TABLE 2.

Elastic, geometric, and electrostatic parameters used in the DNA/protein model

Parameter	Definition	Value
N	Number of the vertices in the circular DNA model	176 (5.28 kbp)
l0	Equilibrium segment length	10 nm
le	Kuhn statistical length of DNA	100 nm
k	Number of elastic segment for each Kuhn statistical length	10
C	Twisting rigidity constant	3.0 × 10−19 erg·cm
kB	Boltzmann's constant	1.38 × 10−23 J/K
T	Absolute temperature	298 K
g	Bending rigidity constant of average DNA	pkBT/l0
h	Stretching rigidity constant
Δt	Time step for Brownian dynamic simulations	600 ps
d0	Radial distance criterion for site juxtaposition	10 nm
cS	Monovalent salt concentration	0.2 M
	Vertices to which a Hin dimer can bind	1, 34
	Vertices to which a Fis dimer can bind	5, 6
	Equilibrium tilt-like and roll-like bends on an ihin vertex by a Hin dimer	−18°, 0°
	Equilibrium tilt-like and roll-like bends on an ifis vertex by a Fis dimer	60°, 0°
	Computational tilt-like and roll-like bending rigidity for ihin vertices	g, g
	Computational tilt-like and roll-like bending rigidity for ifis vertices	3.0 g, 3.0 g
κ	Inverse Debye length (salt-dependent, here for 0.2 M)	1.477 nm−1
λ	Effective linear charge density of double helix (here for 0.2 M)	40.9 e/nm
ε	Relative dielectric constant of aqueous medium	80
	Number of effective charges for a DNA segment, a Hin-dimer/DNA complex, and a Fis-dimer/DNA complex, respectively	5, 200, 100
μ	Computational short-range repulsion force	35 pN
ρ0	Hydrodynamic radius of a DNA segment of l0	2.24 nm