2KDQ
Simultaneous recognition of HIV-1 TAR RNA bulge and loop sequences by cyclic peptide mimic of Tat protein
SOLUTION NMR
NMR Experiment | ||||||||
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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 | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Bruker | DRX | 500 |
2 | Bruker | DMX | 600 |
3 | Varian | INOVA | 800 |
4 | Bruker | AVIII | 600 |
NMR Refinement | ||
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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 | |
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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 | ||||
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# | 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 |