Biology subjects

Harmon, T. S.

Publications and source records attributed to Harmon, T. S..

6 recordsLinked to original sources

bioRxiv2026

Mechanical regulation of endocytosis by protein droplet capillary forces

Clathrin-mediated endocytosis (CME) is the primary pathway for internalization of extracellular and membrane cargo in eukaryotic cells. It is characterized by a patch of the plasma membrane invaginating and pinching off to generate a cytoplasmic vesicle. Recently, experimental evidence has begun to accumulate in support of proteins assembling into liquid-like condensates at nascent CME sites, but potential functional consequences are not understood. Given that condensate capillary forces can influence membrane bending, we constructed complementary analytical and numerical model systems to probe the mechanical influence of a protein droplet on endocytosis. Model evaluations and analysis reveal that a droplet can regulate the progression of endocytosis by stalling invagination until the droplet grows past a threshold size. After the droplet-mediated brake is released, the droplet provides a force that can drive the membrane bud toward scission. Thus, we propose a ``mechanical timer'' mechanism as a function for protein phase separation in cellular membrane trafficking.

biophysics↗

bioRxiv2025

Born to Condense: Polysomes Drive Co-Translational Condensation of Biomolecular Condensate Proteins

Biomolecular condensates formed by protein liquid-liquid phase separation (LLPS) are ubiquitous in cells and play crucial roles in cellular regulation. While the physics and functions of LLPS are well studied, its interplay with protein synthesis - translation - remains largely unexplored. Here we introduce a theoretical framework for Co-Translational Condensation (CTC), in which nascent protein chains of polysomes - multiple ribosomes on one mRNA - interact with condensates, localizing translation to condensate surfaces. Using coarse-grained simulations, we show that protein domain architecture dictates the thermodynamics of CTC, consistent with a Langmuir adsorption model. Bioinformatic analysis of more than 7,500 proteins reveals that most condensate-associated proteins have architectures favoring CTC, with strong interaction regions of nascent chains exposed on polysomes. At the dynamical level, simulation and reaction-diffusion modeling reveal that CTC is kinetically feasible within typical polysome lifetimes, either through large polysomes nucleating new condensates or via diffusion to pre-existing condensates. As a case study, we demonstrate that CTC enhances post-translational modifications by minimizing unmodified intermediates. More broadly, we anticipate CTC may also influence protein folding, misfolding, and signal-integration latency. Together, our results establish CTC as a general mechanism coupling translation with phase separation, with broad implications for protein evolution, cellular organization, and synthetic biology.

biophysics↗

bioRxiv2025

Droplet-assisted folding of long regulatory RNAs

Long regulatory RNA regions orchestrate complex cellular processes, including gene expression and epigenetic modifications. How these RNAs dynamically fold and refold in response to cellular signals remains poorly understood. Given that RNAs interact with ubiquitous RNA-binding proteins (RBPs) prone to form biomolecular condensates, we explore how protein droplets interacting along an RNA impact its folding process. Attached droplets prevent premature folding by competing with RNA:RNA interactions. When droplets dissolve due to cellular signals, capillary effects cause the RNA to collapse while refolding. We test this process of condensate-guided RNA folding by adapting established RNA secondary structure predictors to mimic various folding pathways and supplement this with coarse-grained simulations. We find that interactions with transient droplets robustly leads to the formation of long-range RNA contacts, which are otherwise hard to achieve. Our results compare favorably with available experimental data. We propose that this strategy, which we call droplet-assisted RNA folding, represents a previously unexplored mechanism for shaping RNA structures. Given the widespread propensity of RBPs to form condensates, this process could play a fundamental role in the structural organization, conditional reshaping, and functional regulation of long regulatory RNAs. SignificanceComplex non-coding RNA regions (e.g. lncRNAs, 3UTRs, etc.) perform several important functions in higher organisms. However, the longer an RNA, the more likely it is to misfold. How can such regulatory regions of more than 1000 nts be reliably folded, considering that premature co-transcriptional folding favors local interactions? We present a mechanism by which biomolecular condensates of RNA-binding proteins (RBPs) assist and control the folding of complex RNAs. Here, droplets of RBPs nucleate around RNA binding motifs, prevent premature misfolding through their RNA chaperone function, and allow robust folding of initially distant regions through coordinated droplet dissolution and detachment. This mechanism provides an alternative perspective on how long RNAs acquire their structures in a context that is functionally dynamic.

molecular biology↗

bioRxiv2024

Transport kinetics across interfaces between coexisting liquid phases

Biomolecular condensates provide compartments that organize biological processes in the cell. Spatial organization of condensates relies on transport across phase boundaries. We investigate the kinetics of molecule transport across interfaces in phase-separated mixtures. Using non-equilibrium thermodynamics we derive the interfacial kinetics, describing the movement of the interface, and of molecular transport across the interface. In the limit of a thin interface, we show that breaking local equilibrium at the interface introduces a local transport resistance. Subsequently, using a continuum approach, we explore two physical scenarios where such a resistance emerges: a mobility minimum and a potential barrier at the interface. These scenarios lead to the same effective transport model in the sharp interface limit, characterized by a single interface resistance parameter. We discuss experimental conditions for which interface resistance could be observed and how these scenarios could be distinguished.

biophysics↗

bioRxiv2024

The Impact of Coiled-Coil Domains on the Phase Behavior of Biomolecular Condensates

Spatial organization is fundamental to biological systems, with biomolecular condensates as a key subset. Many studies show that folded domains play important roles in condensate formation by facilitating interactions. However, little is known about how the presence of large structured elements impacts condensate formation. Using coarse-grained simulations, we investigated a model system of two multivalent proteins, one containing a coiled-coil domain (CCD), which undergoes liquid-liquid phase separation (LLPS). We found that CCDs promote LLPS by preventing loop-closure defects, enabling protein networking. Replacing the CCD with a flexible linker abolishes LLPS due to formation of oligomeric clusters. There is a critical length of the CCD where the system rapidly changes from no LLPS to LLPS at low concentrations. This highlights their potential in regulating condensate formation and properties. This study provides insights into the phase behavior of biomolecular condensates and offers a framework for designing synthetic condensates with tunable phase behaviors.

biophysics↗

bioRxiv2017

Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins

Many intracellular membraneless bodies appear to form via reversible phase transitions of multivalent proteins. Two relevant types of phase transitions are sol-gel transitions (gelation) and phase separation plus gelation. Gelation refers to the formation of a system spanning molecular network. This can either be enabled by phase separation or it can occur independently. Despite relevance for the formation and selectivity of compositionally distinct protein and RNA assemblies, the determinants of gelation as opposed to phase separation plus gelation remain unclear. Here, we focus on linear multivalent proteins that consist of interaction domains that are connected by disordered linkers. Using results from computer simulations and theoretical analysis we show that the lengths and sequence-specific features of disordered linkers determine the coupling between phase separation and gelation. Thus, the precise nature of phase transitions for linear multivalent proteins should be biologically tunable through genetic encoding of or post-translational modifications to linker sequences.

cell biology↗