IRES-targeting Small Molecule Inhibits Enterovirus 71 Replication via Allosteric Stabilization of a Ternary Complex
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-1H NOESY | 200 uM Selective Deuteration; Fully Deuteration for U and C; Selective Deuteration for A and G rNTP, 800 uM DMA135 | 100% D2O | 20 mM | 6.5 | 1 atm | 303 | Bruker AVANCE 800 |
| 2 | 2D 1H-1H NOESY | 200 uM Selective Deuteration; EQUIMOLAR MIX:ATP, GTP, CTP, UTP rNTP, 800 uM DMA135 | 100% D2O | 20 mM | 6.5 | 1 atm | 303 | Bruker AVANCE 800 |
| 3 | 2D 1H-1H NOESY | 200 uM Selective Deuteration; Fully Deuteration for U and C; Selective Deuteration for A and G rNTP | 100% D2O | 20 mM | 6.5 | 1 atm | 303 | Bruker AVANCE 800 |
| 4 | 2D 1H-1H NOESY | 200 uM Selective Deuteration; EQUIMOLAR MIX:ATP, GTP, CTP, UTP rNTP | 100% D2O | 20 mM | 6.5 | 1 atm | 303 | Bruker AVANCE 800 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 900 |
| 2 | Bruker | AVANCE | 700 |
| 3 | Bruker | AVANCE | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | Amber | |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 16 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | Amber | Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman | |
| 2 | chemical shift assignment | NMRView | Johnson, One Moon Scientific | |
| 3 | chemical shift assignment | Sparky | Goddard | |
| 4 | collection | TopSpin | Bruker Biospin | |
| 5 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 6 | processing | NMRDraw | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
