFTWARE, VERSION 2.17.0 (SCHWIETERS ET AL., 2003). 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 TEMPERATURE IN 15000 STEPS IN THE FIRST SLOW-COOL ANNEALING STAGE. | TopSpin |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 500 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (closest to the average) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | TopSpin | 2.0 | Bruker Biospin |
| 2 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 3 | chemical shift assignment | NMRView | Johnson, One Moon Scientific | |
| 4 | data analysis | NMRView | Johnson, One Moon Scientific | |
| 5 | peak picking | NMRView | Johnson, One Moon Scientific | |
| 6 | geometry optimization | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 7 | structure solution | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 8 | refinement | X-PLOR NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 9 | data analysis | ProcheckNMR | Laskowski and MacArthur | |
| 10 | data analysis | MOLMOL | Koradi, Billeter and Wuthrich | |
