Sun et al. 10.1073/pnas.0408867102. |
Fig. 7.
Total energy and bending energy of the solenoid model with parallel nucleosomes as a function of Monte Carlo (MC) simulation steps at 200 mM salt concentration.Fig. 8.
Distributions of q and f of the nucleosomal array at different monovalent salt concentrations.Table 3. Parameters used in the model of nucleosomal array
Parameter | Description | Value |
l 0 | Equilibrium segment length | 3.0 nm |
h | Stretching constant | 5000 kBT/l02 |
C | Twisting constant | 3.0 × 10−12 erg·nm |
g | Bending constant | lp ·kBT/l0 |
lp | Elastic bending persistence length of DNA | 50 nm |
θ 0 | Angular separation between linker segments | 90° |
r 0 | Radius of wound DNA supercoiled | 4.8 nm |
2ω 0 | Width of wound DNA supercoiled | 3.6 nm |
k ex | Excluded volume parameter | 0.001 kBT |
σ 1 | Core/linker excluded volume parameter | 2.5 nm |
σ 2 | Core/core excluded volume parameter | 1.5 nm |
Table 4. Geometrical values of nucleosomal array obtained from MC simulations at different salt concentrations
Salt, mM | Radius of gyration, nm | θ, ° | f, ° |
10 | 41 ± 3 | 64 ± 15 | 147 ± 30 |
30 | 31 ± 3 | 60 ± 22 | 109 ± 39 |
50 | 24 ± 3 | 48 ± 23 | 82 ± 35 |
100 | 19 ± 1 | 50 ± 21 | 56 ± 34 |
200 | 19 ± 1 | 41 ± 17 | 58 ± 39 |
Values are ±SD.
Table 5. Energy components at different salt concentrations
Salt, | Stretching, | Bending, | Twisting, | van der Waals, | Electrostatics, | Total, |
mM | kcal/mol | kcal/mol | kcal/mol | kcal/mol | kcal/mol | kcal/mol |
10 | 25 ± 4 | 86 ± 7 | 24 ± 4 | 7 ± 2 | 3 ± 5 | 145 ± 8 |
30 | 25 ± 4 | 75 ± 5 | 24 ± 4 | 10 ± 3 | −48 ± 8 | 86 ± 9 |
50 | 25 ± 4 | 70 ± 5 | 28 ± 4 | 14 ± 3 | −86 ± 8 | 51 ± 10 |
100 | 25 ± 4 | 60 ± 5 | 25 ± 4 | 19 ± 4 | −108 ± 10 | 22 ± 10 |
200 | 25 ± 4 | 57 ± 5 | 26 ± 4 | 24 ± 4 | −117 ± 8 | 16 ± 9 |
Values are ±SD.