Facilitated Dissociation Kinetics of Dimeric Nucleoid-Associated Proteins Follow a Universal Curve

Abstract

Recent experimental work has demonstrated facilitated dissociation of certain nucleoid-associated proteins that exhibit an unbinding rate that depends on the concentration of freely diffusing proteins or DNA in solution. This concentration dependence arises due to binding competition with these other proteins or DNA. The identity of the binding competitor leads to different qualitative trends, motivating an investigation to understand observed differences in facilitated dissociation. We use a coarse-grained simulation that takes into account the dimeric nature of many nucleoid-associated proteins by allowing an intermediate binding state. The addition of this partially bound state allows the protein to be unbound, partially bound, or fully bound to a DNA strand, leaving opportunities for other molecules in solution to participate in the unbinding mechanism. Previous models postulated symmetric binding energies for each state of the coarse-grained protein corresponding to the symmetry of the dimeric protein; this model relaxes this assumption by assigning different energies for the different steps in the unbinding process. Allowing different unbinding energies not only has equilibrium effects on the system, but kinetic effects as well. We were able to reproduce the unbinding trends seen experimentally for both DNA and protein competitors. All trends collapse to a universal curve regardless of the unbinding energies used or the identity of the dissociation facilitator, suggesting that facilitated dissociation can be described with a single set of scaling parameters that are related to the energy landscape and geometric nature of the competitors.

Effects of electrostatic interactions on ligand dissociation kinetics

“…However, high non-electrostatic binding strengths also enhance the separation of bound and semi-bound states of the ligands. This allows clearer observation of FD [23,24].…”

“…Besides univalent salt ions, an excess amount of free ligands in solution can also facilitate dissociation of a bound ligand by decreasing the lifetime of the ligand on the binding site [19][20][21][22][23][24][25][26][27]. The free ligands can be identical to the initially bound ligand [21,22,[27][28][29][30].…”

Force-dependent facilitated dissociation can generate protein-DNA catch bonds

“…We adapt a coarse-grained Brownian dynamics simulation model for DNA-binding proteins binding that demonstrates both spontaneous and facilitated dissociation ( Fig. 1B) (53,87). DNA is represented by a strand of N = 100 beads, indexed by i, of radius a = 4 nm at positions r i .…”

“…The binding state of a DNA bead, denoted by Ω i , is updated with a Monte Carlo step everyτ M C = 0.05. This time step is chosen to ensure that if an (implicit) protein is found to have diffused so that it is near the DNA binding site, the subsequent binding time, τ b , matches the diffusion time, τ D , of a single bead (53). A random number, 0 ≤ ζ < 1, is generated, and for DNA site i in state Ω i = A, the binding update occurs as follows:…”

“…We develop a coarse-grained simulation model and a corresponding theoretical model for DNA-bending proteins interacting with DNA, and we explore their force-dependent facilitated dissociation kinetics in the geometry of a common in vitro single-molecule experiment ( Fig. 1B) (51,53,87). Within the model, we identify several distinct types of force-dependent dissociation kinetics: classical slip bonds, catch bonds, delayed onset catch bonds, and force-insensitive bonds.…”