| simulated annealing | THE STRUCTURES WERE CALCULATED BY SIMULATED ANNEALING IN TORSION ANGLE SPACE (SCHWIETERS AND CLORE (2001) J MAGN RESON 152, 288-302) AGAINST A TARGET FUNCTION COMPRISING THE EXPERIMENTAL NMR RESTRAINTS (NOE-DERIVED INTERPROTON DISTANCE, TORSION ANGLE, 3J COUPLING, 13CALPHA/13CBETA SHIFTS AND DIPOLAR COUPLINGS). THE NON-BONDED CONTACTS IN THE TARGET FUNCTION ARE REPRESENTED BY A QUARTIC VAN DER WAALS REPULSION TERM, SUPPLEMENTED BY TORSION ANGLE (KUSZEWSKI ET AL. J. MAGN. RESON 125, 171-177 (1997)) BASE-BASE POSITIONAL (KUSZEWSKI ET AL. J AM CHEM SOC 123, 3903-3918 (2001)) DATABASE POTENTIALS OF MEAN FORCE.
IN THIS ENTRY THE LAST NUMERICAL COLUMN IS THE RMS OF
THE 80 INDIVIDUAL SIMULATED ANNEALING STRUCTURES (FOR
EACH HALF OF THE COMPLEX) ABOUT THE MEAN COORDINATE
POSITIONS: RESIDUES 75-103 OF THE PROTEIN ARE
DISORDERED IN THE COMPLEX. ALTHOUGH THE SINGLE-STRANDED
DNA IS B-LIKE, THE COORDINATES OF THOSE PORTIONS OF THE
SS-DNA NOT IN CONTACT WITH THE PROTEIN COULD NOT BE
ACCURATELY DETERMINED (BASES 201-203, 212-215 AND
223-229). THEREFORE THE COORDINATES ARE PRESENTED IN
TWO HALVES: THE KH3 HALF OF THE COMPLEX (RESIDUES 1-74
OF THE PROTEIN AND BASES 216-222 OF THE SS-DNA) AND THE
KH4 HALF OF THE COMPLEX (RESIDUES 104-174 OF THE
PROTEIN AND BASES 204-211 OF THE SS-DNA). THE
COORDINATE ACCURACY IS CALCULATED FOR THE TWO HALVES OF
THE COMPLEX SEPARATELY. THE APPROXIMATE ORIENTATION OF
AND SEPARATION BETWEEN THE TWO DOMAINS COULD BE DERIVED
FROM ANALYSIS OF HETERONUCLEAR RELAXATION MEASUREMENTS.
THE ORIENTATIONS OF THE TWO HALVES OF THE COMPLEX IN
THESE COORDINATES REFLECTS THE RESULTS OF THE
RELAXATION MEASUREMENTS. THE AVERAGE ORIENTATION OF THE
TWO HALVES OF THE COMPLEX IS PARALLEL WITH AN AVERAGE
INTERHELICAL ANGLE OF ABOUT 1 DEGREE BETWEEN THE THIRD
HELIX OF EACH DOMAIN. THE OVERALL ROTATIONAL
CORRELATION TIME OF THE COMPLEX IS 21.5 NS WITH A
DIFFUSION ANISOTROPY OF 1.85. THE TIME SCALE FOR THE
INTERDOMAIN MOTIONS IS AROUND 4 NS AND THE TWO DOMAINS
WOBBLE INDEPENDENTLY IN CONES WITH SEMI-ANGLES OF ABOUT
30 DEGREES. THE OVERALL LENGTH OF THE COMPLEX IS ABOUT
100 ANGSTROMS AND THE SEPARATION BETWEEN THE TWO HALVES
OF THE COMPLEX IS AROUND 35 ANGSTROMS. THE RESTRAINED
REGULARIZED MEAN STRUCTURE FOR THE TWO HALVES OF THE
COMPLEX IS OBTAINED BY RESTRAINED REGULARIZATION OF THE
AVERAGE COORDINATES AGAINST THE SAME TARGET FUNCTION
USED TO CALCULATE THE SIMULATED ANNEALING STRUCTURES.
SOLVED BY MULTI HETERONUCLEAR NMR AND IS BASED ON
3153 EXPERIMENTAL NMR RESTRAINTS
KH3 HALF KH4 HALF
DISTANCES 1095 949
TORSION ANGLES 244 261
3JHNA COUPLINGS 33 36
13CA/CB SHIFTS 120 121
1DNH DIPOLARS 61 61
1DNC' DIPOLARS 47 39
2DHNC' DIPOLARS 46 40
BREAKDOWN OF INTRAMOLECULAR PROTEIN DISTANCE RESTRAINTS
INTRARESIDUE 157 169
SEQUENTIAL 274 216
MEDIUM RANGE 247 155
LONG RANGE 260 216
BACKBONE H-BONDS 33 36
INTRA-DNA DISTANCES 41 53
INTERMOLECULAR DISTANCES 50 68 | X-PLOR NIH |
