Solution structure of synthetic cyclic peptide mimicking the loop of HIV-1 gp41 glycoprotein envelope
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 2mM and 4mM peptide ; 500 ul DMSO-D6 | 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 angle dynamics energy minimisation | 50 initial random strucutres were produced using simulated annealing in DYANA software.Refinement was done with 500 steps restrained minimization , 35ps MD in vacuo at 300K for equilibration and 200ps MD under NMR restraints and 750 steps conjugeted gradient EM using DISCOVER module of MSI software. | XwinNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | target function |
| Conformers Calculated Total Number | 50 |
| Conformers Submitted Total Number | 1 |
| Representative Model | 1 (minimized average structure) |
| Additional NMR Experimental Information | |
|---|---|
| Details | This structure was determined using standard 2D homonuclear techniques. NOESY experiments with mixing times from 80ms to 800ms were reccorded in order to define the best conditions avoiding spin diffusion. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | XwinNMR | 2.6 | Bruker brmH |
| 2 | processing | XwinNMR | 2.6 | Bruker brmH |
| 3 | data analysis | XEASY | Bartels C.,Xia T. , Billeter M., Guentert P. and Wthrich K. J. Biomolecular 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 | Molecular SImulation Inc., San Diego |
