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FORMATION OF AN AMINO ACID BINDING POCKET THROUGH ADAPTIVE ZIPPERING-UP OF A LARGE DNA HAIRPIN LOOP, NMR, 9 STRUCTURES
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
NOESY
100% D2O
100 mM
6.35
1 atm
277
2
TOCSY
100% D2O
100 mM
6.35
1 atm
277
3
ROESY
100% D2O
100 mM
6.35
1 atm
277
4
1H-15N HMQC
100% D2O
100 mM
6.35
1 atm
277
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Varian
VARIAN UNITY-PLUS
600
NMR Refinement
Method
Details
Software
DISTANCE GEOMETRY, MOLECULAR DYNAMIC
TWENTY STARTING STRUCTURES WERE GENERATED BY METRICMATRIX DISTANCE GEOMETRY (FROM X-PLOR) AND WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE 2-D NMR DATA SETS. NINE FIN AL NMR-DISTANCE REFINED STRUCTURES WERE SELECTED BASED ON THE CRITERION OF LOW TOTAL ENERGY AND LOW RESTRAINTS VIOLATIONS.
X-PLOR
NMR Ensemble Information
Conformer Selection Criteria
LEAST NOE, VDW, AND BOND ANGLE VIOLATION, LEAST TOTAL ENERGY
Conformers Calculated Total Number
20
Conformers Submitted Total Number
9
Additional NMR Experimental Information
Details
THE INTER-PROTON DISTANCE RESTRAINTS WERE DERIVED FROM 2-D NOE BUILD UP EXPERIMENTS RECORDED AT 50, 90, 150, AND 90 AND 135 MIXING TIME FOR EXCHANGEABLE PROTONS 200 MS MIXING TIME FOR NON-EXCHANGEABLE PROTONS AND AT 600 MHZ