1JAA
Solution structure of lactam analogue (DapE) 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 | 3 mM peptide in 500 ul DMSO-D6 | 100% DMSO-D6 | ambiant | 298 | |||
2 | DQF-COSY | 3 mM peptide in 500 ul DMSO-D6 | 100% DMSO-D6 | ambiant | 298 | |||
3 | TOCSY | 3 mM peptide in 500 ul DMSO-D6 | 100% DMSO-D6 | ambiant | 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 structure were generatd in DYANA software , followed by 500 ps restrained minimization + 35 ps MD in vacuo at 300K, 200 ps under NMR restraints and 750ps conjugated gradient EM using the DISCOVER module of MSI software | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | all calculated structures submitted |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 50 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | The structure was determined using standard 2D homonuclear techniques. Different NOESY experiments , with mixing times from 80 ms to 800 ms , were recorded in order to determined the best conditions avoiding 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 | refinement | DYANA | 1.5 | Guentert P., Mumethaler C.and Wuethrich K. (1997) J. Mol. Biol., 273, 283-298 |
5 | refinement | Discover | 3 | Molecular Simulation Inc., san Diego |