| simulated annealing |
GENERATION OF THIS MODEL OF THE SWITCH ARC MUTANT INVOLVED A COMBINATION OF EXPERIMENTAL AND SIMU
LATED DISTANCE RESTRAINTS. FOR RESIDUES 7-14, 81 NOE CROSSPEAKS WERE OBTAINED FROM A 50-MS 2D NOES
Y SPECTRUM AND WERE TRANSLATED INTO STRONG (1.8-2.8 A), MEDIUM (1.8-3.3 A), MEDIUM-WEAK (1.8-3.8 A
) AND WEAK (1.8-4.3 A) DISTANCE RESTRAINTS.18 ADDITIONAL CROSSPEAKS WERE OBTAINED FROM A 150-MS 3D
NOESY SPECTRUM AND WERE ASSIGNED LOOSER RESTRAINTS (1.8 TO 4.0 A OR 1.8 TO 6.0 A)BECAUSE OF THE L
ONGER MIXING TIME USED IN THIS EXPERIMENT. TO SIMULATE THE STRUCTURE OF RESIDUES 14 TO 53 (RESIDUE
14 WAS DESCRIBED BY BOTH ACTUAL AND COMPUTED RESTRAINTS), A LIST OF 1635 DISTANCES WAS GENERATED
BETWEEN PAIRS OF HEAVY ATOMS WITHIN 4 A OF EACH OTHER IN THE WILD-TYPE ARC CRYSTAL STRUCTURE, AND
THE INTERATOMIC DISTANCES WERE CONSTRAINED TO BE WITHIN + OR - 1.0 A OF THIS VALUE. 28 INITIAL STR
UCTURES WITH RANDOM CONFIGURATIONS FOR RESIDUES 1 TO 13 WERE GENERATED BY PERFORMING A SET OF CALC
ULATIONS WITH ONLY THE SIMULATED RESTRAINTS FOR RESIDUES 14 TO 53. THEN, 28 MODEL STRUCTURES WERE
GENERATED BY INCLUDING THE EXPERIMENTAL RESTRAINTS FOR RESIDUES 7 TO 14. NO RESTRAINTS WERE USED F
OR RESIDUES 1 TO 6, WHICH APPEAR TO BE DISORDERED. AMBIGUITIES IN INTRA- AND INTERMOLECULAR NOE AS
SIGNMENT RESULTING FROM ARC'S TWOFOLD SYMMETRY WERE RESOLVED COMPUTATIONALLY AS DESCRIBED (M. NILG
ES, PROTEIN STRUCT. FUNCT. GENET. 17, 297 (1993).19 OF 28 STRUCTURES WERE ACCEPTED WITH NO NOE VIO
LATIONS GREATER THAN 0.3 A. THE FIVE STRUCTURES WITH THE HIGHEST ENERGY, WHICH ALSO CONTAINED BACK
BONE DIHEDRAL ANGLES IN DISALLOWED REGIONS OF RAMACHANDRAN SPACE, WERE DISCARDED. THE REMAINING 14
STRUCTURES, WHICH HAD PAIRWISE RMSD'S OF 0.6 A (BACKBONE) AND 1.6 A (HEAVY), WERE USED TO GENERAT
E A MINIMIZED AVERAGE MODEL. |
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