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. | NMRPipe |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 1 |
| Conformers Submitted Total Number | 1 |
| Representative Model | 1 (fewest violations) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | processing | NMRPipe | Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax | |
| 2 | data analysis | Sparky | Goddard | |
| 3 | structure solution | Custom | Grishaev | |
| 4 | refinement | CNS | 1.0 | Brunger, Adams, Clore, Gros, Nilges and Read |
| 5 | refinement | Custom | Grishaev | |
