Biology subjects

Abel, S. M.

Publications and source records attributed to Abel, S. M..

15 recordsLinked to original sources

bioRxiv2026

The reticulon homology domain of Pex30 generates membrane curvature at ER subdomains for lipid droplet biogenesis

Lipid droplets (LDs) are dynamic organelles that store neutral lipids and form in the endoplasmic reticulum (ER) membrane. Formation of new LDs is a controlled process and requires proteins with specific functions to form and grow from the ER membrane without any defect. In vitro studies have suggested a role for membrane curvature in LD emergence from the ER. Here, we use the membrane-shaping protein Pex30 to investigate the impact of ER membrane curvature on LD biogenesis and morphology. We modified the reticulon homology domain (RHD) of Pex30, which is responsible for tubulating the ER membrane, by extending the short hairpin transmembrane domains (TMD). The Pex30 (TMD) mutants cannot tubulate the ER membrane and generate less local membrane curvature that WT Pex30. Additionally, these mutants are unable to restore delayed LD biogenesis observed in cells devoid of Pex30. Our results indicate that Pex30 RHD generates local membrane curvature at ER subdomains that drives formation of new LDs.

cell biology↗

bioRxiv2026

Viral Capsid-Membrane Interactions Propel Non-Brownian Movements of Non-enveloped Reoviruses during Entry

Understanding how non-enveloped viruses breach host cell membranes is critical for developing strategies to block viral entry, a key step in infection. Despite extensive study, how viral capsids and host lipid membranes dynamically cooperate during membrane penetration remains poorly defined. Here, using reovirus as a model non-enveloped virus and planar model membranes, we identify previously unrecognized non-Brownian membrane motions of infectious subvirion particles (ISVPs) by single-virus tracking. We then integrate experiments with computational modeling to dissect the stepwise, processive capsid-membrane interactions encoded in these distinct dynamics. We show that ISVP motion transitions from an initial phase of directed translocation to progressively confined diffusion. This behavior reflects a multistep entry mechanism in which initial capsid-membrane contact triggers release of the membrane-active 1N peptide. As 1N accumulates within the bilayer, it generates membrane-associated viral retention sites that promote further virus adsorption and increasingly constrain particle mobility. By directly visualizing these motion signatures, we resolve transient and cooperative capsid-membrane interactions that are difficult to capture using conventional biochemical approaches. Together, these findings provide new insight into early membrane penetration events of non-enveloped viruses. SIGNIFICANCE STATEMENTNon-enveloped viruses must penetrate host cell membranes to initiate infection, yet the dynamic mechanisms by which viral capsids engage and remodel lipid membranes remain poorly understood. By directly visualizing the motion of individual reovirus particles on model membranes, we uncover previously unrecognized non-Brownian dynamics that encode stepwise capsid-membrane interactions during viral entry. Integrating single-virus tracking with computational modeling reveals how peptide-mediated membrane remodeling feeds back to regulate viral engagement. This work provides the first direct visualization of processive, stepwise capsid-membrane interactions during non-enveloped virus entry and establishes viral particle dynamics as a quantitative readout for dissecting membrane penetration mechanisms.

biophysics↗

bioRxiv2025

Crowding-induced collapse and adsorption of polymers with nonuniform bending stiffness

Macromolecular crowding can significantly impact the behavior of biopolymers, with crowding-induced depletion interactions influencing both the conformations and surface adsorption of individual polymers. Although previous studies have explored the influence of homogeneous polymer stiffness in crowded conditions, biomolecules such as DNA can exhibit sequence-dependent stiffness, and DNA origami nanoparticles can be designed with alternating stiff and flexible domains. In this work, we use Langevin dynamics simulations to characterize how nonuniform bending stiffness modulates the conformations and adsorption of polymers in crowded environments. By systematically varying the relative length and arrangement of flexible and semiflexible domains along a linear chain, we show that increasing osmotic pressure leads to a pattern-dependent collapse of the polymer, as revealed by a decrease in the radius of gyration. In general, large flexible regions promote polymer collapse, although flexible domains separating extended semi-flexible regions can facilitate their contact, leading to stable folded conformations. When a surface is present, large semiflexible domains promote adsorption, and the pattern of stiffness can be used to control the adsorption threshold. Our findings provide insight into the impact of spatially varying stiffness on the behavior of polymers in crowded environments, highlighting mechanisms relevant to biopolymers and deformable nanoparticles in both cellular and cell-free contexts.

biophysics↗

bioRxiv2024

Polarity sorting of actin filaments by motor-driven cargo transport

During the active transport of cellular cargo, forces generated by cargo-associated molecular motors propel the cargo along cytoskeletal tracks. However, the forces impact not only the cargo, but also the underlying cytoskeletal filaments. To better understand the interplay between cargo transport and the organization of cytoskeletal filaments, we employ coarse-grained computer simulations to study actin filaments interacting with cargo-anchored myosin motors in a confined domain. We show that cargo transport can lead to the segregation of filaments into domains of preferred filament polarity separated by clusters of aggregated cargoes. The formation of polarity-sorted filament domains is enhanced by larger numbers of cargoes, more motors per cargo, and longer filaments. Analysis of individual trajectories reveals dynamic and heterogeneous behavior, including locally stable aggregates of cargoes that undergo rapid coalescence into larger clusters when sufficiently close. Our results provide insight into the impact of motor-driven organelle transport on actin filaments, which is relevant both in cells and in synthetic environments. O_TEXTBOXSIGNIFICANCE The actin cytoskeleton is vital for intracellular transport, and there is an intricate interplay between the organization of the actin network and cargo transport by molecular motors. In this work, we use computer simulations to demonstrate that the transport of cargoes by teams of molecular motors can lead to the emergence of filament domains, separated by clusters of cargoes, that are sorted by the polarity of filaments. The results, which highlight feedback between transport and filament organization, provide insight into mechanisms influencing the cytoskeleton in cells and in reconstituted systems. C_TEXTBOX

biophysics↗

bioRxiv2024

Morphometric analysis of actin networks

The organization of cytoskeletal elements is pivotal for coordinating intracellular transport in eukaryotic cells. Several quantitative measures based on image analysis have been proposed to characterize morphometric features of fluorescently labeled actin networks. While helpful in detecting differences in actin organization between treatments or genotypes, the accuracy of these measures could not be rigorously assessed due to a lack of ground-truth data to which they could be compared. To overcome this limitation, we utilized coarse-grained computer simulations of actin filaments and crosslinkers to generate synthetic actin networks with varying levels of bundling. We converted the simulated networks into pseudo-fluorescence images similar to images obtained using confocal microscopy. Using both published and novel analysis procedures, we extracted a series of morphometric parameters and benchmarked them against analogous measures based on the ground-truth actin configurations. Our analysis revealed a set of parameters that reliably reports on actin network density, orientation, ordering, and bundling. Application of these morphometric parameters to root epidermal cells of Arabidopsis thaliana revealed subtle changes in network organization between wild-type and mutant cells. This work provides robust measures that can be used to quantify features of actin networks and characterize changes in actin organization for different experimental conditions.

biophysics↗

bioRxiv2023

Particle deformability enables control of interactions between membrane-anchored nanoparticles

Nanoparticles adsorbed on a membrane can induce deformations of the membrane that give rise to effective interactions between the particles. Previous studies have focused primarily on rigid nanoparticles with fixed shapes. However, DNA origami technology has enabled the creation of deformable nanostructures with controllable shapes and mechanical properties, presenting new opportunities to modulate interactions between particles adsorbed on deformable surfaces. Here we use coarse-grained molecular dynamics simulations to investigate deformable, hinge-like nanostructures anchored to lipid membranes via cholesterol anchors. We characterize deformations of the particles and membrane as a function of the hinge stiffness. Flexible particles adopt open configurations to conform to a flat membrane, whereas stiffer particles induce deformations of the membrane. We further show that particles spontaneously aggregate and that cooperative effects lead to changes in their shape when they are close together. Using umbrella sampling methods, we quantify the effective interaction between two particles and show that stiffer hinge-like particles experience stronger and longer-ranged attraction. Our results demonstrate that interactions between de-formable, membrane-anchored nanoparticles can be controlled by modifying mechanical properties of the particles, suggesting new ways to modulate the self-assembly of particles on deformable surfaces.

biophysics↗

bioRxiv2023

Exchange between compartments regulates steady states and stochastic switching of a multisite phosphorylation network

The phosphoregulation of proteins with multiple phosphorylation sites is governed by biochemical reaction networks that can exhibit multistable behavior. However, the behavior of such networks is typically studied in a single reaction volume, while cells are spatially organized into compartments that can exchange proteins. In this work, we use stochastic simulations to study the impact of compartmentalization on a two-site phosphorylation network. We characterize steady states and fluctuation-driven transitions between them as a function of the rate of protein exchange between two compartments. Surprisingly, the rate of stochastic switching between states depends nonmonotonically on the protein exchange rate, with the highest rate of switching occurring at intermediate exchange rates. At sufficiently small exchange rates, the state of the system and rate of switching are controlled largely by fluctuations in the balance of enzymes in each compartment. This leads to negatively correlated states in the compartments. For large exchange rates, the two compartments behave as a single effective compartment. However, when the compartmental volumes are unequal, the behavior differs from a single compartment with the same total volume. These results demonstrate that exchange of proteins between distinct compartments can regulate the emergent behavior of a common signaling motif.

biophysics↗

bioRxiv2023

Propulsive cell entry diverts pathogens from immune degradation by remodeling the phagocytic synapse

Phagocytosis is a critical immune function for infection control and tissue homeostasis. This process is typically described as non-moving pathogens being internalized and degraded in phagolysosomes. For pathogens that evade immune degradation, the prevailing view is that virulence factors that biochemically disrupt the biogenesis of phagoslysosomes are required. In contrast, here we report that physical forces exerted by pathogens during cell entry divert them away from the canonical phagolysosomal degradation pathway, and this altered intracellular fate is determined at the time of phagocytic synapse formation. We used the eukaryotic parasite Toxoplasma gondii as a model because live Toxoplasma uses gliding motility to actively invade into host cells. To differentiate the effect of physical forces from that of virulence factors in phagocytosis, we developed a strategy that used magnetic forces to induce propulsive entry of inactivated Toxoplasma into macrophage cells. Experiments and computer simulations collectively reveal that large propulsive forces suppress productive activation of receptors by hindering their spatial segregation from phosphatases at the phagocytic synapse. Consequently, the inactivated parasites, instead of being degraded in phagolysosomes, are engulfed into vacuoles that fail to mature into degradative units, following an intracellular pathway strikingly similar to that of the live motile parasite. Using opsonized beads, we further confirmed that this mechanism is general, not specific to the parasite used. These results reveal previously unknown aspects of immune evasion by demonstrating how physical forces exerted during active cell entry, independent of virulence factors, can help pathogens circumvent phagolysosomal degradation.

biophysics↗

bioRxiv2023

Topographical analysis of immune cell interactions reveals a biomechanical signature for immune cytolysis

Immune cells live intensely physical lifestyles characterized by structural plasticity, mechanosensitivity, and force exertion. Whether specific immune functions require stereotyped patterns of mechanical output, however, is largely unknown. To address this question, we used super-resolution traction force microscopy to compare cytotoxic T cell immune synapses with contacts formed by other T cell subsets and macrophages. T cell synapses were globally and locally protrusive, which was fundamentally different from the coupled pinching and pulling of macrophage phagocytosis. By spectrally decomposing the force exertion patterns of each cell type, we associated cytotoxicity with compressive strength, local protrusiveness, and the induction of complex, asymmetric interfacial topographies. These features were further validated as cytotoxic drivers by genetic disruption of cytoskeletal regulators, direct imaging of synaptic secretory events, and in silico analysis of interfacial distortion. We conclude that T cell-mediated killing and, by implication, other effector responses are supported by specialized patterns of efferent force.

immunology↗

bioRxiv2022

Organization and Dynamics of Crosslinked Actin Filaments in Confined Environments

The organization of the actin cytoskeleton is impacted by the interplay between physical confinement, features of crosslinking proteins, and deformations of semiflexible actin filaments. Some crosslinking proteins preferentially bind filaments in parallel, while others bind more indiscriminately. However, a quantitative understanding of how the mode of binding influences the assembly of actin networks in confined environments is lacking. Here we employ coarse-grained computer simulations to study the dynamics and organization of semiflexible actin filaments in confined regions upon the addition of crosslinkers. We characterize how the emergent behavior is influenced by the system shape, the number and type of crosslinking proteins, and the length of filaments. Structures include isolated clusters of filaments, highly connected filament bundles, and networks of interconnected bundles and loops. Elongation of one dimension of the system promotes the formation of long bundles that align with the elongated axis. Dynamics are governed by rapid crosslinking into aggregates, followed by a slower change in their shape and connectivity. Crosslinking decreases the average bending energy of short or sparsely connected filaments by suppressing shape fluctuations. However, it increases the average bending energy in highly connected networks because filament bundles become deformed and small numbers of filaments exhibit long-lived, highly unfavorable configurations. Indiscriminate crosslinking promotes the formation of high-energy configurations due to the increased likelihood of unfavorable, difficult-to-relax configurations at early times. Taken together, this work demonstrates physical mechanisms by which crosslinker binding and physical confinement impact the emergent behavior of actin networks, which is relevant both in cells and in synthetic environments. SIGNIFICANCEThe actin cytoskeleton is vital for intracellular transport, yet it remains challenging to understand how its organization is impacted by the interplay between physical confinement and the crosslinking of semiflexible actin filaments. In this study, we explore how the mode of crosslinker binding and the shape of the confining region impact the assembly and organization of actin filaments. The dynamics are governed by rapid crosslinking of spatially proximal filaments into aggregates, followed by slower relaxation of their shape and connectivity. Indiscriminate crosslinking promotes more highly connected networks, greater curvature of long filament bundles, and a subset of filaments in highly unfavorable configurations. The results provide insight into mechanisms influencing the cytoskeleton in cells and in reconstituted systems.

biophysics↗

bioRxiv2022

Membrane-mediated interactions between hinge-like particles

Adsorption of nanoparticles on a membrane can give rise to interactions between particles, mediated by membrane deformations, that play an important role in self-assembly and membrane remodeling. Previous theoretical and experimental research has focused on nanoparticles with fixed shapes, such as spherical, rod-like, and curved nanoparticles. Recently, hinge-like DNA origami nanostructures have been designed with tunable mechanical properties. Inspired by this, we investigate the equilibrium properties of hinge-like particles adsorbed on an elastic membrane using Monte Carlo and umbrella sampling simulations. The configurations of an isolated particle are influenced by competition between bending energies of the membrane and the particle, which can be controlled by changing adsorption strength and hinge stiffness. When two adsorbed particles interact, they effectively repel one another when the strength of adhesion to the membrane is weak. However, a strong adhesive interaction induces an effective attraction between the particles, which drives their aggregation. The configurations of the aggregate can be tuned by adjusting the hinge stiffness: Tip-to-tip aggregation occurs for flexible hinges, whereas tip-to-middle aggregation also occurs for stiffer hinges. Our results highlight the potential for using the mechanical features of deformable nanoparticles to influence their self-assembly when the particles and membrane mutually influence one another.

biophysics↗

bioRxiv2021

Adsorption of semiflexible polymers in crowded environments

Macromolecular crowding is a feature of cellular and cell-free systems that, through depletion effects, can impact the interactions of semiflexible biopolymers with surfaces. In this work, we use computer simulations to study crowding-induced adsorption of semiflexible polymers on otherwise repulsive surfaces. Crowding particles are modeled explicitly, and we investigate the interplay between the bending stiffness of the polymer and the volume fraction and size of crowding particles. Adsorption is promoted by stiffer polymers, smaller crowding particles, and larger volume fractions of crowders. We characterize transitions from non-adsorbed to partially and strongly adsorbed states as a function of the bending stiffness. The crowding-induced transitions occur at smaller values of the bending stiffness as the volume fraction of crowders increases. Concomitant effects on the size and shape of the polymer are reflected by crowding- and stiffness-dependent changes to the radius of gyration. We also demonstrate that curvature of the confining surface can induce desorption when the bending stiffness is sufficiently large. The results of our simulations shed light on the interplay of crowding and bending stiffness on the spatial organization of biopolymers in encapsulated cellular and cell-free systems.

biophysics↗

bioRxiv2019

Mechanical feedback enables catch bonds to selectively stabilize scanning microvilli at T-cell surfaces

T cells use microvilli to search the surfaces of antigen-presenting cells for antigenic ligands. The active motion of scanning microvilli provides a force-generating mechanism that is intriguing in light of single-molecule experiments showing that applied forces on stimulatory receptor-ligand bonds increase their lifetimes (catch-bond behavior). In this work, we introduce a theoretical framework to explore the motion of a microvillus tip above an antigen-presenting surface when receptors on the tip stochastically bind to ligands on the surface and dissociate from them in a force-dependent manner. Forces on receptor-ligand bonds impact the motion of the microvillus, leading to feedback between binding and microvillar motion. We use computer simulations to show that the average microvillus velocity varies in a ligand-dependent manner, that catch bonds generate responses in which some microvilli almost completely stop while others move with a broad distribution of velocities, and that the frequency of stopping depends on the concentration of stimulatory ligands. Typically, a small number of catch bonds initially immobilize the microvillus, after which additional bonds accumulate and increase the cumulative receptor-engagement time. Our results demonstrate that catch bonds can selectively slow and stabilize scanning microvilli, suggesting a physical mechanism that may contribute to antigen discrimination by T cells.

biophysics↗

bioRxiv2018

Synergistic interactions between confinement and macromolecular crowding spatially order transcription and translation in cell-free expression

Synergistic interactions between macromolecular crowding and confinement spatially organize transcription and translation in cells. Yet, reproducing such spatial ordering in cell-free expression platforms has proven to be elusive. Here we report crowding- and confinement-driven spatial self-organization of cell-free expression that mimics expression behavior within and around the nucleoid of prokaryotes. These experiments use Ficoll-70 to approximate cellular macromolecular crowding conditions within cell-size lipid vesicles. Intriguingly, there was an abrupt change in transcriptional dynamics when crowding reached physiologically relevant levels. Imaging experiments revealed that this change in transcriptional dynamics was coincident with localization of plasmid DNA and mRNA at the vesicle wall. Computer simulations demonstrated that crowding leads to an entropically induced attraction between plasmid DNA and the wall, causing localization of DNA near the wall at sufficiently high crowding levels. The experiments demonstrate cell-like spatial organization of translation, where translational activity is controlled by chromosomally-templated positioning of mRNA. This cell-free system provides a flexible experimental platform to probe the underlying mechanisms of self-organization of membrane-less structures in cells and the spatial control of gene expression.

synthetic biology↗

bioRxiv2018

The Cdc42 GEF, Gef1, promotes uniform protein distribution along the actomyosin ring to enable concentric furrowing

During cytokinesis, fission yeast coordinates actomyosin ring constriction with septum ingression, resulting in concentric furrow formation. Mechanisms coordinating septum ingression with the actomyosin ring remain unclear. We report that cells lacking the Cdc42 activator Gef1, combined with an activated allele of the formin, Cdc12, display non-concentric furrowing. Although cells that furrow non-concentrically display normal actomyosin rings, the scaffold Cdc15 is unevenly distributed along the ring. This suggests that after ring assembly, uniform Cdc15 distribution along the ring drives proper furrow formation. We find that Cdc15 levels at the ring are reduced in the activated cdc12 mutant, or upon disruption of Arp2/3 complex-dependent endocytic patches. Furthermore, Cdc15 levels in endocytic patches increase in gef1 mutants. We hypothesize that assembled rings recruit Cdc15 from endocytic patches. Patches with higher Cdc15 levels and slower ring-association rate lead to uneven Cdc15 distribution. Based on this hypothesis we developed a mathematical model that captures experimentally observed Cdc15 distributions along the ring. We propose that, at the ring, Gef1 and endocytic events promote uniform Cdc15 distribution to enable proper septum ingression and concentric furrow formation.\n\nSummary StatementGef1 and endocytic events at the assembled actomyosin ring facilitate uniform Cdc15 distribution along the ring thus enabling concentric furrow formation.

cell biology↗