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Solution structure of beta3 analogue peptide (HCYS) 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
2mM peptide in 500ul DMSO-D6
DMSO-D6
ambient
298
2
DQF-COSY
4mM peptide in 500ul DMSO-D6
DMSO-D6
ambient
298
3
TOCSY
4mM peptide in 500ul DMSO-D6
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 angle dynamics, molecular dynamics, energy minimization.
50 initial random structures were generated using simulated annealing in DYANA software, followed using the DISCOVER module of MSI software, by 500 steps restrained minimization, 35 ps MD in vacuo at 300K, 200ps MD under NMR restraints and 750ps conjugated gradient EM.
XwinNMR
NMR Ensemble Information
Conformer Selection Criteria
target function
Conformers Calculated Total Number
50
Conformers Submitted Total Number
24
Representative Model
1 (lowest energy)
Additional NMR Experimental Information
Details
This structure was determined using standard 2D homonuclear techniques. NOESY experiments were recorded with mixing times from 80ms to 800ms in order to determined the best conditions to avoid 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 K., (1995) , J. Biomol. NMR, 5, 1-10
4
structure solution
DYANA
1.5
Guentert P., Mumenthaler C. and Wuethrich K. (1997) J. Mol. Biol., 273, 283-298