Hi, I am analyzing a protein-DNA complex in which DNA is severely curved. The protein could constrain negative DNA supercoils in vitro and I am trying to find some clues to the structural basis of DNA supercoiling from the parameters of DNA calculated by 3dna (listed as following).
Is it possible to infer whether the supercoils come from DNA unwinding or writhing (e.g., the DNA fragment in nucleosome) from these parameters? If so, how to make it? And the DNA has an average h-twist value of 35.29 and thus a h=(360/35.29)=10.20 bp/turn. Does it means that the DNA is over-twisted, since h is less than 10.5 bp/turn?
Thanks
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3DNA (v1.5, Nov. 2002) by Xiang-Jun Lu at Wilma K. Olson's Lab.
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1. The list of the parameters given below correspond to the 5' to 3' direction
of strand I and 3' to 5' direction of strand II.
2. All angular parameters, except for the phase angle of sugar pseudo-
rotation, are measured in degrees in the range of [-180, +180], and all
displacements are measured in Angstrom units.
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RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)
Strand I Strand II Helix
1 (0.006) B:.101_:[.DG]G-----C[.DC]:.116_:C (0.005) |
2 (0.012) B:.102_:[.DT]T-----A[.DA]:.115_:C (0.007) |
3 (0.012) B:.103_:[.DA]A-----T[.DT]:.114_:C (0.010) |
4 (0.013) B:.104_:[.DA]A-----T[.DT]:.113_:C (0.011) |
5 (0.007) B:.105_:[.DT]T-----A[.DA]:.112_:C (0.010) |
6 (0.008) B:.106_:[.DT]T-----A[.DA]:.111_:C (0.008) |
7 (0.008) B:.107_:[.DA]A-----T[.DT]:.110_:C (0.007) |
8 (0.003) B:.108_:[.DC]C-----G[.DG]:.109_:C (0.008) |
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Detailed H-bond information: atom-name pair and length [ON]
1 G-----C [3] O6 - N4 3.04 N1 - N3 2.96 N2 - O2 2.83
2 T-----A [2] N3 - N1 2.64 O4 - N6 2.96
3 A-----T [2] N6 - O4 2.98 N1 - N3 2.70
4 A-----T [2] N6 - O4 3.02 N1 - N3 2.80
5 T-----A [2] N3 - N1 2.77 O4 - N6 3.11
6 T-----A [2] N3 - N1 2.76 O4 - N6 2.94
7 A-----T [2] N6 - O4 2.96 N1 - N3 2.85
8 C-----G [3] O2 - N2 2.70 N3 - N1 2.86 N4 - O6 2.93
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Overlap area in Angstrom^2 between polygons defined by atoms on successive
bases. Polygons projected in the mean plane of the designed base-pair step.
Values in parentheses measure the overlap of base ring atoms only. Those
outside parentheses include exocyclic atoms on the ring. Intra- and
inter-strand overlap is designated according to the following diagram:
i2 3' 5' j2
/| |
| |
Strand I | | II
| |
| |
| |/
i1 5' 3' j1
step i1-i2 i1-j2 j1-i2 j1-j2 sum
1 GT/AC 6.35( 1.96) 0.00( 0.00) 0.00( 0.00) 4.55( 2.68) 10.90( 4.64)
2 TA/TA 6.08( 1.15) 0.00( 0.00) 0.00( 0.00) 4.32( 0.15) 10.40( 1.30)
3 AA/TT 4.44( 2.23) 0.00( 0.00) 0.00( 0.00) 4.94( 0.85) 9.39( 3.08)
4 AT/AT 6.30( 2.60) 0.00( 0.00) 0.00( 0.00) 6.15( 2.46) 12.45( 5.06)
5 TT/AA 7.53( 1.30) 0.00( 0.00) 0.00( 0.00) 6.47( 4.32) 14.00( 5.62)
6 TA/TA 1.38( 0.00) 0.00( 0.00) 0.00( 0.00) 1.68( 0.00) 3.05( 0.00)
7 AC/GT 4.96( 3.39) 0.00( 0.00) 0.00( 0.00) 4.71( 1.07) 9.67( 4.46)
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Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in
the coordinate system of the given structure
bp Ox Oy Oz Nx Ny Nz
1 G-C 12.62 21.58 20.04 -0.13 -0.82 -0.56
2 T-A 12.06 19.25 18.00 -0.13 -0.81 -0.57
3 A-T 11.05 16.20 17.25 -0.01 -0.86 -0.50
4 A-T 10.44 10.39 17.09 0.24 -0.91 0.35
5 T-A 11.26 7.86 18.38 0.15 -0.89 0.44
6 T-A 11.48 4.89 19.71 0.11 -0.78 0.62
7 A-T 11.67 1.50 20.79 0.16 -0.80 0.57
8 C-G 11.36 -1.21 22.97 0.18 -0.79 0.58
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Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 G-C -0.45 -0.09 0.09 0.54 -5.10 1.29
2 T-A -0.05 -0.26 -0.07 6.55 -6.73 4.61
3 A-T 0.12 -0.15 0.19 24.95 -9.76 4.64
4 A-T 0.05 -0.08 -0.31 -18.35 2.76 3.14
5 T-A -0.18 -0.10 0.09 -0.15 -4.90 6.04
6 T-A -0.10 -0.16 -0.22 10.46 -1.22 1.56
7 A-T 0.12 -0.10 0.18 9.68 -10.37 -2.26
8 C-G 0.38 -0.18 0.02 6.90 -7.15 1.29
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.01 -0.14 -0.00 5.07 -5.31 2.54
s.d. 0.24 0.06 0.18 12.23 4.35 2.63
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Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 GT/AC -0.25 -0.27 3.13 0.87 -0.36 30.76
2 TA/TA 0.22 1.27 3.03 1.86 8.58 26.99
3 AA/TT -0.06 1.39 5.67 -0.67 52.71 20.29
4 AT/AT 0.13 -0.28 2.95 -4.54 6.16 22.16
5 TT/AA -0.29 0.44 3.22 5.15 11.21 23.56
6 TA/TA -0.16 1.20 3.35 -1.96 -3.80 46.76
7 AC/GT 0.78 -0.48 3.37 0.51 -1.07 34.74
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. 0.05 0.47 3.53 0.17 10.49 29.32
s.d. 0.37 0.82 0.96 3.05 19.41 9.19
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Local base-pair helical parameters
step X-disp Y-disp h-Rise Incl. Tip h-Twist
1 GT/AC -0.45 0.63 3.13 -0.68 -1.63 30.77
2 TA/TA 0.64 -0.02 3.28 17.79 -3.85 28.35
3 AA/TT -5.03 -0.01 3.41 70.43 0.89 56.22
4 AT/AT -2.55 -1.68 2.69 15.46 11.40 23.43
5 TT/AA -2.02 1.99 2.99 25.36 -11.64 26.55
6 TA/TA 1.82 0.04 3.25 -4.77 2.47 46.94
7 AC/GT -0.63 -1.23 3.40 -1.79 -0.86 34.76
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -1.17 -0.04 3.16 17.40 -0.46 35.29
s.d. 2.26 1.20 0.26 26.03 6.94 11.97
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Structure classification:
This is a right-handed nucleic acid structure
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lambda: virtual angle between C1'-YN1 or C1'-RN9 glycosidic bonds and the
base-pair C1'-C1' line
C1'-C1': distance between C1' atoms for each base-pair
RN9-YN1: distance between RN9-YN1 atoms for each base-pair
RC8-YC6: distance between RC8-YC6 atoms for each base-pair
bp lambda(I) lambda(II) C1'-C1' RN9-YN1 RC8-YC6
1 G-C 53.9 57.6 10.7 9.0 9.9
2 T-A 56.4 57.4 10.2 8.6 9.7
3 A-T 57.8 56.4 10.1 8.5 9.6
4 A-T 56.8 56.9 10.4 8.7 9.8
5 T-A 56.1 59.7 10.3 8.8 9.9
6 T-A 55.1 55.1 10.5 8.8 9.8
7 A-T 54.1 53.1 10.7 8.9 9.8
8 C-G 55.7 54.1 10.6 8.9 9.8
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Classification of each dinucleotide step in a right-handed nucleic acid
structure: A-like; B-like; TA-like; intermediate of A and B, or other cases
step Xp Yp Zp XpH YpH ZpH Form
1 GT/AC -3.34 9.13 -0.26 -3.78 9.12 -0.37 B
2 TA/TA -3.96 8.37 -1.67 -3.36 8.49 0.82 B
3 AA/TT -2.69 8.83 -0.20 -7.13 3.48 8.11
4 AT/AT -3.51 9.24 -0.46 -6.12 9.03 2.03 B
5 TT/AA -3.56 9.17 -0.77 -5.55 8.66 3.10 B
6 TA/TA -2.33 8.54 -0.27 -0.62 8.50 -0.92 B
7 AC/GT -3.00 9.15 -0.14 -3.60 9.15 -0.41 B
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Minor and major groove widths: direct P-P distances and refined P-P distances
which take into account the directions of the sugar-phosphate backbones
(Subtract 5.8 Angstrom from the values to take account of the vdw radii
of the phosphate groups, and for comparison with FreeHelix and Curves.)
Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of
Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343.
Minor Groove Major Groove
P-P Refined P-P Refined
1 GT/AC --- --- --- ---
2 TA/TA --- --- --- ---
3 AA/TT 21.4 --- 18.1 ---
4 AT/AT 20.0 18.2 19.2 17.8
5 TT/AA 16.7 --- 17.2 ---
6 TA/TA --- --- --- ---
7 AC/GT --- --- --- ---
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Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 3.05(1.38)
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Main chain and chi torsion angles:
Note: alpha: O3'(i-1)-P-O5'-C5'
beta: P-O5'-C5'-C4'
gamma: O5'-C5'-C4'-C3'
delta: C5'-C4'-C3'-O3'
epsilon: C4'-C3'-O3'-P(i+1)
zeta: C3'-O3'-P(i+1)-O5'(i+1)
chi for pyrimidines(Y): O4'-C1'-N1-C2
chi for purines(R): O4'-C1'-N9-C4
Strand I
base alpha beta gamma delta epsilon zeta chi
1 G --- --- 64.2 139.7 173.0 -98.2 -101.4
2 T -79.7 -178.8 65.7 141.6 -92.2 -110.8 -108.0
3 A 44.1 -118.3 -163.7 78.9 -152.3 -77.1 -108.4
4 A -55.3 -166.5 51.7 145.7 -179.4 -91.4 -92.9
5 T -74.6 166.0 59.8 89.2 -163.3 -88.2 -126.8
6 T -58.3 169.8 45.2 144.4 -123.1 169.8 -85.9
7 A -58.4 136.5 49.9 136.4 -165.5 -94.8 -105.6
8 C -54.2 163.2 33.4 87.3 --- --- -129.2
Strand II
base alpha beta gamma delta epsilon zeta chi
1 C -59.3 159.3 52.0 84.9 --- --- -132.6
2 A -56.2 173.3 43.7 124.7 -175.6 -101.0 -97.6
3 T -62.4 -174.8 57.6 121.1 -170.5 -93.4 -106.8
4 T -71.4 175.2 46.9 81.2 -145.2 -85.3 -116.6
5 A -72.2 164.0 51.5 92.3 -176.6 -79.6 -119.8
6 A -66.2 -160.2 53.5 141.7 -166.8 -89.6 -96.4
7 T -72.1 -164.1 56.1 132.0 170.1 -100.3 -108.7
8 G --- --- -156.5 152.2 175.2 -98.8 -115.2
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Sugar conformational parameters:
Note: v0: C4'-O4'-C1'-C2'
v1: O4'-C1'-C2'-C3'
v2: C1'-C2'-C3'-C4'
v3: C2'-C3'-C4'-O4'
v4: C3'-C4'-O4'-C1'
tm: amplitude of pseudorotation of the sugar ring
P: phase angle of pseudorotation of the sugar ring
Strand I
base v0 v1 v2 v3 v4 tm P Puckering
1 G -16.2 29.8 -31.7 23.4 -4.7 32.2 169.6 C2'-endo
2 T -38.2 46.7 -37.8 17.5 12.5 45.9 145.5 C2'-endo
3 A -13.9 -12.8 32.7 -41.9 35.3 41.4 37.8 C4'-exo
4 A -4.7 23.7 -32.8 30.5 -16.5 33.4 190.4 C3'-exo
5 T -43.9 22.5 5.7 -31.3 46.7 47.3 83.0 O4'-endo
6 T -36.5 47.9 -40.3 21.1 9.4 46.7 149.6 C2'-endo
7 A -16.9 27.4 -27.6 18.8 -1.4 28.7 164.2 C2'-endo
8 C -26.1 2.7 19.9 -35.3 38.6 38.8 59.2 C4'-exo
Strand II
base v0 v1 v2 v3 v4 tm P Puckering
1 C -30.9 7.3 17.6 -36.3 42.2 41.8 65.1 C4'-exo
2 A -24.4 28.0 -21.0 7.6 10.5 27.7 139.5 C1'-exo
3 T -20.2 21.0 -14.8 3.6 10.4 21.5 133.5 C1'-exo
4 T -25.9 -0.4 24.3 -39.9 41.4 42.4 55.0 C4'-exo
5 A -34.2 15.6 7.3 -27.3 38.7 38.3 79.0 O4'-endo
6 A -7.7 22.5 -28.3 24.2 -10.6 28.3 183.0 C3'-exo
7 T -24.9 32.7 -28.4 14.9 6.2 32.5 150.8 C2'-endo
8 G -10.0 30.0 -37.3 32.5 -14.4 37.4 183.5 C3'-exo
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Same strand P--P and C1'--C1' virtual bond distances
Strand I Strand II
base P--P C1'--C1' base P--P C1'--C1'
1 G/T --- 4.9 1 C/A 6.8 4.3
2 T/A 6.7 4.9 2 A/T 6.7 4.9
3 A/A 7.0 6.4 3 T/T 5.5 6.5
4 A/T 6.9 4.5 4 T/A 6.4 5.1
5 T/T 6.3 5.2 5 A/A 6.7 4.4
6 T/A 6.7 5.1 6 A/T 6.7 5.3
7 A/C 6.8 4.5 7 T/G --- 5.2
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Helix radius (radial displacement of P, O4', and C1' atoms in local helix
frame of each dimer)
Strand I Strand II
step P O4' C1' P O4' C1'
1 GT/AC 10.3 7.1 6.7 9.5 6.0 5.5
2 TA/TA 8.9 6.1 5.2 9.5 6.2 5.5
3 AA/TT 7.5 8.4 7.9 8.3 8.5 8.1
4 AT/AT 9.7 6.9 6.2 12.2 9.3 8.5
5 TT/AA 12.1 9.2 8.4 8.5 6.0 5.2
6 TA/TA 8.6 5.8 5.4 8.4 5.4 5.2
7 AC/GT 9.0 5.6 5.1 10.6 7.7 7.3
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Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
for each dinucleotide step
bp Px Py Pz Hx Hy Hz
1 GT/AC 12.94 20.61 18.63 -0.10 -0.81 -0.57
2 TA/TA 11.12 17.96 17.25 -0.24 -0.92 -0.30
3 AA/TT 12.02 13.05 21.41 -0.83 -0.51 0.22
4 AT/AT 8.86 9.60 19.91 -0.04 -0.98 0.18
5 TT/AA 11.85 7.51 21.52 -0.33 -0.83 0.45
6 TA/TA 13.12 3.09 19.63 0.20 -0.75 0.64
7 AC/GT 11.36 -0.66 20.85 0.15 -0.79 0.60
Topic: How to determine DNA topology form parameters (Read 6204 times)