1J8N
Solution structure of beta3-analogue peptide corresponding to the gp41 600-612 loop of HIV.
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 ; 500ul DMSO-D6 | DMSO-D6 | ambient | 298 | |||
2 | DQF-COSY | 4mM peptide ; 500ul DMSO-D6 | DMSO-D6 | ambient | 298 | |||
3 | 2D NOESY | 4mM peptide ; 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 CALCULATED USING SIMULATED ANNEALING IN DYANA SOFTWARE. REFINEMENT WAS DONE WITH 500 STEPS RESTRAINED MINIMIZATION, 35PS MD IN VACUO AT 300K FOR EQUILIBRATION, 200PS MD UNDER NMR RESTRAINTS, AND 750PS CONJUGATED GRADIENT EM USING DISCOVER MODULE OF MSI SOFTWARE. | XwinNMR |
NMR Ensemble Information | |
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Conformer Selection Criteria | target function |
Conformers Calculated Total Number | 50 |
Conformers Submitted Total Number | 27 |
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 WITH MIXING TIMES FROM 80MS TO 800MS WERE RECORDED IN ORDER TO DEFINE THE BEST CONDITIONS IN ORDER TO AVOID SPIN DIFFUSION. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | collection | XwinNMR | 2.6 | Bruker GMBH |
2 | data analysis | XEASY | 1.2 | Bartels C., Xia T., Billeter M., Guentert P. and Wuethrich K., (1995)J. Biomolecular NMR 5, 1-10 |
3 | refinement | DYANA | 1.5 | Guentert P., Mumenthaler C., Wuethrich K. |
4 | refinement | Discover | 3 | Molecular Simulation Inc., San Diego |