| simulated annealing |
THE 3D STRUCTURE OF THE GAGA FACTOR/DNA COMPLEX WAS SOLVED
BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED
NMR AND IS BASED ON 1475 EXPERIMENTAL NMR RESTRAINTS:
(A) INTRAPROTEIN: 188 SEQUENTIAL (|I- J|=1), 134 MEDIUM
RANGE (1 < |I-J| <=5) AND 95 LONG RANGE (|I-J| >5)
INTERRESIDUES AND 275 INTRARESIDUE APPROXIMATE INTERPROTON
DISTANCE RESTRAINTS; 140 TORSION ANGLE RESTRAINTS; 33
THREE-BOND HN-HA COUPLING CONSTANT RESTRAINTS; AND 94
(48 CALPHA AND 46 CBETA) 13C SHIFT RESTRAINTS. (NUMBERS
OF RESIDUES 10 - 61)
(B) INTRA-DNA: 124 INTRARESIDUE, 112 SEQUENTIAL
INTRASTRAND, 21 INTERSTRAND INTERPROTON DISTANCE
RESTRAINTS; 102 TORSION ANGLE RESTRAINTS (FOR ALPHA, BETA,
GAMMA, DELTA, EPSILON AND AND ZETA BACKBONE TORSION
ANGLES).
(C) INTERMOLECULAR: 75 INTERPROTON DISTANCE RESTRAINTS.
THE EXPERIMENTAL NMR RESTRAINTS ARE SUPPLEMENTED BY
HYDROGEN BONDING RESTRAINTS: 24 DISTANCES FOR 12 BACKBONE
HYDROGEN BONDS WITHIN THE PROTEIN, 58 DISTANCES FOR
WATSON-CRICK BASE-PAIRING WITHIN THE DNA, AND 10 AMBIGUOUS
DISTANCE RESTRAINTS BETWEEN THE PROTEIN AND THE DNA. THE
RESTRAINTS HAVE BEEN DEPOSITED.
THE STRUCTURES WERE CALCULATED USING THE SIMULATED
ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229,
129-136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED
TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J.
MAGN. RESON. SERIES B 104, 99-103) AND CARBON CHEMICAL
SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B
106, 92-96) RESTRAINTS, AND A CONFORMATIONAL DATABASE
POTENTIAL (KUSZEWSKI ET AL.(1996) PROTEIN SCI. 5, 1067-1080
THE RESTRAINED REGULARIZED MEAN STRUCTURE IS PRESENTED IN
THIS ENTRY AND 50 STRUCTURES ARE PRESENTED IN ENTRY 1YUJ.
IN THE RESTRAINED REGULARIZED MEAN COORDINATES THE LAST
COLUMN REPRESENTS THE AVERAGE RMS DIFFERENCE BETWEEN THE
INDIVIDUAL SIMULATED ANNEALING STRUCTURES AND THE MEAN
COORDINATE POSITIONS. THE LAST COLUMN IN THE INDIVIDUAL SA
STRUCTURES HAS NO MEANING. BEST FITTING TO GENERATE THE
AVERAGE STRUCTURE IS WITH RESPECT TO RESIDUES 14 - 58 OF
THE PROTEIN AND BASE PAIRS 1 - 11 OF THE DNA (RESIDUES 10 -
13 AND 59 - 61 ARE DISORDERED IN SOLUTION). RESIDUE 10
CORRESPONDS TO RESIDUE 319 OF THE NATURAL SEQUENCE. NOTE
THE OCCUPANCY FIELD HAS NO MEANING. |
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