| 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 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 EXPERIMENTAL RESTRAINTS ARE GIVEN IN
R2GATMR.
THE STRUCTURES ARE BASED ON A TOTAL OF 1830 EXPERIMENTAL
NMR RESTRAINTS COMPRISING: 1444 INTERPROTON DISTANCE
RESTRAINTS DERIVED FROM NOE MEASUREMENTS; 296 TORSION
ANGLE RESTRAINTS; 90 RESIDUAL DIPOLAR COUPLINGS (52 N-H
AND 38 C-H). THE NOE RESTRAINTS ARE SUBDIVIDED AS FOLLOWS:
(A) WITHIN THE PROTEIN: 242 INTERRESIDUE SEQUENTIAL
(|I-J|=1); 161 INTERRESIDUE SHORT RANGE (1(LESS
THAN)|I-J|(LESS THAN)=5); 182 INTERRESIDUE LONG RANGE
(|I-J|(GREATER THAN)5); AND 334 INTRARESIDUE. (B) WITHIN
THE DNA: 157 INTRARESIDUE; 180 SEQUENTIAL INTRASTRAND; 34
INTERSTRAND; AND 37 H-BONDS (C) BETWEEN PROTEIN AND DNA:
117. THE TORSION ANGLE RESTRAINTS ARE SUBDIVIDED AS
FOLLOWS: 144 ANGLES FOR THE PROTEIN (58 PHI, 56 PSI, 26
CHI1 AND 4 CHI2) AND 152 FOR THE DNA. THE TORSION ANGLE
RESTRAINTS FOR THE DNA COMPRISE LOOSE RESTRAINTS ON THE
BACKBONE TORSION ANGLES ALPHA, BETA, GAMMA, EPSILON AND
ZETA TO PREVENT PROBLEMS ASSOCIATED WITH LOCAL MIRROR
IMAGES.
THE FOLLOWING TWO SETS OF COORDINATES DEFINE THE PRINCIPAL
AXIS OF THE MAGNETIC SUSCEPTIBILITY TENSOR:
MODEL 1
POINT 1 0.378 -50.982 -38.862
POINT 2 0.472 -49.836 -37.853
MODEL 2
POINT 1 9.054 -65.114 92.057
POINT 2 9.125 -63.952 93.051
MODEL 3
POINT 1 159.392 0.215 -60.612
POINT 2 159.391 1.382 -59.623
MODEL 4
POINT 1 1.446 -13.082 18.709
POINT 2 1.560 -11.891 19.663
MODEL 5
POINT 1 36.350 -69.900 58.948
POINT 2 36.375 -68.721 59.923
MODEL 6
POINT 1 126.484 -20.411 -50.611
POINT 2 126.594 -19.266 -49.602
MODEL 7
POINT 1 88.897 -14.889 116.035
POINT 2 89.009 -13.746 117.045
MODEL 8
POINT 1 33.575 14.467 0.174
POINT 2 33.645 15.627 1.168
MODEL 9
POINT 1 83.455-111.061-109.708
POINT 2 83.524-109.891-108.724
MODEL 10
POINT 1 54.992 12.813 -1.197
POINT 2 55.119 13.958 -0.188
MODEL 11
POINT 1 -5.927 -98.366 8.457
POINT 2 -5.849 -97.197 9.441
MODEL 12
POINT 1 -16.731 -79.619 -28.952
POINT 2 -16.693 -78.486 -27.923
MODEL 13
POINT 1 69.885 -59.142 22.056
POINT 2 69.992 -57.968 23.033
MODEL 14
POINT 1 60.771 80.864 -67.242
POINT 2 60.765 82.035 -66.258
MODEL 15
POINT 1 88.367-100.303 26.657
POINT 2 88.485 -99.179 27.688
MODEL 16
POINT 1 71.362 19.714 75.498
POINT 2 71.461 20.908 76.450
MODEL 17
POINT 1 55.206 36.123 129.402
POINT 2 55.272 37.358 130.301
MODEL 18
POINT 1 -0.207 63.643 9.656
POINT 2 -0.119 64.869 10.566
MODEL 19
POINT 1 50.329 42.850 -53.654
POINT 2 50.424 44.067 -52.731
MODEL 20
POINT 1 51.532 -39.600 87.552
POINT 2 51.620 -38.437 88.540
MODEL 21
POINT 1 9.452 -38.136 23.088
POINT 2 9.459 -36.990 24.103
MODEL 22
POINT 1 52.844 16.158 -59.776
POINT 2 52.863 17.351 -58.818
MODEL 23
POINT 1 55.060 6.778 -32.793
POINT 2 55.121 7.966 -31.831
MODEL 24
POINT 1 63.527 -10.417 -15.482
POINT 2 63.570 -9.300 -14.436
MODEL 25
POINT 1 43.182 -28.794 21.016
POINT 2 43.233 -27.638 22.017
MODEL 26
POINT 1 93.739 -3.416 28.751
POINT 2 93.856 -2.334 29.826
MODEL 27
POINT 1 106.589 5.146 33.748
POINT 2 106.637 6.346 34.695
MODEL 28
POINT 1 51.597 -15.726 20.577
POINT 2 51.712 -14.540 21.538
MODEL 29
POINT 1 63.361 -27.745 -32.153
POINT 2 63.448 -26.576 -31.169
MODEL 30
POINT 1 -59.343 5.979 38.193
POINT 2 -59.203 7.083 39.244
MODEL 31
POINT 1 -4.120-119.412 -63.274
POINT 2 -4.040-118.211 -62.331
MODEL 32
POINT 1 38.468 -28.280 -19.797
POINT 2 38.602 -27.192 -18.729
MODEL 33
POINT 1 139.677-206.067 -84.072
POINT 2 139.702-204.924 -83.054
MODEL 34
POINT 1 35.819 -48.400 -10.080
POINT 2 35.876 -47.237 -9.088 | X-PLOR |
