Combined collapse by bridging and self-adhesion in a prototypical polymer model inspired by the bacterial nucleoid

TL;DR

This study models how bridging interactions and self-attraction jointly cause polymer collapse, revealing regimes of classical and switch-like collapse, and showing that bridging can create stable, multi-domain compartments similar to bacterial nucleoid organization.

Contribution

It introduces a combined polymer model with bridging and self-attraction, elucidating their joint effects on collapse and domain formation, inspired by bacterial chromosome behavior.

Findings

Identifies classical and switch-like collapse regimes.

Shows bridging induces stable multi-domain compartments.

Demonstrates stability of domains with uniform attraction above theta point.

Abstract

Recent experimental results suggest that the E. coli chromosome feels a self-attracting interaction of osmotic origin, and is condensed in foci by bridging interactions. Motivated by these findings, we explore a generic modeling framework combining solely these two ingredients, in order to characterize their joint effects. Specifically, we study a simple polymer physics computational model with weak ubiquitous short-ranged self attraction and stronger sparse bridging interactions. Combining theoretical arguments and simulations, we study the general phenomenology of polymer collapse induced by these dual contributions, in the case of regularly-spaced bridging. Our results distinguish a regime of classical Flory-like coil-globule collapse dictated by the interplay of excluded volume and attractive energy and a switch-like collapse where bridging interaction compete with entropy loss terms from the looped arms of a star-like rosette. Additionally, we show that bridging can induce stable compartmentalized domains. In these configurations, different "cores" of bridging proteins are kept separated by star-like polymer loops in an entropically favorable multi-domain configuration, with a mechanism that parallels micellar polysoaps. Such compartmentalized domains are stable, and do not need any intra-specific interactions driving their segregation. Domains can be stable also in presence of uniform attraction, as long as the uniform collapse is above its theta point.