Biology subjects

Malady, B.

Publications and source records attributed to Malady, B..

6 recordsLinked to original sources

bioRxiv2026

Endocytic accessory proteins assemble clathrin while simultaneously destabilizing protein condensates

During endocytosis a dynamic protein network is responsible for assembly of the clathrin coat. Early in the process the Eps15 protein is thought to undergo liquid-liquid phase-separation to form biomolecular condensates. These condensates facilitate clathrin assembly, producing clathrin-coated vesicles that are ultimately excluded from the condensate as the vesicles depart from the plasma membrane. An array of distinct clathrin accessory proteins drive this process, yet their interactions with protein condensates have not been explored. Here we show that clathrin accessory proteins promote the assembly of the clathrin lattice by simultaneously destabilizing protein condensates. By adding diverse accessory proteins to Eps15 condensates, we observed that accessory proteins which cross-linked Eps15 proteins stabilized condensates, while accessory proteins that compete with Eps15-Eps15 interactions destabilized condensates. Interestingly, accessory proteins that destabilized condensates also promoted the assembly of clathrin and its exclusion from condensates. In contrast, accessory proteins that stabilized condensates opposed exclusion of clathrin. Finally, we demonstrated that decreasing condensate stability enhanced clathrin assembly and exclusion, even when no additional clathrin assembly motifs were introduced. Taken together, these results help to explain how condensates can catalyze the assembly of coated vesicles by providing both a substrate for their initiation and a driving force for their exclusion and ultimate departure. Statement of SignificanceThis work is significant because it reveals how biomolecular condensates could actively drive, rather than merely host, clathrin-mediated endocytosis. By showing that clathrin accessory proteins can tune condensate stability to simultaneously promote clathrin lattice assembly and exclusion, this study uncovers a physical mechanism that could link phase separation to membrane trafficking. The finding that condensate destabilization alone enhances clathrin exclusion reframes condensates as dynamic regulators that could provide both an initiation platform and a force for vesicle maturation and release. More broadly, this work advances our understanding of how cells coordinate assembly and disassembly of complex macromolecular structures through regulated changes in condensate material properties.

biophysics↗

bioRxiv2026

Reflectins form multicompartment liquid-liquid phase separated condensates that mirror and may facilitate spatial organization in squid skin Bragg lamellae

Cationic reflectin proteins transduce neuronal signals tuning skin color for dynamic camouflage and communication in Loliginid squid. Neuronally released acetylcholine (ACh) activates phosphorylation of the reflectins, triggering their condensation, folding and hierarchical assembly. This causes osmotic and Gibbs-Donnan dehydration of membrane-enclosed Bragg lamellae containing these proteins in skin cells called iridocytes, changing their refractive index and spacing to finely tune the wavelength of reflected light. Reflectins B and C are enriched in ACh-responsive iridocytes, suggesting they are critical for the neuronally tuned protein phase transitions within the Bragg lamellae. Here, using pH titration as an in vitro surrogate for phosphorylation to reduce protein net charge density, we demonstrate with confocal microscopy that reflectins A1, A2, B and C individually undergo LLPS to form protein dense liquid condensates, while physiological mixtures of these proteins exhibit coordinated phase transitions to form multicompartment condensates whose internal spatial organization is tuned by the proportions and charge densities of the different reflectins. Our findings demonstrate that (i) the charge densities of the different reflectins control their spatial organization within liquid condensates, (ii) the relative proportions of the different reflectins found in the ACh-responsive iridocytes increase the sensitivity of their proteins liquid phase transitions to changes in reflectin charge density; and (iii) the spatial segregation of reflectins A1 and C we observe in their multiphasic liquid condensate mirror their spatial segregation in the Bragg lamellae in vivo, suggesting a mechanistic explanation for the spatial segregation of these reflectins across the iridocytes Bragg lamellae.

biophysics↗

bioRxiv2025

Of condensates and coats - reciprocal regulation of clathrin assembly and the growth of protein networks

Clathrin-mediated endocytosis is essential for membrane traffic, impacting a diverse range of cellular processes including cell signaling homeostasis, cell adhesion, and receptor recycling. During endocytosis, invagination of the plasma membrane is coordinated by a network of proteins that recruit and assemble the clathrin coat. Recent work demonstrated that clathrin accessory proteins which arrive early at endocytic sites, such as Eps15 and Fcho2, form phase-separated condensates that recruit downstream machinery, promoting assembly and maturation of clathrin-coated vesicles. However, the mechanisms by which protein condensates regulate - and are regulated by - clathrin assembly remain unclear. Using in vitro reconstitution and nuclear magnetic resonance spectroscopy, we demonstrate that protein condensates provide a platform for recruitment and assembly of clathrin triskelia. This condensate driven assembly is enhanced in the presence of the accessory protein, AP2, which is readily incorporated within condensates. In turn, clathrin assembly restricted the growth of condensates, exhibiting surfactant-like behavior that stabilized protein-protein interactions while imposing the preferred curvature of the clathrin lattice. This mutual regulation promotes efficient assembly of clathrin-coated vesicles while preventing uncontrolled expansion of protein condensates. More broadly, reciprocal regulation of protein condensates and clathrin coats may provide a framework for understanding how intrinsically disordered and structured protein assemblies can work together to build complex cellular architectures.

biophysics↗

bioRxiv2024

Charge screening and hydrophobicity drive progressive assembly and liquid-liquid phase separation of reflectin protein

The intrinsically disordered reflectin proteins drive tunable reflectivity for dynamic camouflage and communication in the recently evolved Loliginidae family of squid. Previous work revealed that reflectin A1 forms discrete assemblies whose size is precisely predicted by protein net charge density (NCD) and charge screening by the local anion concentration. Using dynamic light scattering (DLS), Forster resonant energy transfer (FRET) and confocal microscopy, we show that these assemblies, of which 95-99% of bulk protein in solution is partitioned into, are dynamic intermediates to liquid protein-dense condensates formed by liquid-liquid phase separation (LLPS). Increasing salt concentration drives this progression by anionic screening of the cationic proteins Coulombic repulsion, and by increasing the hydrophobic effect which tips the balance between short-range attraction and long-range repulsion (SALR) to drive protein assembly and ultimately LLPS. Measuring fluorescence recovery after photobleaching (FRAP) and droplet fusion dynamics, we demonstrate that reflectin diffusivity in condensates is tuned by salt concentration and protein NCD. These results illuminate the physical processes governing reflectin A1 assembly and LLPS, and demonstrate the potential for reflectin A1 condensate-based tunable biomaterials. They also compliment previous observations of liquid phase separation in the Bragg lamellae of activated iridocytes and suggest that LLPS behavior may serve a critical role in governing the tunable and reversible dehydration of the membrane-bounded Bragg lamellae and vesicles containing reflectin in biophotonically active cells.

biophysics↗

bioRxiv2023

Ubiquitin-driven protein condensation promotes clathrin-mediated endocytosis

Clathrin-mediated endocytosis is an essential cellular pathway that enables signaling and recycling of transmembrane proteins and lipids. During endocytosis, dozens of cytosolic proteins come together at the plasma membrane, assembling into a highly interconnected network that drives endocytic vesicle biogenesis. Recently, multiple groups have reported that early endocytic proteins form flexible condensates, which provide a platform for efficient assembly of endocytic vesicles. Given the importance of this network in the dynamics of endocytosis, how might cells regulate its stability? Many receptors and endocytic proteins are ubiquitylated, while early endocytic proteins such as Eps15 contain ubiquitin-interacting motifs. Therefore, we examined the influence of ubiquitin on the stability of the early endocytic protein network. In vitro, we found that recruitment of small amounts of polyubiquitin dramatically increased the stability of Eps15 condensates, suggesting that ubiquitylation could nucleate endocytic assemblies. In live cell imaging experiments, a version of Eps15 that lacked the ubiquitin-interacting motif failed to rescue defects in endocytic initiation created by Eps15 knockout. Furthermore, fusion of Eps15 to a deubiquitylase enzyme destabilized nascent endocytic sites within minutes. In both in vitro and live cell settings, dynamic exchange of Eps15 proteins, a hallmark of liquid-like systems, was modulated by Eps15-Ub interactions. These results collectively suggest that ubiquitylation drives assembly of the flexible protein network responsible for catalyzing endocytic events. More broadly, this work illustrates a biophysical mechanism by which ubiquitylated transmembrane proteins at the plasma membrane could regulate the efficiency of endocytic recycling. Significance StatementThe assembly of proteins into dynamic, liquid-like condensates is an emerging principle of cellular organization. During clathrin-mediated endocytosis, a liquid-like protein network catalyzes vesicle assembly. How do cells regulate these assemblies? Here we show that ubiquitin and endocytic proteins form a dynamic, mutually-reinforcing protein network in vitro and in live cells. To probe the impact of ubiquitylation on the dynamics of endocytosis, we engineered opto-genetic control over recruitment of proteins to nascent endocytic sites. While recruitment of wildtype proteins promoted endocytosis, recruitment of deubiquitylases, enzymes capable of removing ubiquitin, resulted in disassembly of endocytic sites within minutes. These results illustrate that ubiquitylation can regulate the fate of endocytic structures, elucidating a functional connection between protein condensates, endocytosis, and ubiquitin signaling.

cell biology↗

bioRxiv2021

Protein Charge Neutralization is the Proximate Driver Dynamically Tuning a Nanoscale Bragg Reflector

Reflectin is a cationic, block copolymeric protein that mediates the dynamic fine-tuning of color and brightness of light reflected from nanostructured Bragg reflectors in iridocyte skin cells of squids. In vivo, neuronally activated phosphorylation of reflectin triggers its assembly, driving osmotic dehydration of the membrane-bounded Bragg lamellae containing the protein to simultaneously shrink the lamellar thickness and spacing while increasing its refractive index contrast, thus tuning the wavelength and increasing the brightness of reflectance. In vitro, we show that reduction in repulsive net charge of the purified, recombinant reflectin - either (for the first time) by generalized anionic screening with salt, or by pH titration - drives a finely tuned, precisely calibrated increase in size of the resulting multimeric assemblies. The calculated effects of phosphorylation in vivo are consistent with these effects observed in vitro. X-ray scattering analyses confirm the sphericity, size and low polydispersity of the assemblies. Precise proportionality between assembly size and charge-neutralization is enabled by the demonstrated rapid dynamic arrest of multimer growth. The resulting stability of reflectin assemblies with time ensures reciprocally precise control of the particle number concentration, thereby encoding a precise calibration between the extent of neuronal signaling, osmotic pressure, and the resulting optical changes. The results presented here strongly suggest that it is charge neutralization, rather than any change in aromatic content, that is the proximate driver of assembly, fine-tuning a colligative property-based nanostructured biological machine. A physical mechanism is proposed.

molecular biology↗