Ground state sampled during RDC restrained Replica-averaged Metadynamics (RAM) simulations of the HIV-1 TAR complexed with cyclic peptide mimetic of Tat
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | not applicable | 2.0 uM [U-99% 13C; U-99% 15N] Apical region (29-mer) of the HIV-1 TAR RNA element, 2.0 uM [U-99% 13C; U-99% 15N] Cyclic peptide mimetic of HIV-1 Tat, 17 mg/mL Pf1 phage | 100% D2O | 10 mM | 6.6 | 1 atm | 298.15 | Varian INOVA 800 |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 3 | Varian | INOVA | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| molecular dynamics | RAM simulations | Gromacs and Plumed |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | Lowest |
| Conformers Calculated Total Number | 42217 |
| Conformers Submitted Total Number | 10 |
| Representative Model | 1 (lowest energy) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | structure calculation | Xplor-NIH | Schwieters, Kuszewski, Tjandra and Clore | |
| 2 | structure calculation | Gromacs and Plumed | Vendruscolo, Camilloni and others | |
