Biology subjects

Rene Espinosa, J.

Publications and source records attributed to Rene Espinosa, J..

4 recordsLinked to original sources

bioRxiv2024

Dynamically arrested condensate fusion creates complex structures with varying material properties

The cell nucleus and cytosol contain numerous biomolecular condensates which dynamically reshape, fuse and split to accomplish precise compartmentalization of the cell material. While it has been observed that some condensates rapidly coalesce, some others only attach to each other, or do not establish persistent interactions over time. Here, we explain these observations through optical tweezers and Molecular Dynamics simulations focusing on two condensate-forming, RNA-binding proteins--FUS and G3BP1--strongly involved in RNA metabolism and stress responses. We find that the fusion of pure droplets formed by these proteins can give rise to multiphase single-component condensates exhibiting notably different densities, architectures, and material properties. Such behaviour is dictated by the relative timescales of condensate fusion and protein internal mixing. A critical parameter controlling this interplay is the extent of ageing that condensates display; e.g., their progressive hardening driven by the accumulation of inter-protein {beta}-sheet assemblies over time. Strikingly, different degrees of ageing in fusing droplets can lead single-component condensates to form diverse architectures including concentric drops or two-sided condensates. Overall, our results highlight a mechanism, based on the temporal coupling between ageing, fusion, and mixing rate, by which biomolecular condensates form multiphasic structures with markedly different material properties, and hence potentially distinct biological roles.

biophysics↗

bioRxiv2024

Phase behaviour of hnRNPA1 low-complexity domain mutants described by different sequence-dependent models

Intracellular liquid-liquid phase separation (LLPS) of proteins and nucleic acids is a fundamental mechanism by which cells compartmentalize their components and perform essential biological functions. Molecular simulations play a crucial role in providing microscopic insights into the physicochemical processes driving this phenomenon. In this study, we systematically compare six state-of-the-art sequence-dependent, residue-resolution models to evaluate their performance in reproducing the phase behaviour and material properties of condensates formed by seven variants of the low-complexity domain (LCD) of the hnRNPA1 protein (A1-LCD)--a protein implicated in the pathological liquid-to-solid transition of stress granules. Specifically, we assess the HPS, HPS-cation-{pi}, HPS-Urry, CALVADOS2, Mpipi, and Mpipi-Recharged models in their predictions of the condensate saturation concentration, critical solution temperature, and condensate viscosity for the A1-LCD variants. Our analyses demonstrate that, among the tested models, Mpipi, Mpipi-Recharged, and CALVADOS2 provide accurate descriptions of the critical solution temperatures and saturation concentrations for the various A1-LCD variants tested. Regarding the prediction of material properties for condensates of A1-LCD and its variants, Mpipi-Recharged stands out as the most reliable model. Overall, this study benchmarks a range of residue-resolution coarse-grained models for the study of the thermodynamic stability and material properties of condensates and establishes a direct link between their performance and the ranking of intermolecular interactions these models consider.

biophysics↗

bioRxiv2023

Mechano-dependent sorbitol accumulation supports biomolecular condensate

Biomolecular condensates regulate a wide range of cellular functions from signaling to RNA metabolism1, 2, yet, the physiologic conditions regulating their formation remain largely unexplored. Biomolecular condensate assembly is tightly regulated by the intracellular environment. Changes in the chemical or physical conditions inside cells can stimulate or inhibit condensate formation3-5. However, whether and how the external environment of cells can also regulate biomolecular condensation remain poorly understood. Increasing our understanding of these mechanisms is paramount as failure to control condensate formation and dynamics can lead to many diseases6, 7. Here, we provide evidence that matrix stiffening promotes biomolecular condensation in vivo. We demonstrate that the extracellular matrix links mechanical cues with the control of glucose metabolism to sorbitol. In turn, sorbitol acts as a natural crowding agent to promote biomolecular condensation. Using in silico simulations and in vitro assays, we establish that variations in the physiological range of sorbitol, but not glucose, concentrations, are sufficient to regulate biomolecular condensates. Accordingly, pharmacologic and genetic manipulation of intracellular sorbitol concentration modulates biomolecular condensates in breast cancer - a mechano-dependent disease. We propose that sorbitol is a mechanosensitive metabolite enabling protein condensation to control mechano-regulated cellular functions. Altogether, we uncover molecular driving forces underlying protein phase transition and provide critical insights to understand the biological function and dysfunction of protein phase separation.

cell biology↗

bioRxiv2022

Principles of assembly and regulation of condensates of Polycomb repressive complex 1 through phase separation

PRC1 (Polycomb repressive complex 1) plays a significant role in cellular differentiation and development by repressing lineage-inappropriate genes. PRC1 proteins phase separate to form Polycomb condensates (bodies) that are multi-component hubs for silencing Polycomb target genes; however, the molecular principles that underpin the condensate assembly and biophysical properties remain unknown. Here, by using biochemical reconstitution, cellular imaging, and multiscale molecular simulations, we show that PRC1 condensates are assembled via a scaffold-client liquid-liquid phase separation (LLPS) model by which Chromobox 2 (CBX2) is the scaffold and other subunits of the CBX2-PRC1 complex act as clients. The clients induce a reentrant phase transition of CBX2 condensates in a concentration-dependent manner. The composition of the multi-component, heterotypic LLPS systems directs the assembly and biophysical properties of CBX2-PRC1 condensates and selectively promotes the formation of CBX4-PRC1 condensates, but specifically dissolves condensates of CBX6-, CBX7-, and CBX8-PRC1. Additionally, the composition of CBX2-PRC1 condensates controls the enrichment of CBX4-, CBX7-, and CBX8-PRC1 into condensates but the exclusion of CBX6-PRC1 from condensates. Our results show the composition- and stoichiometry-dependent scaffold-client assembly of multi-component PRC1 condensates and supply a conceptual framework underlying the molecular basis and dynamics of Polycomb condensate assembly.

biochemistry↗