1J8Z
Solution structure of beta3 analogue peptide (HCYS) of HIV gp41 600-612 loop.
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 2D NOESY | 2mM peptide in 500ul DMSO-D6 | DMSO-D6 | ambient | 298 | |||
2 | DQF-COSY | 4mM peptide in 500ul DMSO-D6 | DMSO-D6 | ambient | 298 | |||
3 | TOCSY | 4mM peptide in 500ul DMSO-D6 | DMSO-D6 | ambient | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | AVANCE | 400 |
2 | Bruker | AVANCE | 600 |
NMR Refinement | ||
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Method | Details | Software |
torsion angle dynamics, molecular dynamics, energy minimization. | 50 initial random structures were generated using simulated annealing in DYANA software, followed using the DISCOVER module of MSI software, by 500 steps restrained minimization, 35 ps MD in vacuo at 300K, 200ps MD under NMR restraints and 750ps conjugated gradient EM. | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | target function |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 24 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | This structure was determined using standard 2D homonuclear techniques. NOESY experiments were recorded with mixing times from 80ms to 800ms in order to determined the best conditions to avoid spin diffusion. |
Computation: NMR Software | ||||
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# | 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., Xia T., Billeter M., Guentert P. and Wuethrich K., (1995) , J. Biomol. NMR, 5, 1-10 |
4 | structure solution | DYANA | 1.5 | Guentert P., Mumenthaler C. and Wuethrich K. (1997) J. Mol. Biol., 273, 283-298 |
5 | structure solution | Discover | 3 | Molecular Simulation Inc. , San Diego |
6 | refinement | Discover | 3 | Molecular Simulation Inc. , San Diego |