Effects of electrostatic interactions on ligand dissociation kinetics

Abstract

We study unbinding of multivalent cationic ligands from oppositely charged polymeric binding sites sparsely grafted on a flat neutral substrate. Our molecular dynamics (MD) simulations are suggested by single-molecule studies of protein-DNA interactions. We consider univalent salt concentrations spanning roughly a thousandfold range, together with various concentrations of excess ligands in solution. To reveal the ionic effects on unbinding kinetics of spontaneous and facilitated dissociation mechanisms, we treat electrostatic interactions both at a Debye-Hückel (DH, or 'implicit' ions, i.e., use of an electrostatic potential with a prescribed decay length) level, as well as by the more precise approach of considering all ionic species explicitly in the simulations. We find that the DH approach systematically overestimates unbinding rates, relative to the calculations where all ion pairs are present explicitly in solution, although many aspects of the two types of calculation are qualitatively similar. For facilitated dissociation (FD, acceleration of unbinding by free ligands in solution) explicit ion simulations lead to unbinding at lower free ligand concentrations. Our simulations predict a variety of FD regimes as a function of free ligand and ion concentrations; a particularly interesting regime is at intermediate concentrations of ligands where non-electrostatic binding strength controls FD. We conclude that explicit-ion electrostatic modeling is an essential component to quantitatively tackle problems in molecular ligand dissociation, including nucleicacid-binding proteins.

Facilitated Dissociation of Nucleoid Associated Proteins from DNA in the Bacterial Confinement

“…For instance, if we compare the SD (no unbound Fis) and the FD with 20 μ M of unbound Fis in Figure 2A and B for two different binding energies, the low-affinity case (i.e., u = 9 k B T ) is affected by the presence of unbound proteins more strongly as compared to the case where the protein binds tightly to DNA (i.e., u = 12 k B T ). This affinity-dependent behaviour is consistent with the previous simulation studies [29, 38, 46] and theoretical predictions [42], suggesting that low-affinity proteins can be affected from concentration variations more drastically. This behaviour is also in accord with the SD experiments on a smaller yeast TF protein, NHP6A, which binds to DNA with a lower affinity than Fis, but its FD response is at least a factor of two stronger under the equivalent concentration changes [7].…”

“…The total number of binding sites along the DNA chain is n 0 = 120. This number is lower than the consensus sequences determined [41] but high enough to perform statistical analyses for unbinding kinetics [42]. At the beginning of a simulation (i.e., t = 0), each specific binding site, which is 1000 bp apart from the nearest neighbouring sites, is occupied by a single protein.…”

“…Initially, bound proteins are positioned near promoter regions (red beads represent the binding sites in Figure 1A-C) that are spaced evenly along the DNA polymer. Given the smaller size of our model genome, the number of binding sites is chosen as n 0 = 120, which is lower than the consensus sequences determined [37] but high enough to perform statistical analyses of unbinding kinetics [38]. To monitor the concentration-dependent dissociation, a prescribed concentration of initially free proteins, c f , are added at random positions in the simulation boxes in addition to the n 0 = 120 initially bound proteins.…”

“…Previous MD simulations used a two-bead model for simulating Fis protein [7, 29, 38]. Although the twobead model was sufficient to simulate multivalency, there is no energy penalty for configurational changes of the protein [41].…”

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

“…However, with one species of "light" protein and one species of "dark" (competitor) protein, dissociation rates can be measured by observing the decay of the fluorescence signal along the tethered DNA. This experiment can probe kinetics at various tensile forces and competitor concentrations, and other physical variables, such as ionic concentration or composition, can be varied to tune transition energy barriers (22,29,65,95) or preferred binding geometry (89).…”