Biology subjects

Faltova, L.

Publications and source records attributed to Faltova, L..

4 recordsLinked to original sources

bioRxiv2025

Competition between protein-RNA clustering and phase separation drives re-entrant phase behavior of hnRNPA1

Phase separation of RNA-binding proteins plays crucial roles in the cell and is modulated by RNA, including promotion and suppression at low and high RNA concentrations, respectively. In complex coacervates, suppression of phase separation is rationalized by charge inversion when increasing the concentration of one component. Here, we show that suppression of biomolecular condensates of the RNA-binding protein hnRNPA1 at high RNA concentration is driven by a different mechanism, namely the competition with formation of nano-sized protein-RNA clusters in the dilute phase. We show that the competition is modulated not only by RNA concentration, but also by the type of RNA, with specific RNA being more effective in promoting cluster formation than unspecific RNA. We further show that protein-RNA clusters convert into amyloid fibrils over a longer time-scale compared to condensates, therefore providing higher kinetic stability. The competition between clustering and phase separation reported in this study provides a unifying framework to understand the distinct assemblies of hnRNPA1 in the nucleus and the cytoplasm, where the protein is exposed to different types and concentrations of RNA.

biophysics↗

bioRxiv2025

De novo design of peptides localizing at the interface of biomolecular condensates

The interface of biomolecular condensates has been shown to play an important role in processes such as protein aggregation and biochemical reactions. Targeted modulation of these interfaces could, therefore, serve as an effective strategy for engineering condensates and modifying aberrant behaviors. However, the molecular grammar driving the preferential localization of molecules at condensate interfaces remains largely unknown. In this study, we developed a computational pipeline that combines highthroughput coarse-grained simulations, machine learning, and mixed-integer linear programming to design peptides that selectively partition at the interfaces of specific condensate targets. Using this workflow, we designed and synthesized peptides that localize at the interface of three distinct condensates formed by different intrinsically disordered protein regions (IDRs). These peptides exhibit surfactant-like architectures, with one tail incorporated into the condensate and the other excluded from the dense phase. In all cases, the tail entering the condensates is enriched in aromatic residues, while the sequence of the excluded tail varies among the IDRs. For hnRNPA1- and LAF1-IDRs, the excluded tail is enriched in lysines and matches the net charge of the condensate-forming protein, promoting electrostatic repulsion. In the case of DDX4-IDR, which exhibits the lowest charge density, the excluded tail mainly consists of uncharged valine residues, which exhibit negligible interactions with the scaffold protein. These results highlight the importance of the net charge of the scaffold as a key physicochemical parameter for designing peptides with preferential interfacial localization. Overall, our pipeline represents a promising strategy for the rational design of interface-localizing peptides and the identification of the corresponding molecular grammar. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC="FIGDIR/small/653111v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@eab174org.highwire.dtl.DTLVardef@2852d6org.highwire.dtl.DTLVardef@156960corg.highwire.dtl.DTLVardef@1952e1d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Enhancement of Enzymatic Activity by Biomolecular Condensates through pH Buffering

Biomolecular condensates can affect enzymatic reactions by locally changing not only concentrations of molecules but also their environment. Since protein conformations can differ between the dense and dilute phase, phase separation can particularly modulate enzymes characterized by a conformation-dependent activity. Here, we generate enzymatic condensates based on a lipase from Bacillus thermocatenulatus, which exhibits an equilibrium between a closed, inactive state, and an open, active conformation. We show that the activity of the enzyme increases inside the dense phase, leading to an enhancement of the overall reaction rate in the phase-separated system. Moreover, we demonstrate that these condensates can generate a more basic environment compared to the surrounding solution. As a consequence, the phase-separated system maintains a high enzymatic activity even in acidic conditions that would be otherwise less favourable for the lipase. We further show that the formation of two phases with distinct pH values optimizes a cascade reaction involving two enzymes with different optimal pH conditions. Our results demonstrate that biomolecular condensates can also affect the dependence of enzymatic rates on solution pH, thereby expanding the accessible pH interval and enabling network reactions with enzymes that require distinct pH values. These findings have crucial implications in biology and biotechnology for biocatalytic engineering.

biochemistry↗

bioRxiv2022

The interface of condensates of the hnRNPA1 low complexity domain promotes formation of amyloid fibrils

The maturation of liquid-like protein condensates into amyloid fibrils has been associated with neurodegenerative diseases. Here, we analyze the amyloid formation mediated by condensation of the low-complexity domain of hnRNPA1, a protein involved in Amyotrophic Lateral Sclerosis (ALS). We show that phase separation and fibrillation are connected but distinct processes which are independently mediated by different regions of the protein sequence. By monitoring the spatial and temporal evolution of amyloid formation we demonstrate that the formation of fibrils does not occur homogeneously inside the droplets but is promoted at the interface of the condensates. Consistently, we further show that coating the interface of the droplets with surfactant molecules inhibits fibril formation. Our results indicate that the interface of biomolecular condensates can act as an important catalyst for fibril formation, and therefore could represent a possible therapeutic target against the formation of aberrant amyloids mediated by condensation.

biophysics↗