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solution structure of 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
2D NOESY
3mMpeptide in 500ul solvent
100% DMSO-D6
atmospheric atm
298
2
DQF-COSY
3mMpeptide in 500ul solvent
100% DMSO-D6
atmospheric atm
298
3
TOCSY
3mMpeptide 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, energy minimization, molecular dynamics
50 initial random strucutre were generated using DYANA software, followed by 500 steps energy minimization. Then using DISCOVER 3 35 ps MD in vacuo at 300K, 200 steps energy minimization under NMR restraints and 750 steps conjugate gradient EM.
XwinNMR
NMR Ensemble Information
Conformer Selection Criteria
target function
Conformers Calculated Total Number
50
Conformers Submitted Total Number
25
Representative Model
1 (lowest energy)
Additional NMR Experimental Information
Details
Typical 2D ho;onuclear techniques were applied. Different NOESY experiment 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., Xia T., 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