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Solution structure of lactam analogue DapD of HIV gp41 600-612 loop
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D NOESY
4mM peptide in 500 ul solvent
100% DMSO-D6
ambient
298
2
DQF-COSY
4mM peptide in 500 ul solvent
100% DMSO-D6
ambient
298
3
TOCSY
4mM peptide in 500 ul solvent
100% DMSO-D6
ambient
298
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AVANCE
400
2
Bruker
AVANCE
600
NMR Refinement
Method
Details
Software
torsion dynamics, molecular dynamics, energy minimization
50 initial structures were generated using DYANA software, followed by 500 steps restrained minimization.Then using DISCOVER 3, 35 ps MD and 750 steps conjugate gradient EM.
DYANA
NMR Ensemble Information
Conformer Selection Criteria
structures with the lowest energy
Conformers Calculated Total Number
50
Conformers Submitted Total Number
20
Representative Model
1 (lowest energy)
Additional NMR Experimental Information
Details
Classical 2D homonuclear NMR technques were used. Different NOESY with different mixing time (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 P., Mumenthaler C. and Wuethrich K. (1997) J. Mol. Biol., 273,283-298