Protein structural transitions critically transform the network connectivity and viscoelasticity of RNA-binding protein condensates but RNA can prevent it

Abstract

Biomolecular condensates, some of which are liquid-like during health, can age over time becoming gel-like pathological systems. One potential source of loss of liquid-like properties during ageing of RNA-binding protein condensates is the progressive formation of inter-protein β-sheets. To bridge microscopic understanding between accumulation of inter-protein β-sheets over time and the modulation of FUS and hnRNPA1 condensate viscoelasticity, we develop a multiscale simulation approach. Our method integrates atomistic simulations with sequence-dependent coarse-grained modelling of condensates that exhibit accumulation of inter-protein β-sheets over time. We reveal that inter-protein β-sheets notably increase condensate viscosity but does not transform the phase diagrams. Strikingly, the network of molecular connections within condensates is drastically altered, culminating in gelation when the network of strong β-sheets fully percolates. However, high concentrations of RNA decelerate the emergence of inter-protein β-sheets. Our study uncovers molecular and kinetic factors explaining how the accumulation of inter-protein β-sheets can trigger liquid-to-solid transitions in condensates, and suggests a potential mechanism to slow such transitions down.

Repulsive interaction and secondary structure of highly charged proteins in regulating biomolecular condensation

“…Therefore, we speculate that the driving force for the other Hero protein's anti-aggregation function may also be the strong electrostatic repulsion. Interestingly RNA, which is also highly charged, has also been shown to induce concentration-dependent reentrant phase behaviors of many RNA-binding proteins [27,47,67,68]. Particularly, one recent computational study shows that a high concentration of RNA can slow down the ageing of condensates formed by proteins composed of β-sheet secondary structures [68].…”

“…Interestingly RNA, which is also highly charged, has also been shown to induce concentration-dependent reentrant phase behaviors of many RNA-binding proteins [27,47,67,68]. Particularly, one recent computational study shows that a high concentration of RNA can slow down the ageing of condensates formed by proteins composed of β-sheet secondary structures [68]. Although the computational models and target systems are different, the results of RNA's deceleration effect are highly consistent with Hero11's anti- interactions to the framework of the sticker-spacer or scaffold-ligand models can extend their applicability to describe formation, regulation, or destruction of biomolecular condensation.…”

Time-dependent material properties of ageing biomolecular condensates from different viscoelasticity measurements in molecular dynamics simulations

“…In that respect, computer simulations are a powerful tool to uncover the molecular mechanisms that explain the changes in viscosity within biomolecular condensates over time 31,51,63,[73][74][75][76] . From atomistic force fields [77][78][79][80][81][82] to coarse-grained (CG) models [83][84][85][86][87][88][89][90][91][92] , including lattice-based simulations [93][94][95] and mean-field theory [96][97][98] , computer simulations have significantly contributed to elucidating factors behind condensate phaseseparation such as protein and RNA length [99][100][101] , amino acid patterning 91,[102][103][104][105] , multivalency 35,[106][107][108][109] , conformational flexibility 89,110 or multicomponent composition 90,111,…”

“…Remarkably, coarse-grained models have uncovered the impact of enhancement of inter-protein interactions in condensate rigidification 51,74 , as well as the formation of kinetically-arrested multiphase condensates from single-component droplets 73,113 . Nevertheless, further insights on the molecular driving forces behind condensate maturation-for instance triggered by inter-protein disordered-to-order structural transitions 50,75,114 , amino acid sequence mutations 115 or relevant variations on the applied thermodynamic conditions 116 -are urgently needed.…”

Surfactants or scaffolds? RNAs of different lengths exhibit heterogeneous distributions and play diverse roles in RNA-protein condensates

“…Moreover, key features of LLPS, such as valency [62,63], topology [64,65] or binding affinity [66][67][68] can be precisely controlled. In that sense, Molecular Dynamics (MD) simulations have proved useful for the study of biomolecular condensates at various levels of resolution: ranging from atomistic force fields to lattice-based physical models [16,51,[69][70][71][72].…”