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Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers

Fig 4

Equilibrium coverage and extension of the polymer in the presence of ligands.

(Panel A): Equilibrium coverage of a polymer as function of the tension F, assuming that the ligands bind to the polymer in a unique mode. The elastic contribution to the free energy of the naked monomers was estimated using the Marko-Siggia formula Eq (2). The equilibrium coverage was computed using both the ideal gas [Eq (18)] and the Tonks gas [Eq (20)] models. We also consider that the maximum possible coverage is 100%. (Panel B): Equilibrium extension of the covered polymer as function of the pulling force, resulting from employing the coverage of Panel A in the force-extension relation Eq (9). In this figure the values of the parameters of the polymer are of the order of those of ssDNA [24]: N = 5080, d0 = 0.57 nm, Lp = 0.715 nm, K0 = 700 pN and KBT = 4.11 pN nm, while, for the ligands, we consider two different binding modes, with parameters of the order of those of E. Coli SSB [47,59] and HmtSSB proteins [61]: m = 65 or 35, a = 5 nm and ϵb = m × 0.5 × KBT.

Fig 4