Conformations of macrocyclic peptides sampled by exact NOEs: models for cell-permeability. Conformation 1 of omphalotin A in apolar solvents.
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 20 uM OmpA | 70 % CDCl3, 30 % n-hexadecane-D34 | 0 | 7 | 1 bar | 278 | Bruker AVANCE III HD 900 |
| 2 | 2D 1H-1H TOCSY | 20 uM OmpA | 70 % CDCl3, 30 % n-hexadecane-D34 | 0 | 7 | 1 bar | 278 | Bruker AVANCE III HD 900 |
| 3 | 2D 1H-13C HSQC | 20 uM OmpA | 70 % CDCl3, 30 % n-hexadecane-D34 | 0 | 7 | 1 bar | 278 | Bruker AVANCE III HD 900 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE III HD | 900 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing | Amber | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 19 |
| Representative Model | 1 (fewest violations) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | chemical shift assignment | CcpNmr Analysis | 2.5 | CCPN |
| 2 | structure calculation | CYANA | 3.98.15 | Guntert, Mumenthaler and Wuthrich |
| 3 | refinement | Amber | 22 | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman |
| 4 | peak picking | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
