Productive complex between MMP-12 and synthetic triple-helical collagen, revealed through paramagnetic NMR
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D 1H-15N HSQC | 0.4 mM [U-99% 15N] MMP, 0.6 mM TOAC labelled in P5 position THP | 90% H2O/10% D2O | 6.6 | ambient | 299 | ||
| 2 | 2D 1H-15N HSQC | 0.25 mM [U-100% 12C; U-100% 15N; U-100% 2H; U-100% 13CH3] MMP, 0.38 mM TOAC labelled in P8' position THP | 90% H2O/10% D2O | 6.6 | ambient | 299 | ||
| 3 | 2D 1H-13C HSQC | 0.25 mM [U-100% 12C; U-100% 15N; U-100% 2H; U-100% 13CH3] MMP, 0.38 mM TOAC labelled in P8' position THP | 90% H2O/10% D2O | 6.6 | ambient | 299 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 800 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| Rigid-body docking, Conformer selection | The Collagen triple helix repeat peptide chain is homology-modeled from 4AUO. The Macrophage metalloelastase enzyme starting structure is 2poj. | TopSpin |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | back calculated data agree with experimental NOESY spectrum |
| Conformers Calculated Total Number | 7500 |
| Conformers Submitted Total Number | 1 |
| Representative Model | 1 (fewest violations) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | TopSpin | Bruker Biospin | |
| 2 | processing | TopSpin | Bruker Biospin | |
| 3 | chemical shift assignment | Analysis | CCPN | |
| 4 | peak picking | Analysis | CCPN | |
| 5 | structure solution | HADDOCK | 2.1 | Alexandre Bonvin |
| 6 | structure solution | q_test.py | Stephen H. Prior | |
| 7 | refinement | GROMOS | van Gunsteren and Berendsen | |
| 8 | refinement | HADDOCK | 2.1 | Alexandre Bonvin |
| 9 | refinement | q_test.py | Stephen H. Prior | |
