Polymer Stiffness Regulates Multivalent Binding and Liquid-Liquid Phase Separation

Abstract

Multivalent binding is essential to many biological processes because it builds high affinity bonds by using several weak binding interactions simultaneously. Multivalent polymers have shown promise as inhibitors of toxins and other pathogens, and they are important components in the formation of biocondensates. Explaining how structural features of these polymers change their binding and subsequent control of phase separation is critical to designing better pathogen inhibitors and also to understanding diseases associated with membraneless organelles. In this work, we will examine the binding of a multivalent polymer to a small target. This scenario could represent a polymeric inhibitor binding to a toxic protein or RNA binding to an RNA-binding protein in the case of liquid-liquid phase separation. We use simulation and theory to show that flexible randomcoil polymers bind more strongly than stiff rod-like polymers and that flexible polymers nucleate condensed phases at lower energies than their rigid analogues. We hope these results will provide insight into the rational design of polymeric inhibitors and improve understanding of membraneless organelles.

Multivalent polymers can control phase boundary, dynamics, and organization of liquid-liquid phase separation

“…Phase separation occurs at lower protein target concentrations and lower T T as valency and binding affinity are increased. nucleated a stable condensed phase, used a combination of visual inspection, the Binder cumulant, and a collapse in the R g as described in previous work [16]. We used visual inspection to look for the proportion of 10 runs in which a condensed droplet of targets and polymers persisted for the last quarter of the simulation time.…”

“…Polymers longer than the critical loop length see limited increases in avidity with longer degrees of polymerization. In these phase separation simulations, this results in a relatively small increase in binding avidity when N p is increased from 16 to 64 (and a correspondingly smaller change in the phase boundary) than when N p is increased from 4 to 16.…”

“…Another theoretical study found that the solvation of polymeric linkers between binding sites controls whether polymers form a cross-linked gel with or without phase separation [6]. In previous work, we showed that polymer flexibility or persistence length can change the effective valency and consequently, the phase boundary of multivalent polymers [16]. In this paper, we further build on the understanding that multivalent polymer characteristics can control the thermodynamics of biocondensates by exploring the effect of non-specific versus specific polymer binding interactions, condensed phase nucleation in smaller systems, and the dynamics of the resulting condensed polymer droplets.…”

“…This phase diagram will serve as a control for the effects of mixing polymers and target proteins. This figure is adapted from Zumbro et al with permission from Elsevier [16].…”

Multivalent polymers can control phase boundary, dynamics, and organization of liquid-liquid phase separation

“…Another theoretical study found that the solvation of polymeric linkers between binding sites controls whether polymers form a cross-linked gel with or without phase separation [ 6 ]. In previous work, we showed that polymer flexibility or persistence length can change the effective valency and consequently, the phase boundary of multivalent polymers [ 18 ]. In this paper, we further build on the understanding that multivalent polymer characteristics can control the thermodynamics of biocondensates by exploring the effect of non-specific versus specific polymer binding interactions, condensed phase nucleation in smaller systems, and the dynamics of the resulting condensed polymer droplets.…”