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HIGH-RESOLUTION SOLUTION NMR STRUCTURE OF THE TRIMERIC COILED-COIL DOMAIN OF CHICKEN CARTILAGE MATRIX PROTEIN, 20 STRUCTURES
SOLUTION NMR
NMR Experiment
Experiment
Type
Sample Contents
Solvent
Ionic Strength
pH
Pressure
Temperature (K)
Spectrometer
1
2D NOESY
5.5
323
2
2D TOCSY
5.5
323
3
2D 1H-15N HSQC
5.5
323
4
2D 1H-13C HSQC
5.5
323
5
3D 1H-15N NOESY-HSQC
5.5
323
6
3D 1H-15N TOCSY-HSQC
5.5
323
7
3D HCCH-TOCSY
5.5
323
8
3D HNCA
5.5
323
9
3D HNHA
5.5
323
10
3D HNHB
5.5
323
11
2D VERSION OF A 4D 13C/15N HMQC-NOESY-HMQC
5.5
323
12
3D 13C F1-EDITED
5.5
323
13
F3-FILTERED HMQC-NOESY
5.5
323
NMR Spectrometer Information
Spectrometer
Manufacturer
Model
Field Strength
1
Varian
UNITY
600
NMR Refinement
Method
Details
Software
DISTANCE GEOMETRY/ SIMULATED ANNEALING
ALL STRUCTURE CALCULATIONS WERE PERFORMED USING X-PLOR VERSION 3.1. FIRST 60 MONOMER STRUCTURES WERE CALCULATED FROM INTRACHAIN DISTANCE RESTRAINTS, TOGETHER WITH THE DIHEDRAL ANGLE RESTRAINTS FOR PHI AND CHI1 AND THE HYDROGEN BOND RESTRAINTS, USING THE HYBRID DISTANCE GEOMETRY-DYNAMICAL SIMULATED ANNEALING METHOD (NILGES, M.; CLORE, G.M.; GRONENBORN, A.M. (1988); FEBS LETT. 229, 317-324). THE 30 BEST MONOMER STRUCTURES WERE USED AS INPUT FOR THE GENERATION OF TRIMER STARTING STRUCTURES. EACH SELECTED HELIX MONOMER WAS FIRST ORIENTED SUCH THAT ITS GEOMETRIC CENTER COINCIDED WITH THE ORIGIN AND ITS LONG AXIS LAY ALONG THE X-AXIS AND SECOND TRANSLATED BY 10 ANGSTROMS ALONG THE Y-AXIS. COORDINATES FOR THE SECOND AND THIRD SUBUNIT WERE GENERATED BY A ROTATION AROUND THE X-AXIS BY 120 OR 240 DEGREES, RESPECTIVELY. THE 30 GENERATED TRIMER STARTING STRUCTURES WERE USED AS INPUT FOR A SECOND RUN OF SIMULATED ANNEALING INCLUDING THE INTERCHAIN DISTANCE RESTRAINTS. IN THE RESULTING STRUCTURES THE INTERCHAIN DISULFIDE BONDS WERE INTRODUCED AND A FINAL RUN OF SIMULATED ANNEALING AND REFINEMENT PERFORMED. THE LAST STEPS OF REFINEMENT INCLUDED ADDITIONALLY NON-CRYSTALLOGRAPHIC SYMMETRY (NCS) CONSTRAINTS AND R^(-6)-SUM AVERAGED DISTANCE RESTRAINTS FOR AMBIGUOUS NOES (NILGES, M. (1993); PROTEINS 17, 297-309).