1JAA

Solution structure of lactam analogue (DapE) of HIV gp41 600-612 loop.


SOLUTION NMR
NMR Experiment
ExperimentTypeSample ContentsSolventIonic StrengthpHPressureTemperature (K)Spectrometer
12D NOESY3 mM peptide in 500 ul DMSO-D6100% DMSO-D6ambiant298
2DQF-COSY3 mM peptide in 500 ul DMSO-D6100% DMSO-D6ambiant298
3TOCSY3 mM peptide in 500 ul DMSO-D6100% DMSO-D6ambiant298
NMR Spectrometer Information
SpectrometerManufacturerModelField Strength
1BrukerAVANCE400
2BrukerAVANCE600
NMR Refinement
MethodDetailsSoftware
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 softwareXwinNMR
NMR Ensemble Information
Conformer Selection Criteriaall calculated structures submitted
Conformers Calculated Total Number50
Conformers Submitted Total Number50
Representative Model1 (lowest energy)
Additional NMR Experimental Information
DetailsThe 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
#ClassificationVersionSoftware NameAuthor
1collectionXwinNMR2.6Bruker GMBH
2processingXwinNMR2.6Bruker GMBH
3data analysisXEASY1.2Bartels C., Xia T., Billeter M., Guentert P. and Wuethrich K. (1995) J. Biomol. NMR , 5, 1-10
4refinementDYANA1.5Guentert P., Mumethaler C.and Wuethrich K. (1997) J. Mol. Biol., 273, 283-298
5refinementDiscover3Molecular Simulation Inc., san Diego