Solid State NMR structure of the M2 proton channel from Influenza A Virus in hydrated lipid bilayer
SOLID-STATE NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | PISEMA | 5-15 mM [U-15N] entity-1, 5-15 mM [U-15N]-Leu entity-2, 5-15 mM [U-15N]-Ile entity-3, 5-15 mM [U-15N]-Val entity-4, 5-15 mM [U-15N]-Phe entity-5 | 100% H2O | 10 | 7.5 | ambient | 303 | |
| 2 | PISEMA | 5-15 mM [U-15N] entity-1, 5-15 mM [U-15N]-Leu entity-2, 5-15 mM [U-15N]-Ile entity-3, 5-15 mM [U-15N]-Val entity-4, 5-15 mM [U-15N]-Phe entity-5 | 100% H2O | 10 | 7.5 | ambient | 303 | |
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | AVANCE | 600 |
| 2 | Bruker | AVANCE | 900 |
| 3 | Bruker | DRX | 400 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| simulated annealing and molecular dynamics, molecular dynamics | Monomer structure was calculated using solid state NMR constraints by simulated annealing. A preliminary model for tetramer was assembled placing four copies of monomer consistent with NMR derived tilt angles and rotation. The model was annealed again by incorporating distance and orientational restraints.The tetramer model was placed in explicit hydrated lipid bilayer and tetramer model was refined with solid state NMR orientational restraints using NAMD. Finally, The His37-Trp41 geometry was optimized using QM/MM calculations keeping backbone fixed. Note the His-His geometry is consistent with the experimental NMR observation. | X-PLOR NIH |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | structures with the least restraint violations |
| Conformers Calculated Total Number | 8 |
| Conformers Submitted Total Number | 8 |
| Representative Model | 1 (fewest violations) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | X-PLOR NIH | 2.23 | Schwieters, Kuszewski, Tjandra and Clore |
| 2 | structure solution | X-PLOR NIH | 2.23 | Schwieters, Kuszewski, Tjandra and Clore |
| 3 | collection | XwinNMR | 3.6 | Bruker Biospin |
| 4 | refinement | NAMD | 2.7b | Phillips,Braun,Wang,Gumbart ,Tajkhorshid , Villa ,Chipot ,Skeel, Kale , Schulten |
| 5 | chemical shift assignment | PIPATH | Asbury, Quine,Achuthan, Hu, Chapman, Bertram, Cross | |
