NMR REFINED STRUCTURE OF THE 8,9-DIHYDRO-8-(N7-GUANYL)-9-HYDROXY-AFLATOXIN B1 ADDUCT IN A 5'-CPAFBG-3' SEQUENCE
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | 2D NOESY | 99.999% D2O | 0.5 mL of 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.2, in 99.999% D2O | 7.2 | 1 atm | 283 | ||
| 2 | DQF-COSY | 99.999% D2O | 0.5 mL of 0.01 M sodium phosphate buffer containing 0.1 M NaCl and 0.05 mM Na2EDTA at pD 7.2, in 99.999% D2O | 7.2 | 1 atm | 283 | ||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DRX | 500 |
| 2 | Bruker | DRX | 600 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| Data was processed using felix 97. The NOE intensities were converted to distance using RANMARDI module of MARDIGRAS. Starting structures were built using InsightII. XPLOR was used for structural refinement. Final averaged structure was solvated using AMBER. And MD simulated annealing was performed in presence of counter ions using SANDER protocol. The back calculations were performed using CORMA. | The structures are based on 341 distance retraints, 38 empirical H-bond restraints, 17 sugar pucker restraints, and 89 empirical torsion angle restraints | XwinNMR |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | |
| Conformers Calculated Total Number | |
| Conformers Submitted Total Number | 1 |
| Representative Model | 1 (simulated annealing structure, calculaed starting from energy minmized averaged structure from 20 final structures. the enrgy minimized structure was solvated, and md simulation annealing was performed in presence of counter ions) |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | collection | XwinNMR | 3.0 | Bruker |
| 2 | processing | Felix | 97 | Accelrys Inc. |
| 3 | data analysis | MARDIGRAS | 5.2 | Borgias, B. A., and James, T. L. (1990) MARDIGRAS- -a procedure for matrix analysis of relaxation for discerning geometry of an aqueous structure. J. Magn. Reson. 87, 475-487 |
| 4 | refinement | X-PLOR | 3.851 | A.T.Brunger |
| 5 | iterative matrix relaxation | CORMA | 5.2 | Keepers, J. W., and James, T. L. (1984)J. Magn. Reson. 87, 475-487. |
| 6 | structure solution | Amber | 6.0 | Case, D. A., and Pearlman C. A., et al. (1999) Amber 6.0, University of California, San Francisco, CA. |
