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A Correspondence Between Solution-State Dynamics of an Individual Protein and the Sequence and Conformational Diversity of its Family
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D 1H-15N HSQC
0.9 mM [U-100% 13C; U-100% 15N] human ubiquitin
90% H2O/10% D2O
0.05
6.5
ambient
308
1
2D 1H-15N HSQC
0.6-0.9 mM [U-100% 13C; U-100% 15N] human ubiquitin
90% H2O/10% D2O
0.05
6.5
ambient
308
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
AVANCE
700
2
Bruker
DRX
600
3
Bruker
DRX
800
NMR Refinement
Method
Details
Software
Monte Carlo optimization of ensemble members
A 10,000-MEMBER SET OF STRUCTURES WAS GENERATED USING ROSETTA AND BACKRUB CONFORMATIONAL SAMPLING. THE 50-MEMBER ENSEMBLE PRESENTED HERE WAS OPTIMIZED BY SELECTING STRUCTURES FROM THIS SET THAT MAXIMIZE AGREEMENT WITH THE RESIDUAL DIPOLAR COUPLINGS. SEVERAL OF THE STRUCTURES IN ENSEMBLE ARE IDENTICAL AS CHOSEN BY THE OPTIMIZATION ALGORITHM.
Rosetta
NMR Ensemble Information
Conformer Selection Criteria
all calculated structures submitted
Conformers Calculated Total Number
50
Conformers Submitted Total Number
50
Representative Model
1 (n/a)
Computation: NMR Software
#
Classification
Version
Software Name
Author
1
generate structural diversity with backrub conformational sampling
Rosetta
Rosetta Commons
2
optimize a backrub ensemble against the residual dipolar couplings