Complex of the DNA binding core domain of the transcription factor MEF2A with a 20mer oligonucleotide

Solution structure of the MEF2A-DNA complex: structural basis for the modulation of DNA bending and specificity by MADS-box transcription factors

MYOCYTE-SPECIFIC ENHANCER FACTOR 2A, C4 FORM

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SOLVED BY MULTI HETERONUCLEAR NMR AND IS BASED ON 4560 EXPERIMENTAL NMR RESTRAINTS (I.E. 2280 UNIQUE ONES SINCE PROTEIN IS A HOMODIMER AND DNA IS PALINDROMIC). NOE RESTRAINTS: (A) PROTEIN: 664 SEQUENTIAL, 504 MEDIUM RANGE, 212 LONG RANGE, 616 INTRARESIDUE, 174 INTERSUBUNIT. (B) DNA: 428 INTRARESIDUE, 196 SEQUENTIAL INTRASTRAND, 24 INTERSTRAND. (C) PROTEIN- DNA 168. H-BOND RESTRAINTS: PROTEIN 138, DNA 120. TORSION ANGLE RESTRAINTS: PROTEIN 480 (142 PHI, 142 PSI, 112 CHI1, 68 CHI2, 16 CHI3), DNA 228. THREE-BOND HN-HALPHA COUPLING CONSTANTS: 72. SECONDARY 13C SHIFTS: 140 13CALPHA, 140 13CBETA. DIPOLAR COUPLINGS: 1DNH PROTEIN: 70, 1DCH DNA 70. REPULSIVE RESTRAINTS: 106

(1) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN. (2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS. (3) 3D AND 4D HETERONUCLEAR SEPARATED AND FILTERED NOE EXPTS. (4) 2D 12C-FILTERED EXPERIMENTS FOR DNA ASSIGNMENTS. (5) IPAP EXPTS FOR DIPOLAR COUPLINGS DIPOLAR COUPLINGS WERE MEASURED IN A BICELLE LIQUID CRYSTALLINE MEDIUM.

THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136 USING THE PROGRAM XPLOR/CNS MODIFIED TO INCORPORATE COUPLING CONSTANT RESTRAINTS (GARRETT ET AL. (1984) J. MAGN. RESON. SERIES B 104, 99-103), CARBON CHEMICAL SHIFT RESTRAINTS, (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92-96) RESTRAINTS, RESIDUAL DIPOLAR COUPLING RESTRAINTS (CLORE ET AL. J. MAGN. RESON 131, 159-162 (1998); J. MAGN 133, 216-221 (1998)), AND A CONFORMATIONAL DATABASE POTENTIAL FOR PROTEINS AND NUCLEIC ACIDS (KUSZEWSKI ET AL. PROTEIN SCI. 5, 1067-1080 (1996); J. MAGN. RESON 125, 171-177 (1997)).

IN THIS ENTRY THE LAST NUMERICAL COLUMN IS THE RMS OF THE 35 INDIVIDUAL SIMULATED ANNEALING STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS. THE LATTER ARE OBTAINED BY TAKING THE AVERAGE OF THE 35 SIMULATED ANNEALING STRUCTURES BEST-FITTED TO RESIDUES 1-73 AND 101-173 OF THE PROTEIN AND RESIDUES 201-240 OF THE DNA. RESIDUES 74-85 AND 174-185 ARE DISORDERED IN SOLUTION AND ARE THEREFORE NOT INCLUDED IN THE COORDINATES. THE RESTRAINED MINIMIZED MEAN STRUCTURE IS OBTAINED BY RESTRAINED REGULARIZATION OF THE AVERAGE COORDINATES AGAINST THE SAME TARGET FUNCTION USED TO CALCULATE THE SIMULATED ANNEALING STRUCTURES.

BRUNGER,ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE WARREN

DNA BINDING PROTEIN, TRANSCRIPTION FACTOR, MADS-BOX, SAM DOMAIN, TRANSCRIPTION-DNA COMPLEX

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