Suboptimization of a glycine rich peptide allows the combinatorial space exploration for designing novel antimicrobial peptides
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H TOCSY | 100 mM dodecylphosphocholine, 5 % D2O, 1 mM peptide, 5 % sodium 2,2-dimethyl-2-silapentane-5-sulfonate, 90 % H2O | 90% H2O/10% D2O | 0.01 | 4 | 1 atm | 289 | Bruker AVANCE III 500 |
| 2 | 2D 1H-1H NOESY | 100 mM dodecylphosphocholine, 5 % D2O, 1 mM peptide, 5 % sodium 2,2-dimethyl-2-silapentane-5-sulfonate, 90 % H2O | 90% H2O/10% D2O | 0.01 | 4 | 1 atm | 289 | Bruker AVANCE III 500 |
| 3 | 2D 1H-13C HSQC | 100 mM dodecylphosphocholine, 5 % D2O, 1 mM peptide, 5 % sodium 2,2-dimethyl-2-silapentane-5-sulfonate, 90 % H2O | 90% H2O/10% D2O | 0.01 | 4 | 1 atm | 289 | Bruker AVANCE III 500 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE III | 500 |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | |
| Conformers Calculated Total Number | |
| Conformers Submitted Total Number | 10 |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | data analysis | NMRView | Johnson, One Moon Scientific | |
| 2 | structure calculation | X-PLOR NIH | 2.28 | Schwieters, Kuszewski, Tjandra and Clore |
| 3 | refinement | X-PLOR NIH | 2.28 | Schwieters, Kuszewski, Tjandra and Clore |
| 5 | processing | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 4 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 6 | geometry optimization | TALOS | Cornilescu, Delaglio and Bax | |
| 7 | data analysis | QUEEN | Nabuurs, Spronk, Krieger, Maassen, Vriend and Vuister | |
| 8 | data analysis | MOLMOL | Koradi, Billeter and Wuthrich | |
