SOLUTION NMR

NMR Experiment
Experiment Type Sample Contents Ionic Strength Solvent pH Pressure Temprature (K)
1 3D 1H-15N NOESY 1 mM [U-100% 13C; U-100% 15N] FOCAL ADHESION KINASE 1, LINKER, 22-MERIC PEPTIDE FROM PAXILLIN, LINKER, 15-MERIC PEPTIDE FROM PAXILLIN-1, 10 mM potassium phosphate-2, 0.1 % sodium azide-3, 90% H2O/10% D2O 50 90% H2O/10% D2O 6.5 AMBIENT 310
2 3D 1H-13C NOESY 1 mM [U-100% 13C; U-100% 15N] FOCAL ADHESION KINASE 1, LINKER, 22-MERIC PEPTIDE FROM PAXILLIN, LINKER, 15-MERIC PEPTIDE FROM PAXILLIN-1, 10 mM potassium phosphate-2, 0.1 % sodium azide-3, 90% H2O/10% D2O 50 90% H2O/10% D2O 6.5 AMBIENT 310
3 3D HCCH-TOCSY 1 mM [U-100% 13C; U-100% 15N] FOCAL ADHESION KINASE 1, LINKER, 22-MERIC PEPTIDE FROM PAXILLIN, LINKER, 15-MERIC PEPTIDE FROM PAXILLIN-1, 10 mM potassium phosphate-2, 0.1 % sodium azide-3, 90% H2O/10% D2O 50 90% H2O/10% D2O 6.5 AMBIENT 310
4 3D HCCH-COSY 1 mM [U-100% 13C; U-100% 15N] FOCAL ADHESION KINASE 1, LINKER, 22-MERIC PEPTIDE FROM PAXILLIN, LINKER, 15-MERIC PEPTIDE FROM PAXILLIN-1, 10 mM potassium phosphate-2, 0.1 % sodium azide-3, 90% H2O/10% D2O 50 90% H2O/10% D2O 6.5 AMBIENT 310
5 3D HNCA 1 mM [U-100% 13C; U-100% 15N] FOCAL ADHESION KINASE 1, LINKER, 22-MERIC PEPTIDE FROM PAXILLIN, LINKER, 15-MERIC PEPTIDE FROM PAXILLIN-1, 10 mM potassium phosphate-2, 0.1 % sodium azide-3, 90% H2O/10% D2O 50 90% H2O/10% D2O 6.5 AMBIENT 310
6 3D CBCA(CO)NH 1 mM [U-100% 13C; U-100% 15N] FOCAL ADHESION KINASE 1, LINKER, 22-MERIC PEPTIDE FROM PAXILLIN, LINKER, 15-MERIC PEPTIDE FROM PAXILLIN-1, 10 mM potassium phosphate-2, 0.1 % sodium azide-3, 90% H2O/10% D2O 50 90% H2O/10% D2O 6.5 AMBIENT 310
7 3D HNCO 1 mM [U-100% 13C; U-100% 15N] FOCAL ADHESION KINASE 1, LINKER, 22-MERIC PEPTIDE FROM PAXILLIN, LINKER, 15-MERIC PEPTIDE FROM PAXILLIN-1, 10 mM potassium phosphate-2, 0.1 % sodium azide-3, 90% H2O/10% D2O 50 90% H2O/10% D2O 6.5 AMBIENT 310
8 3D HNCACB 1 mM [U-100% 13C; U-100% 15N] FOCAL ADHESION KINASE 1, LINKER, 22-MERIC PEPTIDE FROM PAXILLIN, LINKER, 15-MERIC PEPTIDE FROM PAXILLIN-1, 10 mM potassium phosphate-2, 0.1 % sodium azide-3, 90% H2O/10% D2O 50 90% H2O/10% D2O 6.5 AMBIENT 310
9 2D 1H-15N HSQC 1 mM [U-100% 13C; U-100% 15N] FOCAL ADHESION KINASE 1, LINKER, 22-MERIC PEPTIDE FROM PAXILLIN, LINKER, 15-MERIC PEPTIDE FROM PAXILLIN-1, 10 mM potassium phosphate-2, 0.1 % sodium azide-3, 90% H2O/10% D2O 50 90% H2O/10% D2O 6.5 AMBIENT 310
10 2D 1H-13C HSQC 1 mM [U-100% 13C; U-100% 15N] FOCAL ADHESION KINASE 1, LINKER, 22-MERIC PEPTIDE FROM PAXILLIN, LINKER, 15-MERIC PEPTIDE FROM PAXILLIN-1, 10 mM potassium phosphate-2, 0.1 % sodium azide-3, 90% H2O/10% D2O 50 90% H2O/10% D2O 6.5 AMBIENT 310
NMR Spectrometer Information
Spectrometer Manufacturer Model Field Strength
NMR Refinement
Method Details Software
SIMULATED ANNEALING, TORSION ANGLE DYNAMICS THE SAMPLES USED ARE CONSTRUCTS IN WHICH ONE MOTIF IS TETHERED TO THE C-TERMINUS OF THE FAT DOMAIN VIA A GGSX LINKER AND THE OTHER LD MOTIF IS BOUND AS A FREE PEPTIDE. THE GGS LINKERS ARE UNSTRUCTURED AND COMPARISON OF SPECTRA LEAD US TO BELIEVE THEY DO NOT IMPOSE ANY CONSTRAINT UPON HOW THE TETHERED LD MOTIFS BIND TO FAT. HOWEVER WHEN ANALYZING THE STRUCTURE IN CYANA, THE PRESENCE OF THE GGS LINKER IN THE SEQUENCE INTERFERS WITH CYANA'S INITIAL ALIGNMENT OF THE 20 LOWEST ENERGY STRUCTURES AND THUS CONFUSES RMSD AND TARGET FUNCTION CALCULATIONS. WE FOUND THAT USING PSEUDO LINKERS IN CYANA RESOLVED THIS PROBLEM WITHOUT CHANGING THE STRUCTURES IN QUESTION AND SO WE CHOSE TO SUBMIT THE STRUCTURES IN THAT WAY. 2RP6 REPRESENTS A COMPOSITE STRUCTURE USING CONSTRAINTS OBTAINED FROM THE 2RP7 AND 2RP9 DATA SETS. IT DOES NOT REPRESENT A NEW CONSTRUCT IN ITSELF, BUT MOST ACCURATELY REPRESENTS THE COMPLETE COMPLEX STRUCTURE BETWEEN PAXILLIN AND FOCAL ADHESION KINASE. 1
NMR Ensemble Information
Conformer Selection Criteria target function
Conformers Calculated Total Number 500
Conformers Submitted Total Number 20
Representative Model 1 (lowest energy)
Computation: NMR Software
# Classification Version Software Name Author
1 refinement ? CYANA Guntert, Mumenthaler and Wuthrich
2 structure solution ? CYANA Guntert, Mumenthaler and Wuthrich
3 structure solution 3 Sparky Goddard
4 structure solution ? NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
5 structure solution ? MOLMOL Koradi, Billeter and Wuthrich