1OO9
Orientation in Solution of MMP-3 Catalytic Domain and N-TIMP-1 from Residual Dipolar Couplings
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 15N-separated NOESY; HNCA; HNCO; HN(CO)CA | 0.8mM MMP-3 U-15N, 13C; 0.8mM N-TIMP-1; 20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide; 93% H2O, 7% D2O | 93% H2O/7% D2O | 20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide | 6.6 | ambient | 310 | |
2 | HCCH-TOCSY; HCCH-COSY; | 0.8mM MMP-3 U-15N, 13C; 0.8mM N-TIMP-1; 20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide; 93% H2O, 7% D2O | 93% H2O/7% D2O | 20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide | 6.6 | ambient | 310 | |
3 | 15N-separated NOESY; HNCA; HNCO; HN(CO)CA | 0.66mM N-TIMP-1 U-15N, 13C; 0.66mM MMP-3(E202Q); 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2; 1mM Sodium Azide; 93% H2O; 7% D2O | 93% H2O/7% D2O | 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2;1mM Sodium Azide | 6.7 | ambient | 307 | |
4 | 15N-separated NOESY | 0.3mM 98% 2H/15N N-TIMP-1; 0.3mM MMP-3 (E202Q); 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2; 1mM Sodium Azide; 93% H2O; 7% D2O | 93% H2O/7% D2O | 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2;1mM Sodium Azide | 6.7 | ambient | 307 | |
5 | 15N-separated NOESY | 0.5mM MMP-3 U-2H, 15N; 0.5mM N-TIMP-1; 20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide; 93% H2O, 7% D2O | 93% H2O/7% D2O | 20mM Tris-d11; 100 mM NaCl; 15 mM CaCl2; 3uM ZnCl2; 1mM Sodium Azide | 6.6 | ambient | 310 | |
6 | 15N-separated NOESY | 0.3mM 98% 2H/15N N-TIMP-1; 0.3mM (15N-IV, 15N, 13C-L)MMP-3(E202Q); 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2; 1mM Sodium Azide; 93% H2O; 7% D2O | 93% H2O/7% D2O | 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2;1mM Sodium Azide | 6.7 | ambient | 307 | |
7 | coupled 15N-HSQC; coupled 13C-HSQC; Ha-coupled HNCA | 0.3mM 98% 2H/15N N-TIMP-1; 0.3mM (15N-IV, 15N, 13C-L)MMP-3(E202Q); 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2; 1mM Sodium Azide; 93% H2O; 7% D2O 5% PEG(C12E6)/1-hexanol | 93% H2O; 7% D2O 5% PEG(C12E6)/1-hexanol | 20mM Tris-d11; 125mM NaCl; 15 mM CaCl2; 50uM ZnCl2;1mM Sodium Azide | 6.7 | ambient | 307 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 500 |
2 | Varian | UNITYPLUS | 720 |
3 | Bruker | DRX | 750 |
4 | Varian | INOVA | 600 |
NMR Refinement | ||
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Method | Details | Software |
RIGID BODY MINIMIZATION FOLLOWED BY RESTRAINED SIMULATED ANNEALING | STRUCTURES WERE CALCULATED USING XPLOR-NIH. REFINEMENTS WERE CARRIED OUT FIRST BY RIGID BODY MINIMIZATION (CLORE(2000) PROC.NATL.ACAD.SCI. 97, 9021-9025) FOLLOWED BY RESTRAINED SIMULATED ANNEALING (WANG ET AL. EMBO J. (2000) 19,5635-5649). THE CRYSTAL STRUCTURE OF THE COMPLEX BY BODE ET AL. (NATURE (1997), 389, 77-81; PDB CODE: 1UEA) HAS BEEN USED AS A STARTING POINT WITH PROTONS ATTACHED AND TAKING ONLY N-TERMINAL 126 RESIDUES OF TIMP-1. INTERFACIAL SIDE CHAINS OF THE FOLLOWING RESIDUES WERE ALLOWED TO BE FLEXIBLE: CHAIN A (MMP-3(DC)): 162-169,198-202, 205-206, 211 AND 221-223; CHAIN B (N-TIMP-1): 302-304, 329, 333-335,366-369; A TOTAL OF 49 NOE (46 INTERMOLECULAR AND 3 INTRAMOLECULAR) 75 NH DIPOLAR COULINGS FOR N-TIMP-1, 19 NH DIPOLAR COUPLINGS AND 8 CaHa DIPOLAR COUPLINGS FOR MMP-3 WERE USED FOR REFINEMENT. TARGET FUNCTIONS INCLUDE TERMS FOR NOE RESTRAINTS, DIPOLAR COUPLING RESTRAINTS AND RADIUS OF GYRATION. ALSO, MODULE ( DOSSET ET AL. J. BIOMOL. NMR, (2001),20,223-231) AND PALES (ZWECKSTETTER AND BAX, J. AM. CHEM. SOC (2000), 122, 3791-3792) WERE USED FOR EVALUATING THE ORIENTATION AND STRUCTURES. | XPLOR |
NMR Ensemble Information | |
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Conformer Selection Criteria | lowest energy structure |
Conformers Calculated Total Number | 25 |
Conformers Submitted Total Number | 1 |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | XPLOR | NIH | BRUNGER |
2 | data analysis | PALES | SGI Irix 6.2 | ZWECKSTETTER AND BAX |
3 | data analysis | Module | 1.0 | DOSSET ET AL |