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Solution structure of lactam analogue (DDab)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 500ul DMSO-D6
100% DMSO-D6
none
ambient
298
2
DQF-COSY
4mM peptide in 500ul DMSO-D6
100% DMSO-D6
none
ambient
298
3
TOCSY
4mM peptide in 500ul DMSO-D6
100% DMSO-D6
none
ambient
298
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AVANCE
400
2
Bruker
AVANCE
600
NMR Refinement
Method
Details
Software
torsion angle dynalmics, molecular dynanmics, energy minimization
50 initial radom structure are generated using DYANA software.followed by 500 ps restrained minimization. Followed by 750 ps conjugated gradient EM using the DISCOVER module of MSI software.
XwinNMR
NMR Ensemble Information
Conformer Selection Criteria
target function
Conformers Calculated Total Number
50
Conformers Submitted Total Number
49
Representative Model
1 (lowest energy)
Additional NMR Experimental Information
Details
the structure was calculated using standard 2D homonuclear techniques. Different NOSY experiments were recorded in order to determined the best conditions avoiding 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., Xia T., Billeter M.,Guentert P. and Wuethrich (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