Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers
(Panel A) Temporal evolution of the coverage of the polymer during the binding process when there are two binding modes with different temporal scales: a fast mode 1 and a slow mode 2. (Panel B): Temporal evolution of the extension corresponding to the evolution of the coverage shown in panel (a). This figure corresponds to the following set of parameters: kb1 = 1 s−1, kb2 = 5 ∙ 10−2 s−1, kr1 = 0.1 s−1, kr2 = 10−5 s−1, N = 5080, m1 = 65, m2 = 35, d0 = 0.57 nm, Lp = 0.715 nm, K0 = 700 pN, a1 = a2 = 5 nm, KBT = 4.11 pN nm, and F = 5 pN. For the extension contribution of the naked monomers, we have employed the Marko-Siggia implicit formula [Eq (2)].