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Solution structure of the lactam analogue EDap of HIV gp41 600-612 loop.
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
DQF-COSY
4mM peptide in 500ul solvent
100% DMSO-D6
atmospheric atm
298
2
2D NOESY
4mM peptide in 500ul solvent
100% DMSO-D6
atmospheric atm
298
3
TOCSY
4mM 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 angle dynamics, molecular dynamics, energy minimization.
50 initial structures were generated using DYANA software, followed by 500 ps restrained energy minimization. Then using DISCOVER 35 ps MD, 750ps conjugated gradient EM .
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 the 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, Mumenthaler C. and Wuethrich K. (1997) J.Mol. Biol. 273, 283-298