Biology subjects

Dufresne, E. R.

Publications and source records attributed to Dufresne, E. R..

12 recordsLinked to original sources

bioRxiv2026

Partition Coefficients Reveal Changes in Properties of Low-Contrast Biomolecular Condensates

Biomolecular condensates are domains within cells with distinct compositions, held together by intermolecular cohesion. They are implicated in a variety of cellular processes, and in vitro studies have revealed the molecular driving forces that underly their condensation. However, in vitro condensates do not capture essential features of cellular condensates. In particular, enrichment of proteins, quantified by partition coefficients, is often exaggerated in these simplified systems. We show that the addition of free amino acids and other small molecules to model condensates can bring their partition coefficients within physiological range. In this limit, where there is low biochemical contrast between condensates and their surroundings, we observe striking changes to condensate behavior. Such low-contrast condensates exhibit large fluctuations in shape and composition and show enhanced sensitivity to changes in their environment. These behaviors reflect dramatic shifts to their material properties, including interfacial tension, rheology, and chemical susceptibilities. We note remarkable similarities in these effects across seemingly unrelated two-phase fluid systems. To explain these trends, we reformulate classic models of critical phenomena in terms of partition coefficients. This framework simplifies application of theory to experiments with near-critical fluids and suggests new experimental approaches for assessing condensate physiology in live cells.

biophysics↗

bioRxiv2026

Metabolites Shift Equilibria of Biomolecular Condensates

Biomolecular condensates compartmentalize biochemistry in living cells. While in vitro models of condensates involve only a few components, the cytoplasm is a complex mixture with thousands of components, including many small molecules. While many macromolecular drivers of phase separation have been revealed, the contributions from small molecules have received little attention. To quantify the impact of solutes on biomolecular condensates, we introduce susceptibility, a dimensionless descriptor of condensate response to solute perturbations. We measured how three model condensates, assembled by distinct cohesive mechanisms, respond to diverse solutes including amino acids and nucleotides. Generically, solutes shift condensate phase equilibria, with susceptibilities spanning over four orders of magnitude. These values reflect underlying molecular interactions, consistent with theoretical descriptions including Flory-Huggins and polyphasic linkages. As one example of the predictive power of susceptibility, we exploit enzymatic activity to induce condensation and modulate material properties. Our work establishes susceptibility as an indicator of the sensitivity of biomolecular condensates to solutes, with implications for cell physiology and therapeutic design. SIGNIFICANCE STATEMENTCells compartmentalize biochemistry using biomolecular condensates formed through phase separation. Although cells contain thousands of small molecules, little is known about their influence on condensation. In such complex mixtures, mapping full phase diagrams is infeasible. Alternatively, we introduce susceptibility to characterize system response around a working composition. Using three distinct model condensates and over a dozen solutes, we observe susceptibilities varying over four orders of magnitude. We provide a general thermodynamic framework that clarifies the driving forces behind these responses, rationalizing their magnitude and their dependence on location in the phase diagram. Our work provides a framework for understanding and harnessing solutes to regulate biomolecular condensation, with implications for cell physiology and therapeutic design.

biophysics↗

bioRxiv2025

Dynamic Shape Modulation of Deflated and Adhered Lipid Vesicles

Lipid membrane-bounded organelles often possess intricate morphologies with spatially varying curvatures and large membrane surface areas relative to internal volume (small reduced volumes). These features are thought to be essential for protein sorting and vesicle trafficking, but challenging to reproduce in vitro. Here, we show that weakly adhered giant unilamellar vesicles (GUVs) can be osmotically deflated to reduced volumes as low as 0.1, similar to what is found in flattened, disc-shaped organelles such as Golgi cisternae and ER sheets. Using shape analysis with the Canham-Helfrich model, we determine mechanical parameters including adhesion strength, membrane tension, and pressure of individual vesicles. We find that the rate of shape flattening during deflation is governed by a normalized adhesion strength that combines vesicle size, adhesion energy, and bending rigidity. For highly flattened disc-like vesicles, we identify a geometric relationship that allows the adhesion strength to be estimated solely from the vesicles aspect ratio, size, and bending rigidity. These results provide a quantitative experimental platform for bottom-up studies of membrane shaping mechanisms and shape-dependent phenomena, such as curvature-mediated protein sorting. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/650387v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@f23d45org.highwire.dtl.DTLVardef@194a99borg.highwire.dtl.DTLVardef@10b1ca5org.highwire.dtl.DTLVardef@85bd2d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

Ice and air: Visualisation of freeze-thaw embolism and freezing spread in young L. tulipifera leaves

Spring freezing is an unforgiving stress for young leaves, often leading to death, with consequences for tree productivity and survival. While both the plant water transport system and living tissues are vulnerable to freezing, we do not know whether damage to one or both of these systems causes death in leaves exposed to freezing. Whole saplings of Liriodendron tulipifera were exposed to freezing and thawing trajectories designed to mimic natural spring freezes. We monitored the formation of freeze-thaw xylem embolism and damage to photosynthetic tissues to reveal a predictable progression of ice formation across the leaf surface that is strongly influenced by leaf vein architecture, notably the presence or absence of bundle sheath extensions. Our data also show that freeze-thaw embolism occurs only in the largest vein orders where mean vessel diameter exceeds 30{micro}m. With evidence of both freeze-thaw embolism and damage to photosynthetic tissue, we conclude that this dual-mode lethality may be common among other wide-vesseled angiosperm-leaves, potentially playing a role in limiting geographic distributions, and show that bundle sheath extensions may stall or even prevent freezing spread. HighlightBoth ice and air lead likely lead to death in young L.tulipfera leaves exposed to freezing, with the spread of both governed by physical characteristics of these leaves.

physiology↗

bioRxiv2024

Phase separation of a microtubule plus-end tracking protein into a fluid fractal network

Microtubule plus-end tracking proteins (+TIPs) are involved in virtually all microtubule-based cellular processes, and it has been recently proposed that they function as liquid condensates. However, the formation process and internal organization of +TIP condensates are poorly understood. Here, we have investigated the phase separation of the CLIP-170 family member Bik1, a key +TIP implicated in budding yeast cell division. We found that Bik1 is a rod-shaped dimer whose conformation is dominated by its central coiled-coil domain. Liquid condensation is accompanied by Bik1 conformational rearrangements, leading to a 2-3-fold rise in interactions between the proteins folded and disordered domains. In contrast to classical liquids, the supramolecular structure of the Bik1 condensate is heterogeneous, with a fractal structure of protein-rich and protein-free domains. This observation provides structural evidence in support of recent models of biomolecular condensates based on percolation. More broadly, our results provide insights into the structure, dynamic rearrangement, and organization of a complex, multidomain protein in its dilute and condensed phases. Our experimental framework can be extended to other biomolecular condensates, including more intricate +TIP networks.

biochemistry↗

bioRxiv2023

Phase-Separated Droplets Swim to Their Dissolution

Biological macromolecules can condense into liquid domains. In cells, these condensates form membraneless organelles that can organize chemical reactions1,2. However, little is known about the physical consequences of chemical activity in and around condensates. Working with model bovine serum albumin (BSA) condensates3, we show that droplets swim along chemical gradients. Active BSA droplets loaded with urease swim toward each other. Passive BSA droplets show diverse responses to externally applied gradients of the enzymes substrate and products. In all these cases, droplets swim toward solvent conditions that favor their dissolution. We call this behavior dialytaxis, and expect it to be generic, as conditions which favor dissolution typically reduce interfacial tension, whose gradients are well-known to drive droplet motion4,5. These results suggest alternative physical mechanisms for active transport in living cells, and may enable the design of fluid micro-robots.

biophysics↗

bioRxiv2023

Actin and microtubules position stress granules

Membraneless organelles, composed of protein and nucleic acids, alter the biochemical and physical landscape of the cell. While specific membraneless organelles are found in stereotypical locations, little is known about the physical mechanisms that guide their positioning. Here, we investigate how stress granules, a type of cytoplasmic membraneless organelle, establish their stereotypical perinuclear positioning. We find that actin and microtubules play complementary roles. Lamellar actin confines stress granules, and its retrograde flow drives them toward the cell center. Microtubules, in turn, adhere to stress granules through capillary interactions, which tend to concentrate stress granules in micro-tubule rich regions near the nucleus. Similar physical mechanisms are likely to play a role in the positioning of other membraneless organelles.

biophysics↗

bioRxiv2021

Geometrical frustration of phase-separated domains in Coscinodiscus diatom frustules

Diatoms are single-celled organisms with a cell wall made of silica, called the frustule. Even though their elaborate patterns have fascinated scientists for years, little is known about the biological and physical mechanisms underlying their organization. In this work, we take a top-down approach and examine the micron-scale organization of diatoms from the Coscinodiscus family. We find two competing tendencies of organization, which appear to be controlled by distinct biological pathways. On one hand, micron-scale pores organize locally on a triangular lattice. On the other, lattice vectors tend to point globally toward a center of symmetry. This competition results in a frustrated triangular lattice, populated with geometrically necessary defects whose density increases near the center.

biophysics↗

bioRxiv2021

High interaction valency ensures cohesion and persistence of a microtubule +TIP body at the plus-end of a single specialized microtubule in yeast

Microtubule plus-end tracking proteins (+TIPs) control microtubule specialization and are as such essential notably during eukaryotic cell division. Here, we investigated interactions and functions of the budding yeast Kar9 network consisting of the core +TIPs components Kar9 (functional homologue of APC, MACF, and SLAIN), Bim1 (orthologue of EB1), and Bik1 (orthologue of CLIP-170). Our data indicate that a redundant, multivalent web of interactions links the three +TIPs together to form a "Kar9 body" at the tip of a single cytoplasmic microtubule. They further suggest that this body is a liquid-like condensate, allowing it to persist on both growing and shrinking microtubule tips, and functions as a mechanical coupling device between microtubules and actin cables during mitosis. Our study underlines the power of dissecting the web of low-affinity interactions driving liquid-liquid phase separation of proteins in order to demonstrate the importance and establish the functional roles of condensation processes in vivo.

cell biology↗

bioRxiv2021

Non-specific adhesive forces between filaments and membraneless organelles

Membraneless organelles are liquid-like domains that form inside living cells by phase-separation. While standard physical models of their formation assume their surroundings to be a simple liquid, the cytoplasm is an active viscoelastic environment. To investigate potential coupling of phase separation with the cytoskeleton, we quantify structural correlations of stress granules and microtubules in a human-derived epithelial cell line. We find that microtubule networks are significantly perturbed in the vicinity of stress granules, and that large stress granules conform to the local pore-structure of the microtubule network. When microtubules are depolymerized by nocodazole, tubulin enrichment is localized near the surface of stress granules. We interpret these data using a thermodynamic model of partitioning of particles to the surface and bulk of droplets. This analysis shows that proteins generically have a non-specific affinity for droplet interfaces, which becomes most apparent when they weakly partition to the bulk of droplets and have a large molecular weight. In this framework, our data is consistent with a weak ([lsim] kbT) affinity of tubulin sub-units for stress granule interfaces. As microtubules polymerize their affinity for interfaces increases, providing sufficient adhesion to deform droplets and/or the network. We validate this basic physical phenomena in vitro through the interaction of a simple protein-RNA condensate with tubulin and microtubules.

biophysics↗

bioRxiv2021

Sustained Enzymatic Activity and Flow in Crowded Protein Droplets

Living cells harvest energy from their environments to drive the chemical processes that enable life. We introduce a minimal system that operates at similar protein concentrations, metabolic densities, and length scales as living cells. This approach takes advantage of the tendency of phase-separated protein droplets to strongly partition enzymes, while presenting minimal barriers to transport of small molecules across their interface. By dispersing these microreactors in a reservoir of substrate-loaded buffer, we achieve steady states at metabolic densities that match those of the hungriest microorganisms. We further demonstrate the formation of steady pH gradients, capable of driving microscopic flows. Our approach enables the investigation of the function of diverse enzymes in environments that mimic cytoplasm, and provides a flexible platform for studying the collective behavior of matter driven far from equilibrium.

biophysics↗

bioRxiv2020

Single Gyroid and Inverse b.c.c. Photonic Crystals in Bird Feathers

Vivid, saturated structural colors are conspicuous and important features of many animals. A rich diversity of three-dimensional periodic photonic nanostructures is found in the chitinaceous exoskeletons of invertebrates. Three-dimensional photonic nanostructures have been described in bird feathers, but they are typically quasi-ordered. Here, we report bi-continuous single gyroid {beta}-keratin and air photonic crystal networks in the feather barbs of blue-winged leafbirds (Chloropsis cochinchinensis sensu lato), which have evolved from ancestral quasi-ordered channel-type nanostructures. Self-assembled avian photonic crystals may serve as inspiration for multi-functional applications, as they suggest efficient, alternative routes to single gyroid synthesis at optical length-scales, which has been experimentally elusive.

evolutionary biology↗