Experiment: 2L0J

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