Biology subjects

Tejedor, A. R.

Publications and source records attributed to Tejedor, A. R..

4 recordsLinked to original sources

bioRxiv2022

Reordering of aromatic-rich segments in FUS inhibits ageing of FUS-RNA condensates

Maturation of functional liquid-like biomolecular condensates into solid-like aggregates has been linked to the onset of several neurodegenerative disorders. Low-complexity aromatic-rich kinked segments (LARKS) contained in numerous RNA-binding proteins can promote aggregation by forming inter-protein {beta}-sheet fibrils that accumulate over time and ultimately drive the liquid-to-solid transition of the condensates. Here, we combine atomistic molecular dynamics simulations with sequence-dependent coarse-grained models of various resolutions to investigate the role of LARKS abundance and position within the amino acid sequence in the maturation of condensates. Remarkably, proteins with tail-located LARKS display much higher viscosity over time than those in which the LARKS are placed towards the center. Yet, at very long timescales, proteins with a single LARKS--independently of its location--can still relax and behave as high viscous liquids. However, phase-separated condensates of proteins containing two or more LARKS become kinetically trapped due to the formation of percolated {beta}-sheet networks that display gel-like behaviour. Furthermore, as a work case example, we demonstrate how shifting the location of the LARKS-containing low-complexity domain of FUS protein towards its center effectively precludes the accumulation of {beta}-sheet fibrils in FUS-RNA condensates, maintaining functional liquid-like behaviour without ageing.

biophysics↗

bioRxiv2022

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

Biomolecular condensates are important contributors to the internal organization of the cell material. While initially described as liquid-like droplets, the term biomolecular condensates is now used to describe a diversity of condensed phase assemblies with material properties extending from low to high viscous liquids, gels, and even glasses. Because the material properties of condensates are determined by the intrinsic behaviour of their molecules, characterising such properties is integral to rationalising the molecular mechanisms that dictate their functions and roles in health and disease. Here, we apply and compare three distinct computational methods to measure the viscoelasticity of biomolecular condensates in molecular simulations. These methods are the shear stress relaxation modulus integration (SSRMI), the oscillatory shear (OS) technique, and the bead tracking (BT) method. We find that, although all of these methods provide consistent results for the viscosity of the condensates, the SSRMI and OS techniques outperform the BT method in terms of computational efficiency and statistical uncertainty. We, thus, apply the SSRMI and OS techniques for a set of 12 different protein/RNA systems using a sequence-dependent high-resolution coarse-grained model. Our results reveal a strong correlation between condensate viscosity and density, as well as with protein/RNA length and the number of stickers vs. spacers in the amino-acid protein sequence. Moreover, we couple the SSRMI and the OS technique to nonequilibrium molecular dynamics simulations that mimic the progressive liquid-to-gel transition of protein condensates due to the accumulation of inter-protein {beta}-sheets. We compare the behaviour of three different protein condensates--i.e., those formed by either hnRNPA1, FUS, or TDP-43 proteins--whose liquid-to-gel transitions are associated with the onset of amyotrophic lateral sclerosis and frontotemporal dementia. We find that both SSRMI and OS techniques successfully predict the transition from functional liquid-like behaviour to kinetically arrested states once the network of inter-protein {beta}-sheets has percolated through the condensates. Overall, our work provides a comparison of different modelling rheological techniques to assess the viscosity of biomolecular condensates, a critical magnitude that provides information on the behaviour of biomolecules inside condensates.

biophysics↗

bioRxiv2022

Ageing critically transforms the network connectivity and viscoelasticity of RNA-binding protein condensates but RNA can prevent it

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 {beta}-sheets. To bridge microscopic understanding between accumulation of inter-protein {beta}-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 {beta}-sheets over time. We reveal that inter-protein {beta}-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 {beta}-sheets fully percolates. However, high concentrations of RNA decelerate the emergence of inter-protein {beta}-sheets. Our study uncovers molecular and kinetic factors explaining how the accumulation of inter-protein {beta}-sheets can trigger liquid-to-solid transitions in condensates, and suggests a potential mechanism to slow such transitions down.

biophysics↗

bioRxiv2021

Dual RNA modulation of protein mobility and stability within phase-separated condensates

One of the key mechanisms employed by cells to control their spatiotemporal organization is the formation and dissolution of phase-separated condensates. The balance between condensate assembly and disassembly can be critically regulated by the presence of RNA. In this work, we use a novel sequence-dependent coarse-grained model for proteins and RNA to unravel the impact of RNA in modulating the transport properties and stability of biomolecular condensates. We explore the phase behavior of several RNA-binding proteins such as FUS, hnRNPA1 and TDP-43 proteins along with that of their corresponding prion-like domains and RNA-recognition motifs, from absence to moderately high RNA concentration. By characterising the phase diagram, key molecular interactions, surface tension and transport properties of the condensates, we report a dual RNA-induced behavior: On the one hand, RNA enhances phase separation at low concentration as long as the RNA radius of gyration is comparable to that of the proteins, whilst at high concentration it inhibits the ability of proteins to self-assemble independently of its length. On the other hand, along with the stability modulation, the viscosity of the condensates can be considerably reduced at high RNA concentration as long as the length of the RNA chains is shorter than that of the proteins. Conversely, long RNA strands increase viscosity, even at high concentration, but barely modify protein self-diffusion, which mainly depends on RNA concentration and on its own effect on droplet density. On the whole, our work rationalizes the different routes by which RNA can regulate phase separation and condensate dynamics, as well as the subsequent aberrant rigidification implicated in the emergence of various neuropathologies and age-related diseases.

biophysics↗