2A5R
Complex of tetra-(4-n-methylpyridyl) porphin with monomeric parallel-stranded DNA tetraplex, snap-back 3+1 3' G-tetrad, single-residue chain reversal loops, GAG triad in the context of GAAG diagonal loop, C-MYC promoter, NMR, 6 struct.
SOLUTION NMR
NMR Experiment | ||||||||
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Experiment | Type | Sample Contents | Solvent | Ionic Strength | pH | Pressure | Temperature (K) | Spectrometer |
1 | 1H-1H NOESY | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
2 | 1H-1H TOCSY | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
3 | 1H-31P COSY | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
4 | 1H-1H COSY | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
5 | 1H-15N JRHMQC | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
6 | 1H-15N HMBC | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
7 | 1H-13C JRHM 1H-13C HMBC | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
8 | 1H-13C HSQC | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
9 | 1H-13C sHMBC | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 | |
10 | 1H-31P TOCSY | 70 MM KCL 20 MM POTASSIUM PHOSPHATE, 90% H2O, 10% D2O | 90% H2O/10% D2O | 90 mM | 7.0 | 1 atm | 298 |
NMR Spectrometer Information | |||
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Spectrometer | Manufacturer | Model | Field Strength |
1 | Varian | VARIAN UNITY INOVA | 600 |
2 | Bruker | AVANCE | 800 |
NMR Refinement | ||
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Method | Details | Software |
DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT | X-PLOR |
NMR Ensemble Information | |
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Conformer Selection Criteria | structures with the least restraint violations |
Conformers Calculated Total Number | 6 |
Conformers Submitted Total Number | 6 |
Representative Model | 1 (lowest energy) |
Additional NMR Experimental Information | |
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Details | ONE OF THE EIGHT STRUCTURES OBTAINED FOR FREE DNA TETRAPLEX HAS USED FOR INTERACTIVE MODELING (PDB ID 2A5P). PART OF THE MOLECULE INCLUDING RESIDUES 1,2,3 AND 12 WAS LIFTED AS WHOLE. THE TMPYP4 WAS INTERCALATED BETWEEN THE TETRAD G4-G8-G13-G17 AND BASE PAIR A3-A12, GUIDED BY RESTRAINTS BETWEEN THE DRUG AND DNA, AND FAVORABLE POSITIONS OF THE DRUG. BROKEN BONDS BETWEEN THE RESIDUES 11-12-13 AND 3-4 WERE RESTORED, AND MOLECULE WAS SUBJECTED TO MINIMIZATION ROUNDS AND SUBSEQUENT DYNAMICS, WITH THE IMPOSED DNA AND DRUG-DNA RESTRAINTS. INITIALLY, ALL DRUG-DNA RESTRAINTS EXCEPT THESE INVOLVING RESIDUE 1 WERE TREATED AMBIGUOUSLY WITH SUM AVERAGING FROM CONTRIBUTION OF 8 IDENTICAL PROTON ATOMS. THE RESTRAINTS OF THE RESIDUE 1 WERE SPLIT AS ORIGINATING FROM SINGLE (ONE OF 4) PYRIDYL RINGS OF THE TMPYP4 IN FOUR SETS OF COMPUTATIONS. FROM FOUR MOLECULES OBTAINED ONLY ONE WITH LESS VIOLATIONS HAD POSITION OF THE H1' OF THE RESIDUE T1 AS WELL AS H8 OF THE RESIDUE G2 OVER THE AROMATIC RINGS OF THE PORPHYRIN, THUS ACCOUNTING FOR THE UPFIELD SHIFTS OF THESE PROTONS OBSERVED EXPERIMENTALLY. THE POSITION OF THE DRUG IN THE COMPLEX HAS BEEN INCREMENTALLY CHANGED BY ROTATION BY 15 DEG WITHIN THE BOUNDARIES OF VAN DER WAALS SURFACE OF DNA MOLECULE. THE MOLECULE WITH NEW POSITION OF DRUG WAS SUBJECTED TO CONSTRAINED MINIMIZATION AND DYNAMICS RUNS. AFTER THIS ROUND, PYRIDIL RING WAS ALLOWED TO FREE ROTATE AND DYNAMICS AND MINIMIZATION WAS PERFORMED ON SIX COMPLEXES AGAIN. |
Computation: NMR Software | ||||
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# | Classification | Version | Software Name | Author |
1 | refinement | X-PLOR | 3.851 | AT BRUNGER |
2 | collection | VNMR | 6.0 | VARIAN |
3 | processing | Felix | 2000 | ACCELRYS |
4 | refinement | Insight II | 2000 | ACCELRYS |