| simulated annealing | THE STRUCTURES WERE CALCULATED USING THE SIMULATED
ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT.
229, 129 - 136 AND PROTEIN ENGINEERING 2, 27 - 38 USING
THE PROGRAM X-PLOR MODIFIED TO INCORPORATE COUPLING
CONSTANT RESTRAINTS (GARRETT ET AL. (1994) J. MAGN RESON.
SERIES B 104, 99 - 103), CARBON CHEMICAL SHIFT RESTRAINTS
(KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92
- 96) RESTRAINTS, DIPOLAR COUPLING RESTRAINTS (TJANDRA ET
AL. (1997) NATURE STRUCT BIOL 4, 732-738) AND A
CONFORMATIONAL DATABASE POTENTIAL FOR PROTEINS AND NUCLEIC
ACIDS (KUSZEWSKI ET AL. (1996) PROTEIN SCI 5, 1067 - 1080
AND (1997) J. MAGN. RESON. 125, 171-177)
THE 3D STRUCTURE OF THE COMPLEX OF THE WILD TYPE AREA
DBD-DNA COMPLEX WAS SOLVED BY MULTI-DIMENSIONAL
HETERONUCLEAR-EDITED AND -FILTERED NMR IS BASED ON THE
FOLLOWING 1098 EXPERIMENTAL RESTRAINTS
(A) PROTEIN: 119 SEQUENTIAL (|I-J|=1), 49 SHORT RANGE (1
< |I-J| >=5), 68 LONG RANGE (|I-J|>5), AND 64 INTRARESIDUE
APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; NULL 124
TORSION ANGLE RESTRAINTS (61 PHI, 8 PSI, 39 CHI1, 15 CHI2,
AND 1 CHI3), 41 THREE-BOND HN-HA COUPLING CONSTANT
RESTRAINTS; NULL 77 (41 CALPHA AND 36 CBETA) 13C CHEMICAL
SHIFT RESTRAINTS; NULL 48 RESIDUAL N-H DIPOLAR COUPLING
RESTRAINTS; 20 DISTANCE RESTRAINTS FOR 10 BACKBONE
HYDROGEN BONDS.
(B) DNA: 75 INTRARESIDUE, 115 SEQUENTIAL INTRASTRAND AND
20 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; 66
DISTANCES FOR WATSON-CRICK BASE PAIR HYDROGEN BONDS; 170
TORSION ANGLE RESTRAINTS FOR THE DNA BACKBONE COVERING
VALUES CHARACTERISTIC OF BOTH A AND B DNA.
(C) 48 INTERMOLECULAR INTERPROTON DISTANCE RESTRAINTS
(D) 2 INTERMOLECULAR DISTANCE RESTRAINTS TO PHOSPHATES
(E) 8 'REPULSIVE' RESTRAINTS
(F) 4 DISTANCE RESTRAINTS FOR 2 INTERMOLECULAR H-BONDS
BETWEEN ARG 24 AND BASE OF GUA5.
THE FOLLOWING TWO SETS OF COORDINATES DEFINE THE PRINCIPAL
AXIS OF THE MAGNETIC SUSCEPTIBILITY TENSOR:
MODEL 1
POINT 1 102.092-193.887-255.981
POINT 2 102.732-192.538-255.651
MODEL 2
POINT 1 86.136-234.098 -40.447
POINT 2 86.796-232.777 -40.050
MODEL 3
POINT 1 134.979-162.786-132.132
POINT 2 135.695-161.464-131.850
MODEL 4
POINT 1 -70.103 -54.685 51.419
POINT 2 -69.500 -53.313 51.726
MODEL 5
POINT 1 135.883-100.066-174.175
POINT 2 136.516 -98.700-173.898
MODEL 6
POINT 1 76.125-132.662-107.324
POINT 2 76.655-131.248-107.078
MODEL 7
POINT 1 149.063-111.077 -36.611
POINT 2 149.663-109.715 -36.255
MODEL 8
POINT 1 122.564 -99.258 13.431
POINT 2 123.265 -97.930 13.723
MODEL 9
POINT 1 89.110 -79.702 -46.597
POINT 2 89.824 -78.392 -46.258
MODEL 10
POINT 1 142.398 -66.526 -89.227
POINT 2 143.080 -65.195 -88.905
MODEL 11
POINT 1 131.492-187.153 13.577
POINT 2 132.170-185.854 14.018
MODEL 12
POINT 1 210.687-129.261-129.735
POINT 2 211.314-127.906-129.402
MODEL 13
POINT 1 115.833-147.381-125.532
POINT 2 116.493-146.040-125.205
MODEL 14
POINT 1 213.481 -97.161 -62.866
POINT 2 214.099 -95.785 -62.612
MODEL 15
POINT 1 47.875-239.077 -96.187
POINT 2 48.454-237.709 -95.820
MODEL 16
POINT 1 123.077-156.502-154.067
POINT 2 123.774-155.182-153.731
MODEL 17
POINT 1 89.571 -78.309 3.456
POINT 2 90.142 -76.928 3.784
MODEL 18
POINT 1 35.762-246.462 -37.437
POINT 2 36.440-245.133 -37.101
MODEL 19
POINT 1 121.519-157.548 -7.594
POINT 2 122.144-156.197 -7.236
MODEL 20
POINT 1 113.586 -86.299-148.635
POINT 2 114.193 -84.935-148.298
MODEL 21
POINT 1 91.562-134.645 -78.697
POINT 2 92.233-133.317 -78.335
MODEL 22
POINT 1 118.977-218.365-122.566
POINT 2 119.576-217.008-122.192
MODEL 23
POINT 1 80.952-182.035 -80.709
POINT 2 81.615-180.694 -80.392
MODEL 24
POINT 1 188.361-123.949-146.548
POINT 2 189.022-122.608-146.225
MODEL 25
POINT 1 114.771-280.049 -48.411
POINT 2 115.463-278.730 -48.065
MODEL 26
POINT 1 161.250-143.808 74.628
POINT 2 161.956-142.504 75.004
MODEL 27
POINT 1 143.106-116.338 -57.993
POINT 2 143.761-114.989 -57.690
MODEL 28
POINT 1 114.944-162.825 -21.630
POINT 2 115.575-161.468 -21.310
MODEL 29
POINT 1 89.010-134.313-122.747
POINT 2 89.573-132.932-122.407
MODEL 30
POINT 1 81.718-198.065 -81.738
POINT 2 82.448-196.759 -81.416
MODEL 31
POINT 1 177.911-171.893 -37.695
POINT 2 178.512-170.518 -37.399
MODEL 32
POINT 1 100.216-159.685-185.688
POINT 2 100.906-158.386-185.268
MODEL 33
POINT 1 64.235-177.747 -56.722
POINT 2 64.894-176.431 -56.302
MODEL 34
POINT 1 237.150 -92.701 -2.650
POINT 2 237.781 -91.352 -2.296
MODEL 35
POINT 1 91.957-116.106 -54.093
POINT 2 92.589-114.744 -53.797 | X-PLOR |
