Experiment: 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
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
Spectrometer	Manufacturer	Model	Field Strength
1	Varian	VARIAN UNITY INOVA	600
2	Bruker	AVANCE	800

NMR Refinement
Method	Details	Software
DISTANCE RESTRAINED MOLECULAR DYNAMICS REFINEMENT		X-PLOR

NMR Ensemble Information
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
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.

Additional NMR Experimental Information

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
#	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

2A5R | pdb_00002a5r

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.