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HIGH RESOLUTION SOLUTION NMR STRUCTURE OF MIXED DISULFIDE INTERMEDIATE BETWEEN HUMAN THIOREDOXIN (C35A, C62A, C69A, C73A) MUTANT AND A 13 RESIDUE PEPTIDE COMPRISING ITS TARGET SITE IN HUMAN REF-1 (RESIDUES 59-71 OF THE P50 SUBUNIT OF NFKB), NMR, 31 STRUCTURES
SOLUTION NMR
NMR Refinement
Method
Details
Software
OTHER REFINEMENT REMARKS:
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.
MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL.
(1994) J. MAGN. RESON SERIES B 104 99 - 103), CARBON
CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON.
SERIES B 106, 92 - 96), AND PROTON CHEMICAL SHIFT
(KUSZEWSKI ET AL. (1995) J. MAGN. RESON SERIES B 107,
293 - 297) RESTRAINTS, AND A CONFORMATIONAL DATABASE
POTENTIAL TERM (KUSZEWSKI, GRONENBORN & CLORE (1996)
PROTEIN SCIENCE IN PRESS). ALL STRUCTURAL STATISTICS ARE
GIVEN IN THE REFERENCE.
THE 3D STRUCTURE OF THE HUMAN THIOREDOXIN-NFKB PEPTIDE
COMPLEX IN SOLUTION BY NMR IS BASED ON 3213 EXPERIMENTAL
RESTRAINTS COMPRISING:
2581 STRUCTURE USEFUL INTERPROTON DISTANCE RESTRAINTS
36 RESTRAINTS FOR 18 BACKBONE H-BONDS
321 TORSION ANGLE RESTRAINTS (104 PHI, 76 PSI, 78 CHI1,
AND 30 CHI2 FOR HUMAN THIOREDOXIN, AND 11 PHI,
9 PSI, 9 CHI1, AND 4 CHI2 ANGLES FOR THE REF-1
PEPTIDE
86 HN-HALPHA THREE-BOND COUPLING CONSTANTS
100 13CALPHA AND 97 13CB CHEMICAL SHIFT RESTRAINTS.
442 1H CHEMICAL SHIFT RESTRAINTS (MADE UP OF 113 CAH,
67 METHYL GROUPS AND 262 OTHER NON-EXCHANGEABLE
PROTONS).
THE BREAKDOWN OF THE INTERPROTON DISTANCE RESTRAINTS IS AS
FOLLOWS:
INTRAMOLECULAR HTRX RESTRAINTS:
534 SEQUENTIAL
539 SHORT RANGE (1 < |I-J|<=5)
688 LONG RANGE (|I-J|>5)
682 INTRARESIDUE
INTRAMOLECULAR PEPTIDE RESTRAINTS: 83
INTERMOLECULAR HTRX-NFKB: 55
THE STRUCTURE FOUND IN PDB ENTRY 1CQH IS THE RESTRAINED
MINIMIZED AVERAGE STRUCTURE: (SA)R. THIS IS OBTAINED BY
FIRST AVERAGING THE COORDINATES OF THE INDIVIDUAL 35
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.