Biology subjects

Rangamani, P.

Publications and source records attributed to Rangamani, P..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Coupling between membrane undulations and lipid curvature leads to transient local enrichment of cardiolipin in mitochondrial membranes

Organelles such as mitochondria have characteristic shapes that are critical to their function. Recent efforts have revealed that the curvature contributions of individual lipid species can be a factor in the generation of membrane shape in these organelles. Inspired by lipidomics data from yeast mitochondrial membranes, we used Martini coarse-grained molecular dynamics simulations to investigate how lipid composition facilitates membrane shaping. We found that increasing lipid saturation increases bending rigidity while reducing the monolayer spontaneous curvature. We also found that systems containing cardiolipin exhibited decreased bending rigidity and increased spontaneous curvature when compared to bilayers containing its precursor, phosphatidylglycerol. This finding contradicts some prior experimental results that suggest that bilayers containing tetraoleoyl cardiolipin have greater rigidity than dioleoyl phosphatidylcholine bilayers. To investigate this discrepancy, we analyzed our simulations for correlations between lipid localization and local curvature. We found that there are transient correlations between curved lipids such as cardiolipin (CDL) and phosphatidylethanolamine (PE) and curvature; these interactions enrich specific bilayer undulatory modes and cause bilayer softening. Furthermore, we show that curvature-localization of some lipids such as cardiolipin can influence lipids in the opposing leaflet. These observations add to the emerging evidence that lipid geometric features give rise to local interactions, which can cause membrane compositional heterogeneities. The cross-talk between composition-driven tuning of membrane properties and membrane shape has implications for membrane organization and its related functions. SIGNIFICANCEThe material properties of phospholipid membranes are a function of the lipid composition. Theabundance of cardiolipin in the mitochondrial inner membrane implies a functional role for this special lipid. We explore the interactions of cardiolipin with other lipids with varying lipid saturation using coarse-grained molecular dynamics simulations. We find that membranes containing cardiolipin have higher spontaneous curvature and lower bending rigidity when compared to membranes without cardiolipin - in line with prior models and experiments. We also show that the low bending rigidity of cardiolipin-containing symmetric, and flat bilayered systems is due to the transient partitioning of cardiolipin to undulations due to curvature sensing. This is a mechanism for forming lateral membrane heterogeneities in otherwise symmetric systems.

biophysics↗

bioRxiv2025

Periodic Obstacles Regulate Membrane Tension Propagation to Enable Localized Mechanotransduction

Forces applied to cellular membranes lead to transient membrane tension gradients. The way membrane tension propagates away from the stimulus site into the membrane reservoir is a key property in cellular adaptation. However, it remains unclear how tension propagation in membranes is regulated and how it depends on the cell type. Here, we investigate plasma membrane tension propagation in cultured Caenorhabditis elegans mechanosensory neurons. We show that tension propagation travels quickly and is restricted to a particular distance in the neurites -- projections from the cell body of a neuron. A biophysical model of tension propagation suggests that periodic obstacle density and arrangement play key roles in controlling the propagation of mechanical information. Our experiments show that tension propagation is strongly dependent on the intact actin and microtubule cytoskeleton, whereas membrane lipid properties have minimal impact. In particular, the organization of the /{beta}-spectrin network and the MEC-2 stomatin condensates in periodic scaffold act as barriers to tension propagation, limiting the spread of tension. Our findings suggest that restricting membrane tension propagation in space and time enables precise localized signaling, allows a single neuron to process mechanical signals in multiple distinct domains, thus expanding its computational capacity.

biophysics↗

bioRxiv2024

Glycocalyx-induced formation of membrane tubes

Tubular membrane structures are ubiquitous in cells and in the membranes of intracellular organelles such as the Golgi complex and the endoplasmic reticulum. Tubulation plays essential roles in numerous biological processes, including filopodia growth, trafficking, ion transport, and cellular motility. Understanding the fundamental mechanism of the formation of membrane tubes is thus an important problem in the fields of biology and biophysics. Though extensive studies have shown that tubes can be formed due to localized forces acting on the membrane or by the curvature induced by membrane-bound proteins, little is known about how membrane tubes are induced by glycocalyx, a sugar-rich layer at the cell surface. In this work, we develop a biophysical model that combines polymer physics theory and the Canham-Helfrich membrane theory to investigate how the glycocalyx generates cylindrical tubular protrusions on the cell membrane. Our results show that the glycocalyx alone can induce the formation of tubular membrane structures. This tube formation involves a first-order shape transition without any externally applied force or other curvature-inducing mechanisms. We also find that critical values of glycocalyx grafting density and glycopolymer length are needed to induce the formation of tubular structures. The presence of vertical actin force, line tension, and spontaneous curvature reduces the critical grafting density and length of polymer that triggers the formation of membrane tube, which suggests that the glycocalyx makes tube formation energetically more favorable when combined with an actin force, line tension, and spontaneous curvature. Significance StatementIn many cells, the existence of glycocalyx, a thick layer of polymer meshwork comprising proteins and complex sugar chains coating the outside of the cell membrane, regulates the formation of membrane tubes. Here, we propose a theoretical model that combines polymer physics theory and the Canham-Helfrich membrane theory to study the formation of cylindrical tubular protrusions induced by the glycocalyx. Our findings indicate that glycocalyx plays an important role in the formation of membrane tubes. We find that there exists critical grafting density and length of polymer that triggers the formation of membrane tubes, and the glycocalyx-induced tube formation is facilitated when combined with actin forces, line tension, and spontaneous curvature. Our theoretical model has implications for understanding how biological membranes may form tubular structures.

biophysics↗

bioRxiv2024

Synaptic cleft geometry modulates NMDAR opening probability by tuning neurotransmitter residence time

1Synaptic morphology plays a critical role in modulating the dynamics of neurotransmitter diffusion and receptor activation in interneuron communication. In this study, we investigated how variations in synaptic geometry, including curvature of the synaptic cleft, distance between the presynaptic and postsynaptic membranes, and the surface area-to-volume ratio of the cleft, influence glutamate diffusion and N-Methyl-D-Aspartate receptor (NMDAR) opening probabilities. We developed a stochastic model for receptor activation using reconstructions from realistic synaptic geometries. Our simulations revealed a substantial variability in NMDAR activation, highlighting the significant impact of synaptic structure on receptor dynamics. By exploring the interplay between curvature and surface area-to-volume ratio, we found that increasing the curvature of the synaptic membranes could compensate for reduced NMDAR activation when the synaptic cleft distance was large. We also found that non-parallel membrane configurations, particularly convex presynapses or concave postsynaptic densities (PSDs), maximize NMDAR activation via increased surface area-to-volume ratio, leading to prolonged glutamate residence and reduced leakage. Finally, introducing NMDAR clustering within the PSD significantly enhanced receptor activation across different geometric conditions and mitigated the effects of synaptic morphology on NMDAR opening probabilities. Our findings underscore the complex interplay between synaptic geometry and receptor dynamics, providing insights into how structural modifications can influence synaptic efficacy and plasticity. 2 Significance statementThis study demonstrates that synaptic morphology profoundly shapes neurotransmitter diffusion and NMDA receptor activation, directly impacting synaptic efficacy. Our model shows that factors like synaptic cleft curvature, membrane spacing, and surface area-to-volume ratio significantly influence receptor dynamics. Given the dynamic nature of dendritic spines, which change shape and size during synaptic plasticity, our findings illustrate how purely morphological changes in cleft structure can modulate interneuronal communication and signal strength.

biophysics↗

bioRxiv2024

Nanoscale curvature of the plasma membrane regulates mechanoadaptation through nuclear deformation and rupture

Nuclear translocation of the transcription regulatory proteins YAP and TAZ is a critical readout of cellular mechanotransduction. Recent experiments have demonstrated that cells on substrates with well-defined nanotopographies demonstrate mechanoadaptation through a multitude of effects - increased integrin endocytosis as a function of nanopillar curvature, increased local actin assembly on nanopillars but decreased global cytoskeletal stiffness, and enhanced nuclear deformation. How do cells respond to local nanotopo-graphical cues and integrate their responses across multiple length scales? This question is addressed using a biophysical model that incorporates plasma membrane (PM) curvature-dependent endocytosis, PM curvature-sensitive actin assembly, and stretch-induced opening of nuclear pore complexes (NPCs) in the nuclear envelope (NE). This model recapitulates lower levels of global cytoskeletal assembly on nanopillar substrates, which can be partially compensated for by local actin assembly and NE indentation, leading to enhanced YAP/TAZ transport through stretched NPCs. Using cell shapes informed by electron micrographs and fluorescence images, the model predicts lamin A and F-actin localization around nanopillars, in good agreement with experimental measurements. Finally, simulations predict nuclear accumulation of YAP/TAZ following rupture of the NE and this is validated by experiments. Overall, this study indicates that nanotopography tunes mechanoadaptation through both positive and negative feedback on mechanotransduction. Table of Contents O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/619165v2_ufig1.gif" ALT="Figure 1"> View larger version (84K): org.highwire.dtl.DTLVardef@ec6d5aorg.highwire.dtl.DTLVardef@1ff6ec2org.highwire.dtl.DTLVardef@c09f46org.highwire.dtl.DTLVardef@18df50_HPS_FORMAT_FIGEXP M_FIG C_FIG This study uses experiments and biophysical modeling to examine the response and adaptation of cells to nanoscale topography of surfaces. It is shown that cytoskeletal assembly and nuclear localization of transcription regulatory factors such as YAP/TAZ can be tuned by nanoscale membrane curvature and nuclear deformation and rupture due to substrate nanotopography.

biophysics↗

bioRxiv2024

Biophysical modeling of membrane curvature generation and curvature sensing by the glycocalyx

Generation of membrane curvature is fundamental to cellular function. Recent studies have established that the glycocalyx, a sugar-rich polymer layer at the cell surface, can generate membrane curvature. While there have been some theoretical efforts to understand the interplay between the glycocalyx and membrane bending, there remain open questions about how the properties of the glycocalyx affect membrane bending. For example, the relationship between membrane curvature and the density of glycosylated proteins on its surface remains unclear. In this work, we use polymer brush theory to develop a detailed biophysical model of the energetic interactions of the glycocalyx with the membrane. Using this model, we identify the conditions under which the glycocalyx can both generate and sense curvature. Our model predicts that the extent of membrane curvature generated depends on the grafting density of the glycocalyx and the length of the polymers constituting the glycocalyx. Furthermore, when coupled with the intrinsic membrane properties such as spontaneous curvature and a line tension along the membrane, the curvature generation properties of the glycocalyx are enhanced. These predictions were tested experimentally by examining the propensity of glycosylated transmembrane proteins to drive the assembly of highly-curved filopodial protrusions at the plasma membrane of adherent mammalian cells. Our model also predicts that the glycocalyx has curvature sensing capabilities, in agreement with the results of our experiments. Thus, our study develops a quantitative framework for mapping the properties of the glycocalyx to the curvature generation capability of the membrane. Significance StatementThe glycocalyx is a dense layer of glycosylated transmembrane proteins and lipids distributed on the extracellular surface of eukaryotic cells. It is known to mediate cell-cell interactions and protect cells from invasion by pathogens. However, recently it has been found to play a role in generating membrane curvature, which is essential to diverse cellular functions spanning from endocytosis to cell division. Experiments have revealed that different membrane shapes: spherical vesicles, pearls, and tubes are regulated by the glycocalyx. However, currently, we lack a quantitative physical explanation of how glycocalyx properties determine membrane geometries. Here we develop a polymer brush theory-based model, which suggests that the interplay between glycocalyx polymers and membrane bending captures the wide variety of membrane shapes from spherical buds to elongated pearl-like shapes found in previously published experiments. We predict that the physical properties of glycocalyx polymers, line tension, and membrane elastic parameters play significant roles in regulating membrane morphologies. We find that the glycocalyx prefers higher local membrane curvature indicating that the glycocalyx can sense local curvature.

biophysics↗

bioRxiv2024

Modeling collagen fibril degradation as a function of matrix microarchitecture

Collagenolytic degradation is a process fundamental to tissue remodeling. The microarchitecture of collagen fibril networks changes during development, aging, and disease. Such changes to microarchitecture are often accompanied by changes in matrix degradability. In vitro, collagen matrices of the same concentration but different microarchitectures also vary in degradation rate. How do different microarchitectures affect matrix degradation? To answer this question, we developed a computational model of collagen degradation. We first developed a lattice model that describes collagen degradation at the scale of a single fibril. We then extended this model to investigate the role of microarchitecture using Brownian dynamics simulation of enzymes in a multi-fibril three dimensional matrix to predict its degradability. Our simulations predict that the distribution of enzymes around the fibrils is non-uniform and depends on the microarchitecture of the matrix. This non-uniformity in enzyme distribution can lead to different extents of degradability for matrices of different microarchitectures. Our model predictions were tested using in vitro experiments with synthesized collagen gels of different microarchitectures. Experiments showed that indeed degradation of collagen depends on the matrix architecture and fibril thickness. In summary, our study shows that the microarchitecture of the collagen matrix is an important determinant of its degradability.

biophysics↗

bioRxiv2024

Increasing certainty in systems biology models using Bayesian multimodel inference

Mathematical models are indispensable to the system biology toolkit for studying the structure and behavior of intracellular signaling networks. A common approach to modeling is to develop a system of equations that encode the known biology using approximations and simplifying assumptions. As a result, the same signaling pathway can be represented by multiple models, each with its set of underlying assumptions, which opens up challenges for model selection and decreases certainty in model predictions. Here, we use Bayesian multimodel inference to develop a framework to increase certainty in systems biology models. Using models of the extracellular regulated kinase (ERK) pathway, we first show that multimodel inference increases predictive certainty and yields predictors that are robust to changes in the set of available models. We then show that predictions made with multi-model inference are robust to data uncertainties introduced by decreasing the measurement duration and reducing the sample size. Finally, we use multimodel inference to identify a new model to explain experimentally measured sub-cellular location-specific ERK activity dynamics. In summary, our framework highlights multimodel inference as a disciplined approach to increasing the certainty of intracellular signaling activity predictions.

systems biology↗

bioRxiv2024

Spatial Modeling Algorithms for Reactions and Transport (SMART) in Biological Cells

Biological cells rely on precise spatiotemporal coordination of biochemical reactions to control their many functions. Such cell signaling networks have been a common focus for mathematical models, but they remain challenging to simulate, particularly in realistic cell geometries. Herein, we present our software, Spatial Modeling Algorithms for Reaction and Transport (SMART), a package that takes in high-level user specifications about cell signaling networks and molecular transport, and then assembles and solves the associated mathematical and computational systems. SMART uses state-of-the-art finite element analysis, via the FEniCS Project software, to efficiently and accurately resolve cell signaling events over discretized cellular and subcellular geometries. We demonstrate its application to several different biological systems, including YAP/TAZ mechanotransduction, calcium signaling in neurons and cardiomyocytes, and ATP generation in mitochondria. Throughout, we utilize experimentally-derived realistic cellular geometries represented by well-conditioned tetrahedral meshes. These scenarios demonstrate the applicability, flexibility, accuracy and efficiency of SMART across a range of temporal and spatial scales.

systems biology↗

bioRxiv2024

Liquid-like condensates that bind actin can polymerize and bundle actin filaments

Liquid-like protein condensates perform diverse physiological functions. Previous work showed that VASP, a processive actin polymerase, forms condensates that polymerize and bundle actin. To minimize their curvature, filaments accumulated at the inner condensate surface, ultimately deforming the condensate into a rod-like shape, filled with a bundle of parallel filaments. Here we show that this behavior does not require proteins with specific polymerase activity. Specifically, we found that condensates composed of Lamellipodin, a protein that binds actin but is not an actin polymerase, were also capable of polymerizing and bundling actin filaments. To probe the minimum requirements for condensate-mediated actin bundling, we developed an agent-based computational model. Guided by its predictions, we hypothesized that any condensate-forming protein that binds actin could bundle filaments through multivalent crosslinking. To test this idea, we added an actin-binding motif to Eps15, a condensate-forming protein that does not normally bind actin. The resulting chimera formed condensates that drove efficient actin polymerization and bundling. Collectively, these findings broaden the family of proteins that could organize cytoskeletal filaments to include any actin-binding protein that participates in protein condensation.

biophysics↗

bioRxiv2024

Dynamic mechanisms for membrane skeleton transitions

The plasma membrane and the underlying skeleton form a protective barrier for eukaryotic cells. The molecules forming this complex composite material constantly rearrange under mechanical stress to confer this protective capacity. One of those molecules, spectrin, is ubiquitous in the membrane skeleton and primarily located proximal to the inner leaflet of the plasma membrane and engages in protein-lipid interactions via a set of membrane-anchoring domains. Spectrin is linked by short actin filaments and its conformation varies in different types of cells. In this work, we developed a generalized network model for the membrane skeleton integrated with myosin contractility and membrane mechanics to investigate the response of the spectrin meshwork to mechanical loading. We observed that the force generated by membrane bending is important to maintain a smooth skeletal structure. This suggests that the membrane is not just supported by the skeleton, but has an active contribution to the stability of the cell structure. We found that spectrin and myosin turnover are necessary for the transition between stress and rest states in the skeleton. Our model reveals that the actin-spectrin meshwork dynamics are balanced by the membrane forces with area constraint and volume restriction promoting the stability of the membrane skeleton. Furthermore, we showed that cell attachment to the substrate promotes shape stabilization. Thus, our proposed model gives insight into the shared mechanisms of the membrane skeleton associated with myosin and membrane that can be tested in different types of cells. Significance StatementSpectrin was first observed in red blood cells, as a result of which, many theoretical models focused on understanding its function in this cell type. However, recently, experiments have shown that spectrin is an important skeletal component for many different cell types and that it can form different configurations with actin. In this work, we proposed a model to study the shared mechanisms behind the function of the actin-spectrin meshwork in different types of cells. We found that membrane dynamics in addition to spectrin and myosin turnover are necessary to achieve conformational changes when stresses are applied and to guarantee shape stability when the stresses are removed. We observed that membrane bending is important to support skeletal structure. Furthermore, our model gives insight into how cell shape is maintained despite constant spectrin turnover and myosin contraction.

biophysics↗

bioRxiv2024

Interplay between cortical adhesion and membrane bending regulates microparticle formation

The formation of blebs and microparticle formation requires the bending of the plasma membrane away from the cytosol. There are multiple factors that control the formation of the microparticles including the loss of lipid asymmetry, primarily the exposure of phosphatidylserine on the outer leaflet, detachment of the membrane from the cortical cytoskeleton, and bleb expansion due to pressure. In this work, we develop a biophysical model that accounts for the interaction between these different factors. Our findings reveal that linker attachment is a key determinant of outward budding and lays out the mechanical aspects of outward budding of the plasma membrane. Significance StatementCells release many types of membrane-enclosed vesicles in response to stress, inflammation, or other injuries. Formation of these membrane-enclosed structures is critical for proper function of the coagulation cascade and apoptosis. In many cases, these microparticles are also a part of the long distance intercellular communication and are implicated in chemoresistance. A particular class of vesicles called ectosomes or microparticles are released by the outward budding of the plasma membrane, a process which requires detachment of the membrane from the cortex, exposure of negatively charged, curvature-inducing lipids such as phosphatidylserine from the inner leaflet to the outer leaflet, and pressure-driven expansion of the bleb. Here, we used membrane mechanics coupled with the kinetics of adhesive linker binding-unbinding to investigate how these different factors interact together. Using our models, we predict how linker properties plays an important role in the outward budding of the plasma membrane and identify conditions that can promote or inhibit such curvature generation. These findings have implications not just for conditions that require successful microparticle formation such as the procoagulation cascade but also for inhibiting microparticle formation in cases of chemoresistant drug efflux by tumor cells.

biophysics↗

bioRxiv2024

A spatial model of autophosphorylation of CaMKII in a glutamatergic spine suggests a network-driven kinetic mechanism for bistable changes in synaptic strength.

Long-term potentiation (LTP) is a biochemical process that underlies learning in excitatory glutamatergic synapses in the Central Nervous System (CNS). The critical early driver of LTP is autophosphorylation of the abundant postsynaptic enzyme, Ca2+/calmodulin-dependent protein kinase II (CaMKII). Autophosphorylation is initiated by Ca2+ flowing through NMDA receptors activated by strong synaptic activity. Its lifetime is ultimately determined by the balance of the rates of autophosphorylation and of dephosphorylation by protein phosphatase 1 (PP1). Here we have modeled the autophosphorylation and dephosphorylation of CaMKII during synaptic activity in a spine synapse using MCell4, an open source computer program for creating particle-based stochastic, and spatially realistic models of cellular microchemistry. The model integrates four earlier detailed models of separate aspects of regulation of spine Ca2+ and CaMKII activity, each of which incorporate experimentally measured biochemical parameters and have been validated against experimental data. We validate the composite model by showing that it accurately predicts previous experimental measurements of effects of NMDA receptor activation, including high sensitivity of induction of LTP to phosphatase activity in vivo, and persistence of autophosphorylation for a period of minutes after the end of synaptic stimulation. We then use the model to probe aspects of the mechanism of regulation of autophosphorylation of CaMKII that are difficult to measure in vivo. We examine the effects of "CaM-trapping," a process in which the affinity for Ca2+/CaM increases several hundred-fold after autophosphorylation. We find that CaM-trapping does not increase the proportion of autophosphorylated subunits in holoenzymes after a complex stimulus, as previously hypothesized. Instead, CaM-trapping may dramatically prolong the lifetime of autophosphorylated CaMKII through steric hindrance of dephosphorylation by protein phosphatase 1. The results provide motivation for experimental measurement of the extent of suppression of dephosphorylation of CaMKII by bound Ca2+/CaM. The composite MCell4 model of biochemical effects of complex stimuli in synaptic spines is a powerful new tool for realistic, detailed dissection of mechanisms of synaptic plasticity.

neuroscience↗

bioRxiv2024

Spatiotemporal orchestration of calcium-cAMP oscillations on AKAP/AC nanodomains is governed by an incoherent feedforward loop

The nanoscale organization of enzymes associated with the dynamics of second messengers is critical for ensuring compartmentation and localization of signaling molecules in cells. Specifically, the spatiotemporal orchestration of cAMP and Ca2+ oscillations is critical for many cellular functions. Previous experimental studies have shown that the formation of nanodomains of A-kinase anchoring protein 79/150 (AKAP150) and adenylyl cyclase 8 (AC8) on the surface of pancreatic MIN6 {beta} cells modulates the phase of Ca2+-cAMP oscillations from out-of-phase to in-phase. In this work, we develop computational models of the Ca2+/cAMP pathway and AKAP/AC nanodomain formation that give rise to the two important predictions: instead of an arbitrary phase difference, the out-of-phase Ca2+/cAMP oscillation reaches Ca2+ trough and cAMP peak simultaneously, which is defined as inversely out-of-phase; the in-phase and inversely out-of-phase oscillations associated with Ca2+-cAMP dynamics on and away from the nanodomains can be explained by an incoherent feedforward loop. Factors such as cellular surface-to-volume ratio, compartment size, and distance between nan-odomains do not affect the existence of in-phase or inversely out-of-phase Ca2+/cAMP oscillation, but cellular surface-to-volume ratio and compartment size can affect the time delay for the inversely out-of-phase Ca2+/cAMP oscillation while the distance between two nanodomains does not. Finally, we predict that both the Turing pattern-generated nanodomains and experimentally measured nan-odomains demonstrate the existence of in-phase and inversely out-of-phase Ca2+/cAMP oscillation when the AC8 is at a low level, consistent with the behavior of an incoherent feedforward loop. These findings unveil the key circuit motif that governs cAMP and Ca2+ oscillations and advance our understanding of how nanodomains can lead to spatial compartmentation of second messengers.

systems biology↗

bioRxiv2023

Computational modeling establishes mechanotransduction as a potent entrainment cue for the mammalian circadian clock

Mechanotransduction, which is the integration of mechanical signals from the cells external environment to changes in intracellular signaling, governs many cellular functions. Recent studies have shown that the mechanical state of the cell is also coupled to the cellular circadian clock. To investigate possible interactions between circadian rhythms and cellular mechanotransduction, we have developed a computational model that integrates the two pathways. We postulated that the translocation of the transcriptional regulators YAP/TAZ and MRTF into the nucleus leads to altered expression of circadian proteins. Simulations from our model predict that lower levels of cytoskeletal activity are associated with longer circadian oscillation periods and higher oscillation amplitudes, consistent with recent experimental observations. Furthermore, accumulation of YAP/TAZ and MRTF in the nucleus causes circadian oscillations to decay. These effects hold both at the single-cell level and within a population-level framework. Finally, we investigated the effects of mutations in YAP or lamin A, the latter of which lead to a class of diseases known as laminopathies. Oscillations in circadian proteins are substantially weaker in populations of cells with in silico mutations in YAP or lamin A, suggesting that defects in mechanotransduction can disrupt the circadian clock in certain disease states. However, by reducing substrate stiffness, we were able to restore normal oscillatory behavior, suggesting a possible compensatory mechanism. Thus our study identifies that mechanotransduction could be a potent modulatory cue for cellular clocks and this crosstalk can be leveraged to rescue the circadian clock in disease states.

systems biology↗

bioRxiv2023

Modeling Cardiomyocyte Signaling and Metabolism Predicts Genotype to Phenotype Mechanisms in Hypertrophic Cardiomyopathy

Familial hypertrophic cardiomyopathy (HCM) is a significant precursor of heart failure and sudden cardiac death, primarily caused by mutations in sarcomeric and structural proteins. Despite the extensive research on the HCM genotype, the complex, context-specific nature of many signaling and metabolic pathways linking the HCM genotype to phenotype has hindered therapeutic advancements for patients. To address these challenges, here, we have developed a computational systems biology model of HCM at the cardiomyocyte level. Utilizing a stochastic logic-based ODE method, we integrate subcellular systems in cardiomyocytes that jointly modulate HCM genotype to phenotype, including cardiac signaling, metabolic, and gene regulatory networks, as well as posttranslational modifications linking these networks. After validating with experimental data on changes in activity of signaling species in HCM context and transcriptomes of two HCM mouse models (R403Q-MyHC and R92W-TnT), the model predicts significant changes in cardiomyocyte metabolic functions such as ATP synthase deficiency and a transition from fatty acids to carbohydrate metabolism in HCM. The model indicated major shifts in glutamine-related metabolism and increased apoptosis after HCM-induced ATP synthase deficiency. Aligned with prior experimental studies, we predicted that the transcription factors STAT, SRF, GATA4, TP53, and FoxO are the key regulators of cardiomyocyte hypertrophy and apoptosis in HCM. Using the model, we identified shared (e.g., activation of PGC1 by AMPK, and FHL1 by titin) and context-specific mechanisms (e.g., regulation of Ca2+ sensitivity by titin in HCM patients) that could control genotype to phenotype transition in HCM across different species or mutations. We also predicted potential combination drug targets for HCM (e.g., mavacamten paired with ROS inhibitors) preventing or reversing HCM phenotype (i.e., hypertrophic growth, apoptosis, and metabolic remodeling) in cardiomyocytes. This study provides new insights into mechanisms linking genotype to phenotype in familial hypertrophic cardiomyopathy and offers a framework for assessing new treatments and exploring variations in HCM experimental models.

systems biology↗

bioRxiv2023

Spine apparatus modulates Ca2+ in spines through spatial localization of sources and sinks

Dendritic spines are small protrusions on dendrites in neurons and serve as sites of postsynaptic activity. Some of these spines contain smooth endoplasmic reticulum (SER), and sometimes an even further specialized SER known as the spine apparatus (SA). In this work, we developed a stochastic spatial model to investigate the role of the SER and the SA in modulating Ca2+ dynamics. Using this model, we investigated how ryanodine receptor (RyR) localization, spine membrane geometry, and SER geometry can impact Ca2+ transients in the spine and in the dendrite. Our simulations found that RyR opening is dependent on where it is localized in the SER and on the SER geometry. In order to maximize Ca2+ in the dendrites (for activating clusters of spines and spine-spine communication), a laminar SA was favorable with RyRs localized in the neck region, closer to the dendrite. We also found that the presence of the SER without the laminar structure, coupled with RyR localization at the head, leads to higher Ca2+ presence in the spine. These predictions serve as design principles for understanding how spines with an ER can regulate Ca2+ dynamics differently from spines without ER through a combination of geometry and receptor localization. 1 HighlightsO_LIRyR opening in dendritic spine ER is location dependent and spine geometry dependent. C_LIO_LICa2+ buffers and SERCA can buffer against runaway potentiation of spines even when CICR is activated. C_LIO_LIRyRs located towards the ER neck allow for more Ca2+ to reach the dendrites. C_LIO_LIRyRs located towards the spine head are favorable for increased Ca2+ in spines. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/558941v1_fig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1a2aa64org.highwire.dtl.DTLVardef@60a7c5org.highwire.dtl.DTLVardef@1a68303org.highwire.dtl.DTLVardef@e3743f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO Graphical abstract. Factors governing the dynamics of Ca2+ in dendritic spines include plasma membrane geometry, RyR distribution and ER laminarity. C_FIG

neuroscience↗

bioRxiv2023

Membrane mechanics dictate axonal morphology and function

Axons are thought to be ultrathin membrane cables of a relatively uniform diameter, designed to conduct electrical signals, or action potentials. Here, we demonstrate that unmyelinated axons are not simple cylindrical tubes. Rather, axons have nanoscopic boutons repeatedly along their length interspersed with a thin cable with a diameter of [~]60 nm like pearls-on-a-string. These boutons are only [~]200 nm in diameter and do not have synaptic contacts or a cluster of synaptic vesicles, hence non-synaptic. Our in silico modeling suggests that axon pearling can be explained by the mechanical properties of the membrane including the bending modulus and tension. Consistent with modeling predictions, treatments that disrupt these parameters like hyper- or hypo-tonic solutions, cholesterol removal, and non-muscle myosin II inhibition all alter the degree of axon pearling, suggesting that axon morphology is indeed determined by the membrane mechanics. Intriguingly, neuronal activity modulates the cholesterol level of plasma membrane, leading to shrinkage of axon pearls. Consequently, the conduction velocity of action potentials becomes slower. These data reveal that biophysical forces dictate axon morphology and function and that modulation of membrane mechanics likely underlies plasticity of unmyelinated axons.

neuroscience↗