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Dynamic binding mode of a synaptotagmin-1-SNARE complex in solution
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D 1H-15N HSQC
30 uM [U-100% 13C; U-100% 15N] protein, 25 mM Tris-HCl, 125 mM KSCN, 1 mM CaCl2
90% H2O/10% D2O
7.4
ambient
298
2
2D 1H-13C HMQC
30 uM [U-100% 13C; U-100% 15N] protein, 25 mM Tris-HCl, 125 mM KSCN, 1 mM CaCl2
90% H2O/10% D2O
7.4
ambient
298
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Varian
INOVA
800
2
Varian
INOVA
600
NMR Refinement
Method
Details
Software
molecular dynamics
MOLECULAR DYNAMICS SIMULATIONS WERE USED TO GENERATE STRUCTURES OF THE SYNAPTOTAGMIN-1 C2B DOMAIN-SNARE COMPLEX THAT COULD BE EVALUATED BASED ON HOW WELL THEY FIT THE MEASURED PSEUDOCONTACT SHIFTS. SINCE IT WAS CLEAR FROM THE ANALYSIS THAT THE COMPLEX IS HIGHLY DYNAMICS AND NO SINGLE STRUCTURE CAN FIT ALL THE DATA, THE STRUCTURES FROM THE SIMULATIONS WERE USED TO TRY TO FIT THE MEASURED PSEUDOCONTACT SHIFTS AS ENSEMBLED-AVERAGED VALUES. THE STRUCTURES IN THE DEPOSITION ARE AMONG THOSE THAT CONTRIBUTED TO THE BEST ENSEMBLE-AVERAGE FITS.
NAMD
NMR Ensemble Information
Conformer Selection Criteria
Contribution to fit PCS data
Conformers Calculated Total Number
10000
Conformers Submitted Total Number
5
Representative Model
1 (all these conformers contribute to this dynamics ensemble)