Programmable Viscoelasticity in Protein-RNA Condensates with Disordered Sticker-Spacer Polypeptides

Abstract

The rheological properties of biological matters play a fundamental role in many cell processes. At the organelle level, liquid-liquid phase separation of multivalent proteins and RNAs drives the formation of biomolecular condensates that facilitate dynamic compartmentalization of cellular biochemistry1. With recent advances, it is becoming increasingly clear that the structure and rheological properties of these condensates are critical to their cellular functions2,3. Meanwhile, aberrant liquid-to-solid transitions in some cellular condensates are implicated in neurodegenerative disorders4. Within the limits of two extreme material states, viz., viscous liquid and amorphous or fibrillar solid, there lies a spectrum of materials known as viscoelastic fluids. Viscoelastic fluids behave as an elastic solid at time-scales shorter than their network reconfiguration time but as a viscous fluid at longer time-scales. Viscoelasticity of biomolecular condensates may constitute an adaptive mechanism for sensing mechanical stress and regulating biochemical processes5. From an engineering standpoint, viscoelastic fluids hold great potential for designing soft biomaterials with programmable mechanosensitivity6,7. Here, employing microrheology with optical tweezers, we demonstrate how multivalent disordered sticker-spacer8,9 polypeptides undergoing associative phase separation with RNA can be designed to control the frequency-dependent viscoelastic behavior of their condensates. Utilizing linear repeat polypeptides inspired by natural RNA-binding sequences, we show that polypeptide-RNA condensates behave as Maxwell fluids, with viscoelastic behavior that can be fine-tuned by the identity of the sticker and spacer residues. The sequence heuristics that we uncovered allowed us to create biomolecular condensates spanning two orders of magnitude in their viscous and elastic responses to the applied mechanical stress. This sequence-encoded regulation of viscoelasticity in disordered polypeptide-RNA condensates establishes a link between the molecular architecture of the polypeptide chains and the rheological properties of the resulting condensates at the mesoscale, enabling a route to engineer soft biomaterials with programmable mechanics.

Phase separating RNA binding proteins form heterogeneous distributions of clusters in subsaturated solutions

“…Our findings provide a bridge that connects recent findings regarding dynamic clusters comprising of multivalent molecules (73,74). They also show that chemistry-or site-specific sticker-mediated interactions and solubility determining spacer-mediated interactions can be separable (27,29,43,44,48,49,(75)(76)(77)(78)(79)(80)(81), and suggested to be of importance for biological functions (82).…”

Shear Relaxation Governs Dynamic Processes of Biomolecular Condensates

“…Here denotes the angular frequency. * ( ) data have been reported for some condensates, indicating that they are indeed viscoelastic on the ms to s timescales 10,[29][30][31][32] . To assess the viscocapillary model and to uncover other determinants of the fusion speed, here we used optical tweezers (OT) to measure the complex shear moduli and the interfacial tensions of diverse condensates.…”

Polyphasic linkage and the impact of ligand binding on the regulation of biomolecular condensates

“…22,29 As a result, condensates that form via phase separation–aided percolation transitions are best described as networked viscoelastic materials. 34 …”