| STRUCTURE REFINEMENT OF THE DNA WAS PERFORMED USING COMPLETE RELAXATION MATRIX, RESTRAINED MOLECULAR DYNAMICS. | 303 NOE VOLUME CONSTRAINTS FROM THE 100 MS AND 498 NOE FROM THE 250 MS NOESY DATA WERE USED. IN ADDITION 10 NOE CONSTRAINTS INVOLVING THE IMINO PROTONS OF RESIDUES G1, G5, G6, G8, G10, G14, AND G15 WERE USED AS DISTANCE CONSTRAINTS. FOUR HYDROGEN BONDS WERE USED FOR EACH GUANINE INVOLVED IN A QUARTET. EXPERIMENTAL COUPLING CONSTANTS WERE USED TO GENERATE 45 DIHEDRAL CONSTRAINTS, 15 FROM BASHD-TOCSY EXPERIMENTS (H3*-31P), AND 30 FROM PE-COSY DATA (H1*-C1*- C2*-1H2* AND H1*-C1*-C2*-2H2*). ADDITIONAL CONSTRAINTS WERE USED TO KEEP THE PURINE RINGS PLANAR. THE STARTING STRUCTURE USED WAS THE STRUCTURE OBTAINED IN A PREVIOUS REFINEMENT. THE NON-BONDED INTERACTION CUT-OFF WAS SET TO 11.5 A, USING X-PLOR PROTOCOLS. THE ACTIVE DISTANCE OF THE SWITCHING FUNCTIONS WAS 7.5 TO 10.5 A. THE DISTANCE CUT-OFF FOR THE HYDROGEN BONDING INTERACTIONS WAS 7.5 A. THE SWITCHING FUNCTION FOR HYDROGEN BONDING INTERACTIONS WAS ACTIVE FROM 4.0 TO 6.5 A. THE ENERGY OF THE STARTING STRUCTURE WAS MINIMIZED IN 200 STEPS OF POWELL'S CONJUGATE GRADIENT MINIMIZATION. THE RELAXATION MATRIX REFINEMENTS WERE CARRIED OUT IN VACUUM AT 300K WITH A RELATIVE WEIGHTING OF ALL THE EXPERIMENTAL CONSTRAINTS (NOE, DISTANCE AND DIHEDRAL) OF 60 KCAL/MOL. SUBSEQUENTLY, A 100 PS RELAXATION MATRIX TRAJECTORY WAS CONDUCTED WITH STRUCTURES SAVED EVERY 2 PS. THE TRAJECTORIES STABILIZED AFTER 30 PS. UPON COMPLETION OF THE SIMULATION AN ADDITIONAL 200 STEP CONJUGATE GRADIENT MINIMIZATION WAS CONDUCTED TO PRODUCE THE FINAL STRUCTURES. THE ROOT MEAN SQUARE DEVIATION {OF WHAT?} WAS CALCULATED TO BE 0.14. THE NOE CROSS-PEAK VOLUMES OF THE STRUCTURES OBTAINED BETWEEN 80-100 PS AT INTERVALS OF 2 PS WERE BACKCALCULATED USING THE FELIX 970 SOFTWARE PACKAGE (MSI INC.) PARAMETERS USED IN THE BACKCALCULATION PROTOCOL ARE AS FOLLOWS: A CORRELATION TIME OF 5.0 NS, A Z-LEAKAGE RATE OF 3.0 S-1 AND A DISTANCE CUT OFF OF 7.5 A. NOE SPECTRA OF THESE 10 STRUCTURES WERE THEN BACKCALCULATED AND AVERAGED. 40 NOE INTENSITIES FROM THE EXPERIMENTAL NOESY SPECTRA WERE USED TO NORMALIZE THE BACKCALCULATED TO THE THEORETICAL NOES. THE NORMALIZATION AND AVERAGING PROCESSES WERE CONDUCTED ON A IN HOUSE PROGRAM. THE RMS, R AND Q VALUES OF THE AVERAGED STRUCTURE THAT ARE 0.28, 0.68 AND 0.30. | VNMR |
