Biology subjects

Rangamani, P.

Publications and source records attributed to Rangamani, P..

At least 55 records · Page 3Linked to original sources

bioRxiv2023

Divergent iron-regulatory states contribute to heterogeneity in breast cancer aggressiveness

Primary tumors with similar mutational profiles can progress to vastly different outcomes where transcriptional state, rather than mutational profile, predicts prognosis. A key challenge is to understand how distinct tumor cell states are induced and maintained. In triple negative breast cancer cells, invasive behaviors and aggressive transcriptional signatures linked to poor patient prognosis can emerge in response to contact with collagen type I. Herein, collagen-induced migration heterogeneity within a TNBC cell line was leveraged to identify transcriptional programs associated with invasive versus non-invasive phenotypes and implicate molecular switches. Phenotype-guided sequencing revealed that invasive cells upregulate iron uptake and utilization machinery, anapleurotic TCA cycle genes, actin polymerization promoters, and a distinct signature of Rho GTPase activity and contractility regulating genes. The non-invasive cell state is characterized by actin and iron sequestration modules along with glycolysis gene expression. These unique tumor cell states are evident in patient tumors and predict divergent outcomes for TNBC patients. Glucose tracing confirmed that non-invasive cells are more glycolytic than invasive cells, and functional studies in cell lines and PDO models demonstrated a causal relationship between phenotype and metabolic state. Mechanistically, the OXPHOS dependent invasive state resulted from transient HO-1 upregulation triggered by contact with dense collagen that reduced heme levels and mitochondrial chelatable iron levels. This induced expression of low cytoplasmic iron response genes regulated by ACO1/IRP1. Knockdown or inhibition of HO-1, ACO1/IRP1, MRCK, or OXPHOS abrogated invasion. These findings support an emerging theory that heme and iron flux serve as important regulators of TNBC aggressiveness.

cancer biology↗

bioRxiv2023

Liquid-like condensates mediate competition between actin branching and bundling

Cellular remodeling of actin networks underlies cell motility during key morphological events, from embryogenesis to metastasis. In these transformations there is an inherent competition between actin branching and bundling, because steric clashes among branches create a mechanical barrier to bundling. Recently, liquid-like condensates consisting purely of proteins involved in either branching or bundling of the cytoskeleton have been found to catalyze their respective functions. Yet in the cell, proteins that drive branching and bundling are present simultaneously. In this complex environment, which factors determine whether a condensate drives filaments to branch versus becoming bundled? To answer this question, we added the branched actin nucleator, Arp2/3, to condensates composed of VASP, an actin bundling protein. At low actin to VASP ratios, branching activity, mediated by Arp2/3, robustly inhibited VASP-mediated bundling of filaments, in agreement with agent-based simulations. In contrast, as the actin to VASP ratio increased, addition of Arp2/3 led to formation of aster-shaped structures, in which bundled filaments emerged from a branched actin core, analogous to filopodia emerging from a branched lamellipodial network. These results demonstrate that multi-component, liquid-like condensates can modulate the inherent competition between bundled and branched actin morphologies, leading to organized, higher-order structures, similar to those found in motile cells. SIGNIFICANCE STATEMENTReorganization of actin filaments allows cells to migrate, which is required for embryonic development, wound healing, and cancer metastasis. During migration, the leading-edge of the cell consists of needle-like protrusions of bundled actin, which emanate from a sheet of branched actin. Given that the proteins responsible for both architectures are present simultaneously, what determines whether actin filaments will be branched or bundled? Here we show that liquid-like condensates, composed of both branching and bundling proteins, can mediate the inherent competition between these fundamentally different ways of organizing actin networks. This work demonstrates that by tuning the composition of condensates, we can recapitulate the transition from branched to bundled networks, a key step in cell migration.

biophysics↗

bioRxiv2023

Cell motility modes are selected by the interplay of mechanosensitive adhesion and membrane tension

The initiation of directional cell motion requires symmetry breaking that can happen both with or without external stimuli. During cell crawling, forces generated by the cytoskeleton and their transmission through mechanosensitive adhesions to the extracellular substrate play a crucial role. In a recently proposed 1D model (Sens, PNAS 2020), a mechanical feedback loop between force-sensitive adhesions and cell tension was shown to be sufficient to explain spontaneous symmetry breaking and multiple motility patterns through stick-slip dynamics, without the need to account for signaling networks or active polar gels. We extended this model to 2D to study the interplay between cell shape and mechanics during crawling. Through a local force balance along a deformable boundary, we show that the membrane tension coupled with shape change can regulate the spatiotemporal evolution of the stochastic binding of mechanosensitive adhesions. Linear stability analysis identified the unstable parameter regimes where spontaneous symmetry breaking can take place. Using simulations to solve the fully coupled nonlinear system of equations, we show that starting from a randomly perturbed circular shape, this instability can lead to keratocyte-like shapes. Simulations predict that different adhesion kinetics and membrane tension can result in different cell motility modes including gliding, zigzag, rotating, and sometimes chaotic movements. Thus, using a minimal model of cell motility, we identify that the interplay between adhesions and tension can select emergent motility modes.

biophysics↗

bioRxiv2023

Effective cell membrane tension protects red blood cells against malaria invasion

A critical step in how malaria parasites invade red blood cells (RBCs) is the wrapping of the membrane around the egg-shaped merozoites. Recent experiments have revealed that RBCs can be protected from malaria invasion by high membrane tension. While cellular and biochemical aspects of parasite actomyosin motor forces during the malaria invasion have been well studied, the important role of the biophysical forces induced by the RBC membrane-cytoskeleton composite has not yet been fully understood. In this study, we use a theoretical model for lipid bilayer mechanics, cytoskeleton deformation, and membrane-merozoite interactions to systematically investigate the influence of effective RBC membrane tension, which includes contributions from the lipid bilayer tension, spontaneous tension, interfacial tension, and the resistance of cytoskeleton against shear deformation on the progression of membrane wrapping during the process of malaria invasion. Our model reveals that this effective membrane tension creates a wrapping energy barrier for a complete merozoite entry. We calculate the tension threshold required to impede the malaria invasion. We find that the tension threshold is a nonmonotonic function of spontaneous tension and undergoes a sharp transition from large to small values as the magnitude of interfacial tension increases. We also predict that the physical properties of the RBC cytoskeleton layer - particularly the resting length of the cytoskeleton - play key roles in specifying the degree of the membrane wrapping. We also found that the shear energy of cytoskeleton deformation diverges at the full wrapping state, suggesting the local disassembly of the cytoskeleton is required to complete the merozoite entry. Additionally, using our theoretical framework, we predict the landscape of myosin-mediated forces and the physical properties of the RBC membrane in regulating successful malaria invasion. Our findings on the crucial role of RBC membrane tension in inhibiting malaria invasion can have implications for developing novel antimalarial therapeutic or vaccine-based strategies. SignificanceRBC membrane tension plays an important role in regulating RBC shape and functionality. In particular, recent experimental studies have shown that elevated RBC membrane tension protects against severe malaria infection. In this study, we sought to identify how different contributions to the the effective membrane tension can contribute to this mechanically-driven protection against malaria invasion. Using a mathematical model, we derived a relationship between the effective tension of the RBC membrane - comprising a lipid bilayer and a cytoskeleton layer- and the degree of membrane wrapping during malaria invasion. Our model shows that the shear resistance of the RBC cytoskeleton plays an important role in inhibiting malaria invasion. Our findings can be generalized to the role of cell membrane mechanics in many wrapping phenomena providing insight into the crucial contributions of the host-cell membrane in protection against severe infections.

biophysics↗

bioRxiv2023

Kinetic trapping organizes actin filaments within liquid-like protein droplets

AbstractActin is essential for various cellular functions such as growth, migration, and endocytosis. Recent evidence suggests that several actin-binding proteins phase separate to form condensates and that actin networks have different architectures in these droplets. In this study, we use computational modeling to investigate the conditions under which actin forms different network organizations in VASP droplets. Our simulations reveal that the binding and unbinding rates of actin and VASP determine the probability of formation of shells and rings, with shells being more probable than rings. The different actin networks are highly dependent on the kinetics of VASP-actin interactions, suggesting that they arise from kinetic trapping. Specifically, we showed that reducing the residence time of VASP on actin filaments promotes assembly of shells rather than rings, where rings require a greater degree of actin bundling. These predictions were tested experimentally using a mutant of VASP, which has decreased bundling capability. Experiments reveal an increase in the abundance of shells in VASP droplets, consistent with our predictions. Finally, we investigated the arrangements of filaments within deformed droplets and found that the filament length largely determines whether a droplet will straighten into a bundle or remain kinetically trapped in a ring-like architecture. The sphere-to-ellipsoid transition is favored under a wide range of conditions while the ellipse-to-rod transition is only permitted when filaments have a specific range of lengths. Our findings have implications for understanding how the interactions between phase-separated actin binding proteins and actin filaments can give rise to different actin network architectures.

biophysics↗

bioRxiv2023

Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome

Cristae are high curvature structures in the inner mitochondrial membrane (IMM) that are crucial for ATP production. While cristae-shaping proteins have been defined, analogous mechanisms for lipids have yet to be elucidated. Here we combine experimental lipidome dissection with multi-scale modeling to investigate how lipid interactions dictate IMM morphology and ATP generation. When modulating phospholipid (PL) saturation in engineered yeast strains, we observed a surprisingly abrupt breakpoint in IMM topology driven by a continuous loss of ATP synthase organization at cristae ridges. We found that cardiolipin (CL) specifically buffers the IMM against curvature loss, an effect that is independent of ATP synthase dimerization. To explain this interaction, we developed a continuum model for cristae tubule formation that integrates both lipid and protein-mediated curvatures. The model highlighted a snapthrough instability, which drives IMM collapse upon small changes in membrane properties. We also showed that CL is essential in low oxygen conditions that promote PL saturation. These results demonstrate that the mechanical function of CL is dependent on the surrounding lipid and protein components of the IMM. SynopsisO_LIcritical lipidic breakpoint for yeast mitochondria phenocopies the loss of cristae-shaping proteins in the IMM. C_LIO_LIsaturation controls membrane mechanical properties and modulates ATP synthase oligomerization. C_LIO_LImitochondrial-specific lipid cardiolipin can functionally compensate for increased phospholipid saturation and is required for cristae formation in low oxygen environments. C_LIO_LImathematical model for cristae membrane tubules predicts a snapthrough instability mediated by both protein and lipid-encoded curvatures. C_LI Synopsis Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/532310v3_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@196aefforg.highwire.dtl.DTLVardef@1bafcadorg.highwire.dtl.DTLVardef@122f502org.highwire.dtl.DTLVardef@35afd_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2023

Mechanically induced topological transition of spectrin regulates its distribution in the mammalian cortex

The cell cortex is a dynamic assembly that ensures cell integrity during passive deformation or active response by adapting cytoskeleton topologies with poorly understood mechanisms. The spectrin meshwork ensures such adaptation in erythrocytes and neurons. Erythrocytes rely on triangular-like lattices of spectrin tetramers, which in neurons are organized in periodic arrays. We exploited Expansion Microscopy to discover that these two distinct topologies can co-exist in other mammalian cells such as fibroblasts. We show through biophysical measurements and computational modeling that spectrin provides coverage of the cortex and, with the intervention of actomyosin, erythroid-like lattices can dynamically transition into condensates resembling neuron-like periodic arrays fenced by actin stress fibers. Spectrin condensates experience lower mechanical stress and turnover despite displaying an extension close to the contour length of the tetramer. Our study sheds light on the adaptive properties of spectrin, which ensures protection of the cortex by undergoing mechanically induced topological transitions.

cell biology↗

bioRxiv2022

Serine-129 phosphorylation of α-synuclein is a trigger for physiologic protein-protein interactions and synaptic function

Phosphorylation of -synuclein at the Serine-129 site (-syn Ser129P) is an established pathologic hallmark of synucleinopathies, and also a therapeutic target. In physiologic states, only a small fraction of total -syn is phosphorylated at this site, and consequently, almost all studies to date have focused on putative pathologic roles of this post-translational modification. We noticed that unlike native (total) -syn that is widely expressed throughout the brain, the overall pattern of -syn Ser129P is restricted, suggesting intrinsic regulation and putative physiologic roles. Surprisingly, preventing phosphorylation at the Ser-129 site blocked the ability of -syn to attenuate activity-dependent synaptic vesicle (SV) recycling - widely thought to reflect its normal function. Exploring mechanisms, we found that neuronal activity augments -syn Ser-129P, and this phosphorylation is required for -syn binding to VAMP2 and synapsin - two functional binding-partners that are necessary for -syn function. AlphaFold2-driven modeling suggests a scenario where Ser129P induces conformational changes in the C-terminus that stabilizes this region and facilitates protein-protein interactions. Our experiments indicate that the pathology-associated Ser129P is an unexpected physiologic trigger of -syn function, which has broad implications for pathophysiology and drug-development.

neuroscience↗

bioRxiv2022

The ins and outs of membrane bending by intrinsically disordered proteins

Membrane curvature is essential to diverse cellular functions. While classically attributed to structured domains, recent work illustrates that intrinsically disordered proteins are also potent drivers of membrane bending. Specifically, repulsive interactions among disordered domains drive convex bending, while attractive interactions, which lead to liquid-like condensates, drive concave bending. How might disordered domains that contain both repulsive and attractive domains impact curvature? Here we examine chimeras that combine attractive and repulsive interactions. When the attractive domain was closer to the membrane, its condensation amplified steric pressure among repulsive domains, leading to convex curvature. In contrast, when the repulsive domain was closer to the membrane, attractive interactions dominated, resulting in concave curvature. Further, a transition from convex to concave curvature occurred with increasing ionic strength, which reduced repulsion while enhancing condensation. In agreement with a simple mechanical model, these results illustrate a set of design rules for membrane bending by disordered proteins.

biophysics↗

bioRxiv2022

Biophysical modeling of actin-mediated structural plasticity reveals mechanical adaptation in dendritic spines

Synaptic plasticity is important for learning and memory formation; it describes the strengthening or weakening of connections between synapses. The postsynaptic part of excitatory synapses resides in dendritic spines, which are small protrusions on the dendrites. One of the key features of synaptic plasticity is its correlation with the size of these spines. A long-lasting synaptic strength increase (long-term potentiation, LTP) is only possible through the reconfiguration of the actin spine cytoskeleton. Here, we develop an experimentally-informed three-dimensional computational model in a moving boundary framework to investigate this reconfiguration. Our model describes the reactions between actin and actin-binding proteins (ABPs) leading to the cytoskeleton remodeling and their effect on the spine membrane shape to examine the spine enlargement upon LTP. Moreover, we find that the incorporation of perisynaptic elements enhances spine enlargement upon LTP, exhibiting the importance of accounting for these elements when studying structural LTP. Our model shows adaptation to repeated stimuli resulting from the interactions between spine proteins and mechanical forces. Significance StatementDendritic spines are small protrusions that receive stimulation from presynaptic neurons. Upon stimulation, the dendritic spines change their size, an important feature of synaptic plasticity. This change is achieved by modifications to the actin cytoskeleton and mediated by many actin-binding proteins. To investigate the fundamental mechanics of spine expansion, we developed a 3D biophysical model that accounts for the dynamics of cytoskeleton-membrane interactions. Our simulations predict that spine expansion due to actin remodeling can be enhanced by including the interaction with perisynaptic elements that affect the spines mechanical properties. We also found that mechanical properties can control spine expansion after repeated stimuli, which ensures physiological size. Thus, we predict that spine growth is regulated by its mechanical properties.

biophysics↗

bioRxiv2022

Mechanisms underlying divergent relationships between Ca2+ and YAP/TAZ signaling

Yes-associated protein (YAP) and its homolog TAZ are transducers of several biochemical and biomechanical signals, serving to integrate multiplexed inputs from the microenvironment into higher-level cellular functions such as proliferation, differentiation, apoptosis, migration, and hemostasis. Emerging evidence suggests that Ca2+ is a key second messenger that closely connects microenvironmental input signals and YAP/TAZ regulation. However, studies that directly modulate Ca2+ have reported contradictory YAP/TAZ responses: In some studies, a reduction in Ca2+ influx increases the activity of YAP/TAZ, while in others, an increase in Ca2+ influx activates YAP/TAZ. Importantly, Ca2+ and YAP/TAZ exhibit distinct spatiotemporal dynamics, making it difficult to unravel their connections from a purely experimental approach. In this study, we developed a network model of Ca2+-mediated YAP/TAZ signaling to investigate how temporal dynamics and crosstalk of signaling pathways interacting with Ca2+ can alter YAP/TAZ response, as observed in experiments. By including six signaling modules (e.g., GPCR, IP3-Ca2+, Kinases, RhoA, F-actin, and Hippo-YAP/TAZ) that interact with Ca2+, we investigated both transient and steady-state cell response to Angiotensin II and thapsigargin stimuli. The model predicts stimuli, Ca2+ transient, and frequency-dependent relationships between Ca2+ and YAP/TAZ primarily mediated by signaling species like cPKC, DAG, CaMKII, and F-actin. Model results illustrate the role of Ca2+ dynamics and CaMKII bistable response in switching the direction of changes in Ca2+-induced YAP/TAZ activity for different stimuli. Frequency-dependent YAP/TAZ response revealed the competition between upstream regulators of LATS1/2, leading to the YAP/TAZ non-monotonic response to periodic GPCR stimulation. This study provides new insights into the underlying mechanisms responsible for the controversial Ca2+-YAP/TAZ relationship observed in experiments.

systems biology↗

bioRxiv2022

Computational modeling of AMPK and mTOR crosstalk in glutamatergic synapse calcium signaling

Neuronal energy consumption is vital for information processing and memory formation in synapses. The brain consists of just 2% of the human bodys mass, but consumes almost 20% of the bodys energy budget. Most of this energy is attributed to active transport in ion signaling, with calcium being the canonical second messenger of synaptic transmission. Here, we develop a computational model of synaptic signaling resulting in the activation of two protein kinases critical in metabolic regulation and cell fate, AMP-Activated protein kinase (AMPK) and mammalian target of rapamycin (mTOR) and investigate the effect of glutamate stimulus frequency on their dynamics. Our model predicts that frequencies of glutamate stimulus over 10 Hz perturb AMPK and mTOR oscillations at higher magnitudes by up to 70% and area under curve (AUC) by 10%. This dynamic difference in AMPK and mTOR activation trajectories potentially differentiates high frequency stimulus bursts from basal neuronal signaling leading to a downstream change in synaptic plasticity. Further, we also investigate the crosstalk between insulin receptor and calcium signaling on AMPK and mTOR activation and predict that the pathways demonstrate multistability dependent on strength of insulin signaling and metabolic consumption rate. Our predictions have implications for improving our understanding of neuronal metabolism, synaptic pruning, and synaptic plasticity. Key PointsO_LINeurons consume disproportionate amounts of cellular energy relative to their mass, indicating the importance of energy regulation in information processing in the brain. C_LIO_LIAMP activated protein kinase (AMPK) is thought to be the biochemical link between energy consumption in neuronal information processing and synaptic plasticity. C_LIO_LIComputational model investigating the crosstalk between high-frequency glutamatergic calcium signaling and AMPK activation in neurons predicts multistability in AMPK and mammalian target of rapamycin (mTOR) activation. C_LIO_LIOur models predict a frequency-dependent response in AMPK and mTOR activation that also scales according to insulin signaling and energy consumption. The oscillatory behavior depends on both intracellular and extracellular factors, such as energy consumption and insulin signaling. C_LIO_LIThis work elucidates the role of insulin and insulin resistance in regulating neuronal activity, through computational modeling the metabolic response of energy stress resulting from calcium signaling. C_LI

systems biology↗

bioRxiv2022

A thermodynamically-consistent model for ATP production in mitochondria

AO_SCPLOWBSTRACTC_SCPLOWLife is based on energy conversion. In particular, in the nervous system significant amounts of energy are needed to maintain synaptic transmission and homeostasis. To a large extent, neurons depend on oxidative phosphorylation in mitochondria to meet their high energy demand (Pekkurnaz and Wang, 2022). For a comprehensive understanding of the metabolic demands in neuronal signaling, accurate models of ATP production in mitochondria are required. Here, we present a thermodynamically consistent model of ATP production in mitochondria based on previous work (Pietrobon and Caplan, 1985; Magnus and Keizer, 1997; Metelkin et al., 2006; Garcia et al., 2019). The significant improvement of the model is that the reaction rate constants are set such that detailed balance is satisfied. Moreover, using thermodynamic considerations, the dependence of the reaction rate constants on membrane potential, pH, and substrate concentrations are explicitly provided. These constraints assure the model is physically plausible. Furthermore, we explore different parameter regimes to understand in which conditions ATP production or its export are the limiting steps in making ATP available in the cytosol. The outcomes reveal that, under the conditions used in our simulations, ATP production is the limiting step and not its export. Finally, we performed spatial simulations with nine 3D realistic mitochondrial reconstructions and linked the ATP production rate in the cytosol with morphological features of the organelles. 1. SO_SCPLOWUMMARYC_SCPLOWIn this work, Garcia et al present a thermodynamically consistent model for ATP production in mitochondria, in which reaction rate constants are set such that detailed balance is satisfied. Simulations revealed that ATP production, but not its export, is the limiting step, and simulations with 3D mitochondrial reconstructions linked the ATP production rate in the cytosol with the morphological features of the organelles.

cell biology↗

bioRxiv2022

Design principles of dose-response alignment in coupled GTPase switches

"Dose-response alignment" (DoRA), where the downstream response of cellular signaling path-ways closely matches the fraction of activated receptor, can improve the fidelity of dose information transmission. It is believed that a key component for DoRA is negative feedback and thus a natural question that arises is whether there exist design principles for signaling motifs within such negative feedback loops, which may enable these motifs to attain near-perfect DoRA. Here, we investigated several model formulations of an experimentally validated circuit that couples two molecular switches--mGTPase (monomeric GTPase) and tGTPase (heterotrimeric GTPases) -- with negative feedback loops. We find that, in the absence of feedback, the low and intermediate mGTPase activation levels benefit DoRA in the mass action and Hill-function models, respectively. In other cases, where the mass action model with a high mGTPase activation level or the Hill-function model with a non-intermediate mGTPase activation level, the DoRA can be improved by adding negative feedback loops. Furthermore, we found that DoRA in a longer cascade (i.e., tGTPase) can be obtained using Hill-function kinetics under certain conditions. In summary, we show how ranges of activity of mGTPase, reaction kinetics, the negative feedback, and the cascade length affect DoRA. This work provides a framework for improving the DoRA performance in signaling motifs with negative feedback loops. Significance StatementDose-response alignment helps cells faithfully transmit dose information; how this alignment is achieved in motifs with negative feedback is unclear. Through rigorous studies interrogating a naturally occurring motif comprised of two species of GTPases coupled by negative feedback loops, this work reveals the versatile roles of negative feedback loops and GTPase regulators on DoRA. We find that the negative feedback can enhance DoRA only with specific kinetic forms and with certain ranges of GTPases activation levels. This knowledge advances our understanding of the role of negative feedback on DoRA and sheds light on the importance of dynamic range of signaling processes as an essential determinant of how cells transfer information about stimuli. Findings can help design signaling circuits with better DoRA behavior, and ultimately augment cell signaling studies.

systems biology↗

bioRxiv2022

Formation of protein-mediated tubes is governed by a snapthrough transition

Plasma membrane tubes are ubiquitous in cellular membranes and in the membranes of intracellular organelles. They play crucial roles in trafficking, ion transport, and cellular motility. These tubes can be formed due to localized forces acting on the membrane or by the curvature induced by membrane-bound proteins. Here, we present a mathematical framework to model cylindrical tubular protrusions formed by proteins that induce anisotropic spontaneous curvature. Our analysis revealed that the tube radius depends on an effective tension that includes contributions from the bare membrane tension and the protein-induced curvature. We also found that the length of the tube undergoes an abrupt transition from a short, domeshaped membrane to a long cylinder and this transition is characteristic of a snapthrough instability. Finally, we show that the snapthrough instability depends on the different parameters including coat area, bending modulus, and extent of protein-induced curvature. Our findings have implications for tube formation due to BAR-domain proteins in processes such as endocytosis, t-tubule formation in myocytes, and cristae formation in mitochondria.

cell biology↗

bioRxiv2022

Modeling membrane curvature generation using mechanics and machine learning

The deformation of cellular membranes regulates trafficking processes, such as exocytosis and endocytosis. Classically, the Helfrich continuum model is used to characterize the forces and mechanical parameters that cells tune to accomplish membrane shape changes. While this classical model effectively captures curvature generation, one of the core challenges in using it to approximate a biological process is selecting a set of mechanical parameters (including bending modulus and membrane tension) from a large set of reasonable values. We used the Helfrich model to generate a large synthetic dataset from a random sampling of realistic mechanical parameters and used this dataset to train machine learning models. These models produced promising results, accurately classifying model behavior and predicting membrane shape from mechanical parameters. We also note emerging methods in machine learning that can leverage the physical insight of the Helfrich model to improve performance and draw greater insight into how cells control membrane shape change.

biophysics↗

bioRxiv2022

Spatiotemporal modeling reveals geometric dependence of AMPAR dynamics on dendritic spine morphology

The modification of neural circuits depends on the strengthening and weakening of synaptic connections. Synaptic strength is often correlated to the density of the ionotropic, glutamateric receptors, AMPAR, (-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor) at the postsynaptic density (PSD). While AMPAR density is known to change based on complex biological signaling cascades, the effect of geometric factors such as dendritic spine shape, size, and curvature remain poorly understood. In this work, we developed a deterministic, spatiotemporal model to study the dynamics of AMPAR during long term potentiation (LTP). This model includes a minimal set of biochemical events that represent the upstream signaling events, trafficking of AMPAR to and from the PSD, lateral diffusion in the plane of the spine membrane, and the presence of an extrasynaptic AMPAR pool. Using idealized and realistic spine geometries, we show that the dynamics and increase of bound AMPAR at the PSD depends on a combination of endo- and exocytosis, membrane diffusion, availability of free AMPAR, and intracellular signaling interactions. We also found non-monotonic relationships between spine volume and change in AMPAR at the PSD, suggesting that spines restrict changes in AMPAR to optimize resources and prevent runaway potentiation. Significance StatementSynaptic plasticity involves dynamic biochemical and physical remodeling of small protrusions called dendritic spines along the dendrites of neurons. Proper synaptic functionality within these spines requires changes in receptor number at the synapse, which has implications for down-stream neural functions, such as learning and memory formation. In addition to being signaling subcompartments, spines also have unique morphological features that can play a role in regulating receptor dynamics on the synaptic surface. We have developed a spatiotemporal model that couples biochemical signaling and receptor trafficking modalities in idealized and realistic spine geometries to investigate the role of biochemical and biophysical factors in synaptic plasticity. Using this model, we highlight the importance of spine size and shape in regulating bound AMPAR dynamics that govern synaptic plasticity, and predict how spine shape might act to reset synaptic plasticity as a built-in resource optimization and regulation tool.

neuroscience↗

bioRxiv2022

Liquid-like assembly of VASP drives actin polymerization and bundling

The organization of actin filaments into bundles is required for cellular processes such as motility, morphogenesis, and cell division. Filament bundling is controlled by a network of actin binding proteins. Recently, several proteins that comprise this network have been found to undergo liquid-liquid phase separation. How might liquid-like condensates contribute to filament bundling? Here, we show that the processive actin polymerase and bundling protein, VASP, forms liquid-like droplets under physiological conditions. As actin polymerizes within VASP droplets, elongating filaments partition to the edges of the droplet to minimize filament curvature, forming an actin-rich ring within the droplet. The rigidity of this ring is balanced by the droplets surface tension, as predicted by a continuum-scale computational model. However, as actin polymerizes and the ring grows thicker, its rigidity increases and eventually overcomes the surface tension of the droplet, deforming into a linear bundle. The resulting bundles contain long, parallel actin filaments that grow from their tips. Significantly, the fluid nature of the droplets is critical for bundling, as more solid droplets resist deformation, preventing filaments from rearranging to form bundles. Once the parallel arrangement of filaments is created within a VASP droplet, it propagates through the addition of new actin monomers to achieve a length that is many times greater than the initial droplet. This droplet-based mechanism of bundling may be relevant to the assembly of cellular architectures rich in parallel actin filaments, such as filopodia, stress fibers, and focal adhesions.

biophysics↗