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Solution structure of lactam analogue (DDap) of gp41 600-612 loop of HIV
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D NOESY
2mM peptide in 500ul solvent
100% DMSO-D6
atmospheric atm
298
2
DQF-COSY
2mM peptide in 500ul solvent
100% DMSO-D6
atmospheric atm
298
3
TOCSY
2mM peptide in 500ul solvent
100% DMSO-D6
atmospheric atm
298
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AVANCE
400
2
Bruker
AVANCE
600
NMR Refinement
Method
Details
Software
torsion angles dynamics, molecular dynamics, energy minimization.
50 initial random structures were generated usin DYANA software, followed by 500ps restrained minimization, 35ps MD and 750ps conjugated 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
20
Representative Model
1 (lowest energy)
Additional NMR Experimental Information
Details
classical 2D homonuclear NMR techniques were used. Different NOESY experiments with different mixing times from 80ms to 800ms were recorded in order to determine best conditions without spin diffusion.
Computation: NMR Software
#
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., Billeter M., Guentert P. and Wuethrich K. (1995) J. Biomol. NMR, 5, 1-10
4
refinement
DYANA
1.5
Guentert P., Mumenthaler C.and Wuethrich K. (1997) J. Mol. Biol. 273, 283-298