Biology subjects

Rebane, A. A.

Publications and source records attributed to Rebane, A. A..

4 recordsLinked to original sources

bioRxiv2026

Semidilute Polymer Scaling Controls PEG-induced Protein Phase Separation

When does polyethylene glycol (PEG) mass concentration provide a common measure of crowding strength across polymer chain lengths? Here we use bovine serum albumin (BSA) and PEG as a controlled depletion system and measure both coexisting phases to determine binodals, tie lines, and critical points across PEG molecular weights of 4--100 kDa. Phase diagrams for PEG 20, 35, and 100 kDa approximately collapse in mass-concentration coordinates, consistent with semidilute polymer scaling. Generalized free volume theory (GFVT) describes the BSA binodals and tie lines. It also approximately describes binodals for three additional globular proteins in PEG 35K, extending the comparison across proteins spanning 7.2--66.4 kDa. For the binary PEG mixtures tested, GFVT approximates the binodals using an effective polymer size corresponding to the weight-average molecular weight. These results identify a regime in which PEG mass concentration (g/L) provides a transferable measure of depletion-induced crowding.

biophysics↗

bioRxiv2026

Weak interactions drive selective proteome demixing and tune the differential response to environmental perturbations

The intracellular space is a crowded environment where macromolecules perform distinct tasks despite pervasive "non-specific" interactions. Whether these interactions are functionally relevant and how they influence cellular organization remains unclear. Here, we developed QuPID-MS, which measures the propensity of proteins to phase separate in native cell extracts proteome-wide. We find that weak interactions drive condensation of half of the proteome in a crowding- and temperature-dependent manner and we present evidence that this proteome demixing occurs in cells. Importantly, protein condensation properties are conserved and broadly change when cells adapt to new environments, demonstrating that weak interactions are regulated and linked to function. Indeed, condensation of the growth regulator TORC1 coincides with its rapid inactivation, while high solubility of the stress-activated Hog1 ensures its activity across conditions. We thus uncover a fundamental organizing principle that allows tuning of cell growth to environmental fluctuations while ensuring other processes function robustly despite perturbations.

cell biology↗

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↗

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↗