NMR solution structure of the Dermaseptin antimicrobial peptide analog NC12-K4S4(1-13)a
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | DQF-COSY | 2.2mM peptide; 20:1 molar ratio of DPC-d38 (Cambridge Isotope Laboratories, Inc., USA); 0.02% NaN3 | 90% of 10% strength PBS solution, 10% D2O | 78 mM | 7.4 | ambient | 303 | |
| 2 | 2D TOCSY | 2.2mM peptide; 20:1 molar ratio of DPC-d38 (Cambridge Isotope Laboratories, Inc., USA); 0.02% NaN3 | 90% of 10% strength PBS solution, 10% D2O | 78 mM | 7.4 | ambient | 303 | |
| 3 | 2D NOESY | 2.2mM peptide; 20:1 molar ratio of DPC-d38 (Cambridge Isotope Laboratories, Inc., USA); 0.02% NaN3 | 90% of 10% strength PBS solution, 10% D2O | 78 mM | 7.4 | ambient | 303 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DMX | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| Distance Geometry, Simulated Annealing | The structures are derived from 241 NOE constraints; 109 intraresidual; 44 i+1; 19 i+2; 39 i+3; 30 long-range. | XwinNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy, structures with the least restraint violations |
| Conformers Calculated Total Number | 50 |
| Conformers Submitted Total Number | 15 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | XwinNMR | 3.1 | Bruker |
| 2 | processing | XwinNMR | 3.1 | Bruker |
| 3 | data analysis | Sparky | 3 | Goddard and Kneller |
| 4 | structure solution | X-PLOR | 3.856 | Nilges, Kuszewski and Brnger |
| 5 | data analysis | Procheck | Laskowski, Rullmannn, MacArthur, Kaptein and Thornton | |
| 6 | refinement | X-PLOR | 3.856 | Nilges, Kuszewski and Brnger |
