Abstract
Ion-mediated interactions between polyelectrolytes (PEs) are crucial to the properties of flexible biopolymers such as nucleic acids and proteins but the effect of PE flexibility on such interactions has not been explicitly addressed until now. In this work, the potentials of mean force (PMFs) between like-charged PEs with different bending flexibility have been investigated by Monte Carlo simulations and a cylindrical confinement around each PE was involved to model two PEs in an array. We found that in the absence of trivalent salt, the PMFs between like-charged PEs in an array are apparently repulsive while the bending flexibility can visibly decrease the repulsive PMFs. With the addition of high trivalent salt, the PMFs become significantly attractive whereas the attractive PMFs can be apparently weakened by the bending flexibility. Our analyses reveal that the effect of bending flexibility is attributed to the increased PE conformational space, which allows the PEs to fluctuate away to decrease the monovalent ion-mediated repulsion or to weaken the trivalent ion-mediated attraction through disrupting trivalent ion-bridging configuration. Additionally, our further calculations show that the effect of bending flexibility on the ion-mediated interactions is less apparent for PEs without cylindrical confinement.
Highlights
Ion-mediated interactions between polyelectrolytes (PEs) are crucial to the properties of flexible biopolymers such as nucleic acids and proteins but the effect of PE flexibility on such interactions has not been explicitly addressed until now
Such order of the effective separation D is fully consistent with the increase of Δf(r)’s of condensed ions for the four types of PEs and smaller effective separation D between PEs corresponds to larger Δf(r) of condensed ions; see Figs. 2 and 3. This is because more rotatable/bendable PEs have stronger conformation fluctuation and tendency to nonparallel/ bent configurations and have larger effective separations D. Such conformation fluctuation of two like-charged PEs characterized by effective separation D, would definitely affect the effective interactions between them: (i) for low monovalent salt, more rotatable/bendable PEs have larger conformation space to mutually bend/rotate away to avoid strong repulsions between them, and the bending flexibility can visibly decrease the repulsive PMFs; (ii) with added high trivalent salt, the stronger conformation fluctuation for more rotatable/bendable PEs would cause larger effective separation and weaken the effective trivalentmediated like-charge attraction, through decreasing PE-PE correlations and the associated binding of trivalent ions, which will be discussed in more details
In this work, we investigated the ion-mediated interactions between like-charged PEs with different bending flexibility through Monte Carlo simulations
Summary
Ion-mediated interactions between polyelectrolytes (PEs) are crucial to the properties of flexible biopolymers such as nucleic acids and proteins but the effect of PE flexibility on such interactions has not been explicitly addressed until now. We showed the calculated PMFs between two like-charged parallel PEs, between two rotatable PEs, and between two bendable PEs in a PE array for different 3:3 trivalent salt concentrations, through involving a cylindrical confinement around each PE to model two PEs in an array.
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