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THE 3D STRUCTURE OF THE HUMAN THIOREDOXIN-NFKB PEPTIDE
COMPLEX IN SOLUTION BY NMR IS BASED ON 3213 EXPERIMENTAL
RESTRAINTS COMPRISING:
2546 STRUCTURE USEFUL INTERPROTON DISTANCE RESTRAINTS
36 RESTRAINTS FOR 18 BACKBONE H-BONDS
44 RESTRAINTS FOR 6 BOUND WATER MOLECULES
300 TORSION ANGLE RESTRAINTS (104 PHI, 76 PSI, 78 CHI1
AND 31 CHI2 FOR HUMAN THIOREDOXIN, AND 7 CHI1 AND 4
CHI2 RESTRAINTS FOR THE NFKB PEPTIDE)
88 HN-HALPHA THREE-BOND COUPLING CONSTANTS
102 13CALPHA AND 97 13CB CHEMICAL SHIFT RESTRAINTS.
THE BREAKDOWN OF THE INTERPROTON DISTANCE RESTRAINTS IS AS
FOLLOWS:
INTRAMOLECULAR HTRX RESTRAINTS:
503 SEQUENTIAL
437 SHORT RANGE (1 < |I-J|<=5)
727 LONG RANGE (|I-J|>5)
690 INTRARESIDUE
INTRAMOLECULAR PEPTIDE RESTRAINTS: 115
INTERMOLECULAR HTRX-NFKB: 74
THE STRUCTURES ARE CALCULATED USING THE HYBRID METRIC
MATRIX DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING
METHOD DESCRIBED BY: NILGES, M., CLORE, G.M. &
GRONENBORN, A.M. (1988) FEBS LETT 229, 317 - 324. ALL
STRUCTURAL STATISTICS ARE GIVEN IN THE REFERENCE.
THE STRUCTURE FOUND IN PDB ENTRY 1MDI IS THE RESTRAINED
MINIMIZED AVERAGE STRUCTURE: (SA)R. THIS IS OBTAINED
BY FIRST AVERAGING THE COORDINATES OF THE INDIVIDUAL 60
DYNAMICAL SIMULATED ANNEALING SA STRUCTURES BEST FITTED TO
RESIDUES 1 - 105 OF HTRX AND RESIDUES 57 - 67 OF THE
PEPTIDE AND SUBJECTING THE RESULTING COORDINATES TO
RESTRAINED MINIMIZATION. THE LAST NUMBER COLUMN IN THIS
SET OF COORDINATES (THE B-FACTOR COLUMN IN X-RAY
STRUCTURES) GIVES THE AVERAGE RMS DIFFERENCE BETWEEN THE
INDIVIDUAL SA STRUCTURES AND THE MEAN STRUCTURE. THE
NUMBERS IN THE LAST COLUMN OF THE INDIVIDUAL STRUCTURES
HAVE NO MEANING. |
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