2KQT

Solid-state NMR structure of the M2 transmembrane peptide of the influenza A virus in DMPC lipid bilayers bound to deuterated amantadine

SOLID-STATE NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	2D 13C-13C Spin Diffusion	5.8 mg [U-99% 13C; U-99% 15N] at S31, I32 and D44 M2-TM, 21.6 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, .42 mg [U-2H] d15-1-aminoadamantane*HCl	10mM pH 7.5 phosphate buffer, 50% hydration		7.5	ambient	243
2	2D 13C-13C Spin Diffusion	5.0 mg [U-99% 13C; U-99% 15N] at S31, I32 and D44 M2-TM, 10.4 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, 0.09 mg [U-2H] d15-1-aminoadamantane*HCl	10mM pH 7.5 phosphate buffer, 50% hydration		7.5	ambient	243
3	2D 13C-13C Spin Diffusion	5.2 mg [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34 M2-TM, 19.9 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, 0.38 mg [U-2H] d15-1-aminoadamantane*HCl	10mM pH 7.5 phosphate buffer, 50% hydration		7.5	ambient	243
4	2D 13C-15N HETCOR	5.8 mg [U-99% 13C; U-99% 15N] at S31, I32 and D44 M2-TM, 21.6 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, .42 mg [U-2H] d15-1-aminoadamantane*HCl	10mM pH 7.5 phosphate buffer, 50% hydration		7.5	ambient	243
5	2D 13C-15N HETCOR	5.0 mg [U-99% 13C; U-99% 15N] at S31, I32 and D44 M2-TM, 10.4 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, 0.09 mg [U-2H] d15-1-aminoadamantane*HCl	10mM pH 7.5 phosphate buffer, 50% hydration		7.5	ambient	243
6	2D 13C-15N HETCOR	5.2 mg [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34 M2-TM, 19.9 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, 0.38 mg [U-2H] d15-1-aminoadamantane*HCl	10mM pH 7.5 phosphate buffer, 50% hydration		7.5	ambient	243
7	1D 2H-13C REDOR, single 13C pulse	5.8 mg [U-99% 13C; U-99% 15N] at S31, I32 and D44 M2-TM, 21.6 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, .42 mg [U-2H] d15-1-aminoadamantane*HCl	10mM pH 7.5 phosphate buffer, 50% hydration		7.5	ambient	243
8	1D 2H-13C REDOR, single 13C pulse	5.0 mg [U-99% 13C; U-99% 15N] at S31, I32 and D44 M2-TM, 10.4 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, 0.09 mg [U-2H] d15-1-aminoadamantane*HCl	10mM pH 7.5 phosphate buffer, 50% hydration		7.5	ambient	243
9	1D 2H-13C REDOR, single 13C pulse	5.2 mg [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34 M2-TM, 19.9 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, 0.38 mg [U-2H] d15-1-aminoadamantane*HCl	10mM pH 7.5 phosphate buffer, 50% hydration		7.5	ambient	243
10	1D 2H-13C REDOR, single 13C pulse	5.8 mg [U-99% 13C; U-99% 15N] at S31, I32 and D44 M2-TM, 21.6 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, .42 mg [U-2H] d15-1-aminoadamantane*HCl	10mM pH 7.5 phosphate buffer, 50% hydration		7.5	ambient	243
11	1D 2H-13C REDOR, single 2H pulse	5.8 mg [U-99% 13C; U-99% 15N] at S31, I32 and D44 M2-TM, 21.6 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, .42 mg [U-2H] d15-1-aminoadamantane*HCl	10mM pH 7.5 phosphate buffer, 50% hydration		7.5	ambient	243
12	1D 2H-13C REDOR, single 2H pulse	5.0 mg [U-99% 13C; U-99% 15N] at S31, I32 and D44 M2-TM, 10.4 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, 0.09 mg [U-2H] d15-1-aminoadamantane*HCl	10mM pH 7.5 phosphate buffer, 50% hydration		7.5	ambient	243
13	1D 2H-13C REDOR, single 2H pulse	5.2 mg [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34 M2-TM, 19.9 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, 0.38 mg [U-2H] d15-1-aminoadamantane*HCl	10mM pH 7.5 phosphate buffer, 50% hydration		7.5	ambient	243
14	2H Static Quadrupolar Echo	7 mg [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34 M2-TM, 27 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, 2.0 mg [U-2H] d15-1-aminoadamantane*HCl	10mM pH 7.5 phosphate buffer, 50% hydration		7.5	ambient	243
15	2H Static Quadrupolar Echo	7 mg [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34 M2-TM, 27 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO, 1 mM EDTA, 0.1 mM NaN3, 0.5 mg [U-2H] d15-1-aminoadamantane*HCl	10mM pH 7.5 phosphate buffer, 50% hydration		7.5	ambient	243
16	2H Static Quadrupolar Echo	5.2 mg [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34 M2-TM, 19.9 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, 0.38 mg [U-2H] d15-1-aminoadamantane*HCl	10mM pH 7.5 phosphate buffer, 50% hydration		7.5	ambient	243

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	AVANCE	400
2	Bruker	AVANCE	600

NMR Refinement
Method	Details	Software
simulated annealing, Monte Carlo	The temperature was initially set to 1,000,000K and decreased by 10% every 100 steps until a temperature of 25 K was reached. The constants (CI-CIV) were obtained through a trial-and-error process. Some side chain rotamers were changed to maximize agreement with the radial distances., An ensemble of models was obtained by selecting the top scoring model after one round of Monte Carlo/Simulated Annealing minimization and refining again with the inverse kinematics algorithm. The distance potential constant CIII was set to 50 kcal/mol-radians^2. Since the radial distance provided excellent restraints between the drug and M2, we were able to position the amantidine molecule near with S31 without the need for further minimization. THE POSITION OF THE AMANTADINE LIGAND (PDB CODE 308) IS IDENTICAL IN ALL OF THE MINIMIZED STRUCTURE SINCE IT IS THE AVERAGE LIGAND POSITION RELATIVE TO THE BACKBONE. WE HAVE MEASURED A 13C-2H DIPOLAR COUPLING FROM SEVERAL PEPTIDE BACKBONE AND SIDECHAIN CARBONS TO THE DEUTERONS ON THE 308 LIGAND. WE SIMULATED THE THE RADIUS OF THE M2 CHANNEL PORE FOR THE SITES WHERE WE OBSERVED 13C-2H DIPOLAR COUPLING, AND FOUND PORE RADII FOR THESE SITES THAT CORRESPONDED WITH THE MEASURED 13C-2H DIPOLAR COUPLING AT THAT SITE. THUS, IN THE FINAL STRUCTURE MINIMIZATION, WE USED THE PORE RADII AS A CONSTRAINT RATHER THAN PEPTIDE-DRUG DISTANCES SINCE THE LIGAND IS ROTATING IN THE CHANNEL.	TopSpin

NMR Ensemble Information
Conformer Selection Criteria	structures with the least restraint violations
Conformers Calculated Total Number	24
Conformers Submitted Total Number	17
Representative Model	1 (fewest violations)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	collection	TopSpin	1.3	Bruker Biospin
2	chemical shift assignment	TopSpin	1.3	Bruker Biospin
3	processing	TopSpin	1.3	Bruker Biospin
4	data analysis	TopSpin	1.3	Bruker Biospin
5	peak picking	TopSpin	1.3	Bruker Biospin
6	refinement	X-PLOR_NIH, IN-HOUSE METHOD		Schwieters, Kuszewski, Tjandra and Clore
7	collection	XwinNMR		Bruker Biospin
8	chemical shift assignment	XwinNMR		Bruker Biospin

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.