SOLUTION NMR STRUCTURE OF RECOMBINANT SYRIAN HAMSTER PRION PROTEIN RPRP(90-231) , 25 STRUCTURES
SOLUTION NMR
| NMR Experiment | ||||||||
|---|---|---|---|---|---|---|---|---|
| Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
| 1 | N15 NOESY | 5.2 | 1 atm | 303 | ||||
| 2 | C13 NOESY | 5.2 | 1 atm | 303 | ||||
| NMR Spectrometer Information | |||
|---|---|---|---|
| Spectrometer | Manufacturer | Model | Field Strength |
| 1 | Bruker | DMX | 750 |
| 2 | Bruker | AMX | 600 |
| 3 | Varian | UNITYPLUS | 500 |
| NMR Refinement | ||
|---|---|---|
| Method | Details | Software |
| NMR-RESTRAINED SIMULATED ANNEALING, MOLECULAR DYNAMICS, AND ENERGY MINIMIZATION. | NMR DISTANCE RESTRAINTS WERE ASSIGNED WITH THE AID OF ARIA (AMBIGUOUS RESTRAINTS FOR ITERATIVE ASSIGNMENT) PROCEDURE, RESULTING IN 2778 UNAMBIGUOUS AND 306 AMBIGUOUS DISTANCE RESTRAINTS. 63 J COUPLING CONSTANTS, AND 44 HYDROGEN BOND RESTRAINTS WERE ALSO USED IN THE STRUCTURE CALCULATIONS. 100 STRUCTURES WERE CALCULATED USING XPLOR NMR- RESTRAINED SIMULATED ANNEALING PROTOCOL. RESIDUES 112-231 OF THE 25 STRUCTURES WITH LOWEST TOTAL ENERGY WERE EACH SUBJECTED TO 25PS RESTRAINED MOLECULAR DYNAMICS SIMULATION IN A 6 ANGSTROM SHELL OF WATER FOLLOWED BY ENERGY MINIMIZATION USING AMBER4.1 FORCE FIELD. THE AVERAGE VIOLATION FOR DISTANCE RESTRAINTS IS 0.032A, AND FOR J COUPLING CONSTANTS IS 0.059HZ. THE AVERAGE BACKBONE ATOMIC RMSD TO THE MEAN STRUCTURE IS 0.67A FOR RESIDUES 125-227 OF THE 25 STRUCTURES. THE REFINEMENT HAS BEEN SUBMITTED TO BIOCHEMISTRY WITH THE TITLE "SOLUTION STRUCTURE OF SYRIAN HAMSTER PRION PROTEIN RPRP(90-231)". NOTE, LOWER RESOLUTION STRUCTURES PUBLISHED ON PNAS 94, 10086 (1997) WERE CALCULATED WITH THE PROGRAM DIANA DEVELOPED IN WUTHRICH'S LAB.RESIDUES 90-124 OF RPRP(90-231) ARE LARGELY UNSTRUCTURED. RESIDUES 90-111 WERE EXCLUDED IN THE FINAL STAGE OF STRUCTURE REFINEMENT. THE COORDINATES DEPOSITED TO PDB CONTAIN RESIDUES 125-228. | ARIA |
| NMR Ensemble Information | |
|---|---|
| Conformer Selection Criteria | TOTAL ENERGY |
| Conformers Calculated Total Number | 100 |
| Conformers Submitted Total Number | 25 |
| Representative Model | 1 (n/a) |
| Additional NMR Experimental Information | |
|---|---|
| Details | IONIC_STRENGTH: NULL PRESSURE: 1 ATM SOLVENT SYSTEM: 1MM PROTEIN, H2O, 20 MM SODIUM ACETATE THE 1H, 15N AND 13C RESONANCES WERE ASSIGNED USING TRIPLE RESONANCE NMR EXPERIMENTS HNCA, HNCACB, CBCACONNH, HNCO, HCCH-TOCSY ACQUIRED ON 500 AND 600 MHZ SPECTROMETERS WITH UNIFORMLY 13C/15N-LABELED SAMPLE. DISTANCE RESTRAINTS WERE OBTAINED FROM 750 MHZ 15N-HSQC-NOESY AND 13C-HSQC- NOESY SPECTRA WITH 100MS MIXING TIME. |
| Computation: NMR Software | ||||
|---|---|---|---|---|
| # | Classification | Version | Software Name | Author |
| 1 | refinement | ARIA | M. NILGES | |
| 2 | refinement | XPLOR | A. T. BRUNGER | |
| 3 | refinement | AMBER4.1 | P. A. KOLLMAN | |
| 4 | structure solution | ARIA | ||
| 5 | structure solution | XPLOR | ||
| 6 | structure solution | Amber | ||
