170D

SOLUTION STRUCTURE OF A DNA DODECAMER CONTAINING THE ANTI-NEOPLASTIC AGENT ARABINOSYLCYTOSINE: COMBINED USE OF NMR, RESTRAINED MOLECULAR DYNAMICS AND FULL RELAXATION MATRIX REFINEMENT


SOLUTION NMR Experimental Data


NMR Refinement
Method MOLECULAR DYNAMICS, MATRIX RELAXATION
Details STRUCTURES WERE GENERATED IN THE FOLLOWING MANNER: RESTRAINED MOLECULAR DYNAMICS WAS PERFORMED WITH EXPERIMENTAL DISTANCE AND DIHEDRAL RESTRAINTS GENERATED FROM NOESY AND COSY NMR DATA. THREE STRUCTURES WERE GENERATED STARTING FROM CANONICAL A-TYPE DNA AND THREE STRUCTURES STARTING FROM CANONICAL B-TYPE DNA. FOR BOTH CONTROL AND ARAC STRUCTURES, THE RMSD OF THE SIX STRUCTURES WAS < 0.7 ANGSTROM. THE SIX STRUCTURES WERE AVERAGED, MINIMIZED AND REFINED USING RELAXATION MATRIX REFINEMENT IN A DYNAMICAL SIMULATED ANNEALING PROTOCOL. THE X-PLOR DISTANCE CONSTRAINT AND SUGAR DIHEDRAL CONSTRAINT TABLES USED IN THE RESTRAINED MOLECULAR DYNAMICS CALCULATIONS FOR THE ARAC-CONTAINING DODECAMER ARE AVAILABLE FROM THE PROTEIN DATA BANK AS A SEPARATE ENTRY.
NMR Ensemble Information
Conformers Calculated Total Number 6
Conformers Submitted Total Number 1
Computation: NMR Software
# Classification Software Name Author
1 refinement X-PLOR BRUNGER