141D

SOLUTION STRUCTURE OF A CONSERVED DNA SEQUENCE FROM THE HIV-1 GENOME: RESTRAINED MOLECULAR DYNAMICS SIMULATION WITH DISTANCE AND TORSION ANGLE RESTRAINTS DERIVED FROM TWO-DIMENSIONAL NMR SPECTRA


SOLUTION NMR
NMR Refinement
MethodDetailsSoftware
MOLECULAR DYNAMICS, ENERGY MINIMIZATIONALL COORDINATES AROSE FROM ENERGY MINIMIZED AMBER4 FILES THAT WERE REFORMATTED FOR THE HELIX ANALYSIS PROGRAM CURVES. THEREFORE, ALL HYDROGEN ATOMS WERE REMOVED. THE DEPOSITORS HAVE PROVIDED THREE COORDINATE SETS FOR THIS STRUCTURE. THE FIRST TWO COORDINATE SETS (PROTEIN DATA BANK ENTRIES 140D AND 141D) CONTAIN THE RESULTS OF THE NMR/RESTRAINED MOLECULAR DYNAMICS REFINEMENT WHERE A-DNA AND B-DNA WERE USED AS STARTING MODELS, RESPECTIVELY. THE AUTHORS DENOTED THESE STRUCTURES AS RMD-A AND RMD-B, RESPECTIVELY. THE THIRD COORDINATE SET (PROTEIN DATA BANK ENTRY 142D) REPRESENTS THE FINAL STRUCTURE, DENOTED RMD-FINAL BY THE AUTHORS. ALL STRUCTURES WERE DERIVED BY AVERAGING THE LAST 4 PS OF 30 PS RESTRAINED MD (AMBER4) AND SUBSEQUENT RESTRAINED ENERGY MINIMIZATION. FIVE RMD RUNS WERE AVERAGED TO EACH INTERIM STRUCTURE RMD-A AND RMD-B, DEPENDING ON THE STARTING GEOMETRY. ALL TEN STRUCTURES WERE AVERAGED, RESTRAINED ENERGY MINIMIZED AND A FINAL 20PS RMD RUN WAS PERFORMED, THE LAST 4PS OF WHICH, AFTER AVERAGING AND RESTRAINED ENERGY MINIMIZATION LEAD TO THE FINAL STRUCTURE: RMD-FINAL.AMBER4
NMR Ensemble Information
Conformer Selection Criteria
Conformers Calculated Total Number
Conformers Submitted Total Number1
Additional NMR Experimental Information
DetailsSUGAR PUCKER OF DEOXYRIBOSES HAS BEEN DETERMINED BY SIMULATION OF 2QF-COSY SPECTRA. A LIST OF TORSION ANGLE AND NOE DISTANCE RESTRAINTS IS AVAILABLE FROM THE PROTEIN DATA BANK AS ENTRY R140DMR.
Computation: NMR Software
#ClassificationVersionSoftware NameAuthor
1structure solutionAMBER4
2refinementAMBER4