Experiment: 2KDQ

Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimic of Tat protein

SOLUTION NMR

NMR Experiment
Experiment	Type	Sample Contents	Solvent	Ionic Strength	pH	Pressure	Temperature (K)	Spectrometer
1	3D-13C HMQC NOESY, 3D HCCH TOCSY, IPAP-HSQC	1.0mM [U-98% 13C; U-98% 15N] HIV-1 TAR RNA-5, 1.0mM L-22 CYCLIC PEPTIDE-6	100% D2O	10 mM potassium phosphate	6.6	ambient	298
2	15N HSQC	1.0mM [U-98% 13C; U-98% 15N] HIV-1 TAR RNA-7, 1.0mM L-22 CYCLIC PEPTIDE-8, 90 % H2O, 10% D2O	90% H2O/10% D2O	10 mM potassium phosphate	6.6	ambient	277
3	2D noesy	1.0mM HIV-1 TAR RNA-1, 1.0mM L-22 CYCLIC PEPTIDE-2	100% D2O	10 mM potassium phosphate	6.6	ambient	298
4	2D watergate NOESY	1.0mM HIV-1 TAR RNA-3, 1.0mM L-22 CYCLIC PEPTIDE-4, 90 % H2O, 10% D2O	90% H2O/10% D2O	10 mM potassium phosphate	6.6	ambient	277
5	F1fF2f-type noesy, F1fF2f-type tocsy, 2D HCCH-COSY	1.0mM [U-98% 13C; U-98% 15N] HIV-1 TAR RNA-5, 1.0mM L-22 CYCLIC PEPTIDE-6	100% D2O	10 mM potassium phosphate	6.6	ambient	298
6	2D 1H-1H NOESY	1.0mM [U-2H] HIV-1 TAR RNA-9, 1.0mM L-22 CYCLIC PEPTIDE-10	100% D2O	10 mM potassium phosphate	6.6	ambient	298
7	F1fF2f-type watergate noesy	1.0mM [U-98% 13C; U-98% 15N] HIV-1 TAR RNA-7, 1.0mM L-22 CYCLIC PEPTIDE-8, 90 % H2O, 10% D2O	90% H2O/10% D2O	10 mM potassium phosphate	6.6	ambient	277

NMR Spectrometer Information
Spectrometer	Manufacturer	Model	Field Strength
1	Bruker	DRX	500
2	Bruker	DMX	600
3	Varian	INOVA	800
4	Bruker	AVIII	600

NMR Refinement
Method	Details	Software
simulated annealing	Structures of the HIV-1 TAR RNA/L-22 complex were calculated with Xplor-NIH. Backbone dihedral angle restraints for the peptide were estimated using chemical shift data and TALOS. Structures were originally calculated without RDCs to test for convergence and adherence to the NOE data. RDC restraints were then applied as susceptibility anisotropy restraints with a harmonic potential well.	X-PLOR NIH

NMR Ensemble Information
Conformer Selection Criteria	Lowest energy, least restraint violations
Conformers Calculated Total Number	100
Conformers Submitted Total Number	10
Representative Model	1 (lowest energy)

Computation: NMR Software
#	Classification	Version	Software Name	Author
1	structure solution	X-PLOR NIH	2.16.0	C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clore
2	processing	NMRPipe		Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
3	collection	TopSpin		Bruker Biospin
4	data analysis	TALOS		Cornilescu, Delaglio and Bax
5	peak picking	Sparky		Goddard
6	refinement	X-PLOR NIH	2.16.0	C.D. Schwieters, J.J. Kuszewski, N. Tjandra and G.M. Clore