Structure of the HIV-1 frameshift site RNA bound to a small molecule inhibitor of viral replication
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 0.75 mM RNA (45-MER), 0.75 mM DB213, 20 uM DSS, 20 mM potassium chloride, 10 mM [U-2H] TRIS | 90% H2O/10% D2O | 20 | 7.0 | ambient atm | 283 | |
| 2 | 2D 1H-1H NOESY | 0.75 mM RNA (45-MER), 0.75 mM DB213, 20 uM DSS, 20 mM potassium chloride, 10 mM [U-2H] TRIS | 100% D2O | 20 | 7.0 | ambient atm | 308 | |
| 3 | 2D 1H-1H TOCSY | 0.75 mM RNA (45-MER), 0.75 mM DB213, 20 uM DSS, 20 mM potassium chloride, 10 mM [U-2H] TRIS | 100% D2O | 20 | 7.0 | ambient atm | 308 | |
| 4 | 2D 1H-13C HSQC | 1.5 mM RNA (45-MER), 1.5 mM DB213, 40 uM DSS, 40 mM potassium chloride, 20 mM [U-2H] TRIS | 100% D2O | 20 | 7.0 | ambient atm | 308 | |
| 5 | 2D 1H-13C HSQC | 1.5 mM RNA (45-MER), 1.5 mM DB213, 40 uM DSS, 40 mM potassium chloride, 20 mM [U-2H] TRIS, 4.5 mg Pf1 phage | 100% D2O | 20 | 7.0 | ambient atm | 308 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DMX | 750 |
| 2 | Varian | AVANCE | 900 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| torsion angle dynamics, molecular dynamics | HADDOCK | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 50 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | docking | HADDOCK | 2.0 | Alexandre Bonvin, Utrecht University |
| 2 | refinement | HADDOCK | 2.0 | Alexandre Bonvin, Utrecht University |
| 3 | structure solution | HADDOCK | 2.0 | Alexandre Bonvin, Utrecht University |
| 4 | refinement | Amber | 9.0 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm |
| 5 | structure solution | Amber | 9.0 | Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm |
| 6 | chemical shift assignment | Sparky | Goddard | |
| 7 | data analysis | Sparky | Goddard | |
| 8 | peak picking | Sparky | Goddard | |
| 9 | data analysis | SYBYL | 8.0 | Tripos |
| 10 | geometry optimization | SYBYL | 8.0 | Tripos |
| 11 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 12 | collection | XwinNMR | 3.5 | Bruker Biospin |
| 13 | processing | XwinNMR | 3.5 | Bruker Biospin |
| 14 | collection | VnmrJ | Varian | |
| 15 | data analysis | PALES | Markus Zweckstetter, Ad Bax | |
| 16 | data analysis | PyMOL | DeLano Scientific | |
