1JCP
Solution structure of the lactam analogue EDap of HIV gp41 600-612 loop.
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | DQF-COSY | 4mM peptide in 500ul solvent | 100% DMSO-D6 | atmospheric atm | 298 | |||
| 2 | 2D NOESY | 4mM peptide in 500ul solvent | 100% DMSO-D6 | atmospheric atm | 298 | |||
| 3 | TOCSY | 4mM peptide in 500ul solvent | 100% DMSO-D6 | atmospheric atm | 298 | |||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 400 |
| 2 | Bruker | AVANCE | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| torsion angle dynamics, molecular dynamics, energy minimization. | 50 initial structures were generated using DYANA software, followed by 500 ps restrained energy minimization. Then using DISCOVER 35 ps MD, 750ps conjugated gradient EM . | XwinNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | target function |
| Conformers Calculated Total Number | 50 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | Classical 2D homonuclear NMR techniques were used. Different NOESY experiments with different mixing times from 80ms to 800ms were recorded in order to determine the best conditions without spin diffusion. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | XwinNMR | 2.6 | Bruker GMBH |
| 2 | processing | XwinNMR | 2.6 | Bruker GMBH |
| 3 | data analysis | XEASY | 1.2 | Bartels C., Billeter M., Guentert P. and Wuethrich K. (1995) J. Biomol. NMR, 5, 1-10 |
| 4 | refinement | DYANA | 1.5 | Guentert, Mumenthaler C. and Wuethrich K. (1997) J.Mol. Biol. 273, 283-298 |
| 5 | refinement | Discover | 3 | MSI, San Diego |
