1JD8
Solution structure of lactam analogue DapD of HIV gp41 600-612 loop
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 4mM peptide in 500 ul solvent | 100% DMSO-D6 | ambient | 298 | |||
| 2 | DQF-COSY | 4mM peptide in 500 ul solvent | 100% DMSO-D6 | ambient | 298 | |||
| 3 | TOCSY | 4mM peptide in 500 ul solvent | 100% DMSO-D6 | ambient | 298 | |||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | Avance | 400 |
| 2 | Bruker | Avance | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| torsion dynamics, molecular dynamics, energy minimization | 50 initial structures were generated using DYANA software, followed by 500 steps restrained minimization.Then using DISCOVER 3, 35 ps MD and 750 steps conjugate gradient EM. | DYANA |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the lowest energy |
| Conformers Calculated Total Number | 50 |
| Conformers Submitted Total Number | 20 |
| Representative Model | 1 (lowest energy) |
| Additional NMR Experimental Information | |
|---|---|
| Details | Classical 2D homonuclear NMR technques were used. Different NOESY with different mixing time (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 P., Mumenthaler C. and Wuethrich K. (1997) J. Mol. Biol., 273,283-298 |
| 5 | refinement | DISCOVER | 3 | MSI, San Diego |
