The complex between Ca-Calmodulin and skeletal muscle myosin light chain kinase from combination of NMR and aqueous and contrast-matched SAXS data
SOLUTION SCATTERING - SOLUTION NMR
Solution Scattering Data Acquistion
1
2
Scattering Type
x-ray
x-ray
Radiation/Neutron Source
ADVANCED PHOTON SOURCE
ADVANCED PHOTON SOURCE
Synchrotron
Y
Y
Beamline Type
12-IDB
12-IDC
Detector Type
PILATUS 2M
GOLD CCD
Detector Manufacturer Details
DECTRIS
Temperature (K)
298
298
pH
6.5
6.5
Numer of Time Frames Used
20
20
Protein Concentration Range (mg/mL)
1.2-5.0
5.0 - 9.5
Sample Buffer
25MM HEPES, 150 MM KCL, 3 MM CACL2, 1 MM TCEP, H2O
25MM HEPES, 150 MM KCL, 1 MM TCEP, 3 MICROMOL PBCL2, 65% SUCROSE, H2O
Data Reduction Software
MARDETECTOR, IGOR
MARDETECTOR, IGOR
Guiner Mean Radius Of Gyration (nm)
1.78
1.8
Sigma Mean Radius Of Gyration
0.04
0.2
R(XS-1) Mean Cross Sectional Radii (nm)
R(XS-1) Sigma Mean Cross Sectional Radii
R(XS-2) Mean Cross Sectional Radii (nm)
R(XS-2) Sigma Mean Cross Sectional Radii
P(R) Protein Length (nm)
6.0
Solution Scattering Data Analysis and Model Fitting
Method
Software
Software Authors
Starting Model
Conformers, Number Calculated
Conformers, Number Submitted
Conformers, Selection Criteria
Best Representative Conformer
Other Details
PRIMUS, GNOM
1
BEST-FITTING CONFORMER BASED ON THE FIT OF AQUEOUS SAXS DATA FOR CA-CAM/MLCK, CONTRAST-MATCHED (65% SUCROSE) SAXS DATA FOR PB-CAM/MLCK, AND BACKBONE 1H-15N RESIDUAL DIPOLAR COUPLINGS FOR CAM IN THE CA-CAM/MLCK COMPLEX
1
4000000000000 STARTING RELATIVE POSITIONS OF THE N-TERM (1-75) AND C-TERM (82-148) DOMAINS OF CAM WERE BUILT USING COORDINATES IN THE PDB DEPOSITION 1 ...
4000000000000 STARTING RELATIVE POSITIONS OF THE N-TERM (1-75) AND C-TERM (82-148) DOMAINS OF CAM WERE BUILT USING COORDINATES IN THE PDB DEPOSITION 1MXE:A. TAIL RESIDUES 1-4 AND 144-148 WERE BEST-FITTED TO 1MXE USING MODELS 1J7O AND 1J7P. THESE 4*1011 MODELS SAMPLE IN AN EXHAUSTIVE FASHION ALL POSSIBLE RELATIVE DOMAIN POSITIONS WHICH DIFFER BY NO MORE THAN 1A IN TERMS OF C-TERM DOMAIN PLACEMENT WHEN N-TERM DOMAIN IS FIXED. ROTATIONAL AND TRANSLATIONAL GRIDS OF 2DEG AND 1A WERE USED. THE MODELS WERE THEN FILTERED TO EXHIBIT FIT TO THE RDC DATA NO WORSE THAN 10% HIGHER THAN GLOBAL MINIMUM FOUND BY NLS OPTIMIZATION OF ORIENTATION OF THE C-TERM RELATIVE TO THE N-TERM DOMAIN. ADDITIONAL FILTERS WERE THEN APPLIED INCLUDING ABSENCE OF CLASHES <2.5 A BETWEEN HEAVY BACKBONE AND CB ATOMS, AND RGYR OF 13-19A. FOR THE GEOMETRIES THAT PASSED ABOVE REQUIREMENTS, POSITION OF MLCK FROM 2BBM DEPOSITION WAS BEST-FITTED IN A RIGID-BODY MANNER AGAINST NOE DISTANCE RESTRAINTS FROM 2BBM DEPOSITION AND CLASH AVOIDANCE FUNCTION INCLUDING HEAVY BACKBONE AND CB ATOMS. CAM CONFORMATIONS WHICH EXHIBITED AT LEAST 1 NOE VIOLATION EXCEEDING 3A FOR THE BEST-FITTED MLCK WERE REJECTED. LINKER COORDINATES WERE THEN BUILT FOR RESIDUES 76-81 USING 8-RESIDUE BACKBONE AND CB-CONTAINING SEGMENTS FROM A PDB-BASED DATABASE INCLUDING 2.2 MILLION RESIDUES IN TOTAL. LINKERS WHICH CLASHED WITH CAM DOMAINS OR MLCK OR EXHIBITED RMSD ABOVE 1.2 A FOR RESIDUES 1 AND 8 VS RESIDUES 75 AND 82 OF CAM WERE REJECTED. CAM CONFORMATION FOR WHICH SUCH LINKERS COULD NOT BE BUILT WERE REJECTED LEADING TO A TOTAL OF APPROXIMATELY 75000 STRUCTURES. THESE STRUCTURES WERE FITTED TO THE SAXS AND RDC DATA WITH THE OVERALL BEST-FITTING MODEL RETAINED FOR DEPOSITION. THE COORDINATES OF THE LINKER RESIDUES 76-81 AND SIDECHAINS WERE REGULARIZED BY ENERGY MINIMIZATION VIA XPLOR-NIH PRIOR TO THE DEPOSITION WITH THE ACTIVE ENERGY TERMS INCLUDING BONDS, ANGLES, IMPROPERS, NON-BONDED, AND CONFORMATIONAL DATABASE POTENTIALS OF MEAN FORCE.
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D 1H-15N HSQC
0.3 mM [U-13C; U-15N; U-2H] Calmodulin, 0.3 mM ssMLCK
95% H2O/5% D2O
0.1
6.5
ambient
300
2
2D 1H-15N HSQC
0.06-0.25 mM [U-13C; U-15N; U-2H] Calmodulin, 0.06-0.25 mM ssMLCK
65% w/v sucrose/H2O
0.1
6.5
ambient
300
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Bruker
DRX
600
NMR Refinement
Method
Details
Software
rigid-body optimization, simulated annealing
Relative positions of the N- and C-terminal domains of calmodulin, rigidly held at those of the 1MXE structure, chain A, were optimized via a rotational/translational grid search with steps of 2deg and 1A, respectively with the best model fitted against RDC and scattering intensity data. Coordinates of the calmodulin linker residues (76-81) and the interfacial side chains were regularized via a molecular dynamics/simulated annealing protocol with the backbone atoms and the remaining side chains held fixed at the geometry resulting from the rigid-body grid search of the previous step.
