| MOLECULAR DYNAMICS, MATRIX RELAXATION | TWO STARTING STRUCTURES WERE GENERATED BY MANUALLY DOCKING THE DRUG ONTO A- AND B-FORM DNA USING INSIGHT II AND WERE SUBSEQUENTLY REFINED BY DISTANCE-RESTRAINED MOLECULAR DYNAMICS USING A SET OF INTER-PROTON DISTANCE RESTRAINTS DERIVED FROM THE NMR DATA. TWO INITIAL VELOCITY SEEDS WERE USED FOR EACH STARTING STRUCTURE WHICH YIELDS FOUR DISTANCE-REFINED STRUCTURES. THEY WERE REFINED FURTHER USING RELAXATION-MATRIX BASED NOE INTENSITY-RESTRAINED MOLECULAR DYNAMICS. THE FINAL FOUR STRUCTURES WERE OBTAINED BY TAKING THE AVERAGE COORDINATES OF THE LAST 1.0 PS OF THE DYNAMICS DURING RELAXATION MATRIX REFINEMENT AND ENERGY MINIMIZED. THE R(1/6) VALUE WAS USED TO REFINE THE STRUCTURE DURING RELAXATION MATRIX REFINEMENT. THE SUMMATIONS RUN THROUGH ALL OBSERVED, QUANTIFIABLE NOE CROSSPEAKS IN NOESY SPECTRA RECORDED IN D2O AND MIXING TIMES OF 30, 60, 100, 150 AND 200 MS. THE R(1/6) FACTOR AND THE RMS DEVIATIONS FROM IDEAL GEOMETRY FOR THE FOUR FINAL STRUCTURES ARE: MODEL1 MODEL2 MODEL3 MODEL4 R(1/6) FACTOR 0.039 0.038 0.038 0.036 BOND (ANG) 0.012 0.012 0.012 0.011 ANGLES (DEG) 3.833 3.818 3.776 3.684 IMPROPERS (DEG) 0.251 0.250 0.286 0.219 | |
