scholarly journals An agent-based model of molecular aggregation at the cell membrane

2019 ◽  
Author(s):  
Juliette Griffié ◽  
Ruby Peters ◽  
Dylan M. Owen
Keyword(s):  
Plasma Membrane ◽  
Cell Biology ◽  
Super Resolution ◽  
Cell Types ◽  
Signalling Pathways ◽  
Molecular Aggregation ◽  
Agent Based Model ◽  
Agent Based ◽  
Molecular Clustering ◽  
In Cells

AbstractMolecular clustering at the plasma membrane has long been identified as a key process and is associated with regulating signalling pathways across cell types. Recent advances in microscopy, in particular the rise of super-resolution, have allowed the experimental observation of nanoscale molecular clusters in the plasma membrane. However, modelling approaches capable of recapitulating these observations are in their infancy, partly because of the extremely complex array of biophysical factors which influence molecular distributions and dynamics in the plasma membrane. We propose here a highly abstracted approach: an agent-based model dedicated to the study of molecular aggregation at the plasma membrane. We show that when molecules are modelled as though they can act (diffuse) in a manner which is influenced by their molecular neighbourhood, many of the distributions observed in cells can be recapitulated, even though such sensing and response is not possible for real membrane molecules. As such, agent-based offers a unique platform which may lead to a new understanding of how molecular clustering in extremely complex molecular environments can be abstracted, simulated and interpreted using simple rules.Author summaryMolecular aggregation in cell membranes is a key component of cellular machinery, involved across cell types in inter-cellular communication and signalling pathway initiation. As such, understanding the underlying mechanisms and molecule cluster characteristics at a more theoretical level is a pre-requisite. Complete descriptive molecular models have proven impossible to realise due to the overall complexity of the processes involved, highlighting the need for novel approaches. While conceptual models have been shown to be powerful tools and are routinely used in other fields with high level of complexity such as social sciences or economics, they are overall lacking from the literature when it comes to cell studies. We suggest in this work that the same principle applies to cell biology and in particular, the study of molecular clustering. We propose here a general model, independent of cell types or signalling pathways: an agent-based model dedicated to molecular clustering in the plasma membrane. We show we are able to recapitulate molecular aggregation similar to observations in cells while new properties are highlighted by our model, for instance, clustering is a digitised process.

scholarly journals The nanoscale organization of the Wnt signaling integrator Dishevelled in the development-essential vegetal cortex domain of an egg and early embryo

2021 ◽  
Author(s):  
John H. Henson ◽  
Bakary Samasa ◽  
Charles B. Shuster ◽  
Athula H. Wikramanayake
Keyword(s):  
Plasma Membrane ◽  
Sea Urchin ◽  
Super Resolution ◽  
Cell Types ◽  
Early Embryo ◽  
Ultrastructural Organization ◽  
C Terminus ◽  
Pathway Activation ◽  
Vegetal Cortex ◽  
Canonical Wnt

AbstractWnt/β-catenin (cWnt) signaling is a crucial regulator of development and Dishevelled (Dsh/Dvl) functions as an integral part of this pathway by linking Wnt binding to the frizzled:LRP5/6 receptor complex with β-catenin-stimulated gene expression. In many cell types Dsh has been localized to ill-defined cytoplasmic puncta, however in sea urchin eggs and embryos confocal fluorescence microscopy has shown that Dsh is localized to puncta present in a novel and development-essential vegetal cortex domain (VCD). In the present study, we used super-resolution light microscopy and platinum replica TEM to provide the first views of the ultrastructural organization of Dsh within the sea urchin VCD. 3D-SIM imaging of isolated egg cortices demonstrated the concentration gradient-like distribution of Dsh in the VCD, whereas higher resolution STED imaging revealed that some individual Dsh puncta consisted of more than one fluorescent source. Platinum replica immuno-TEM localization showed that Dsh puncta on the cytoplasmic face of the plasma membrane consisted of aggregates of pedestal-like structures each individually labeled with the C-terminus specific Dsh antibody. These aggregates were resistant to detergent extraction and treatment with drugs that disrupt actin filaments or inhibit myosin II contraction, and coexisted with the first division actomyosin contractile ring. These results confirm and extend previous studies and reveal, for the first time in any cell type, the nanoscale organization of plasma membrane tethered Dsh. Our current working hypothesis is that these Dsh pedestals represent a prepositioned scaffold organization that is important for canonical Wnt pathway activation at the sea urchin vegetal organization and may also be relevant to the submembranous Dsh puncta present in other eggs and embryos.

Microinjection of Fluorescently Labeled 130K Protein into Living Fibroblasts: Localization at the Ends of Actin Microfilament Bundles and in Close Relation to Fibronectin

1980 ◽  
Vol 38 ◽  
pp. 708-711
Author(s):  
J. R. Feramisco ◽  
K. Burridge
Keyword(s):  
Molecular Weight ◽  
Plasma Membrane ◽  
Actin Filaments ◽  
Cell Biology ◽  
Close Relation ◽  
Cell Types ◽  
Living Cells ◽  
Structural Proteins ◽  
Major Goal ◽  
Microfilament Bundles

Understanding the interactions between cell surface components and the underlying cytoskeleton continues to be a major goal in cell biology. In particular, little is known about the molecules involved in linking actin filaments to the plasma membrane in cells such as fibroblasts. A protein with a molecular weight of 130,000 (the 130K protein) was recently purified from smooth muscle by Geiger and localized to the ends of microfilament bundles in a variety of cell types. Independently we had purified this protein and were studying its possible interactions with other structural proteins when we learned of its interesting location, one that would be consistent with some role in the attachment of actin filaments to the plasma membrane. We were prompted to investigate this interesting protein further by microinjection of the f1uorescent1y labeled protein into living cells, a technique which had recently been successfully applied to the study of α-actinin.

Fas ligand is targeted to secretory lysosomes via a proline-rich domain in its cytoplasmic tail

2001 ◽  
Vol 114 (13) ◽  
pp. 2405-2416 ◽  
Author(s):  
Emma J. Blott ◽  
Giovanna Bossi ◽  
Richard Clark ◽  
Marketa Zvelebil ◽  
Gillian M. Griffiths
Keyword(s):  
Plasma Membrane ◽  
Cell Surface ◽  
Fas Ligand ◽  
Cytoplasmic Tail ◽  
Cell Types ◽  
Cell Surface Receptor ◽  
Cell Surface Expression ◽  
Rich Domain ◽  
Secretory Lysosomes ◽  
In Cells

Fas ligand (FasL) induces apoptosis through its cell surface receptor Fas. T lymphocytes and natural killer cells sort newly synthesised FasL to secretory lysosomes but, in cell types with conventional lysosomes, FasL appears directly on the plasma membrane. Here, we define a proline-rich domain (PRD) in the cytoplasmic tail of FasL that is responsible for sorting FasL to secretory lysosomes. Deletion of this PRD results in cell surface expression of FasL in cells with secretory lysosomes. Positively charged residues flanking the PRD are crucial to the sorting motif and changing the charge of these residues causes mis-sorting to the plasma membrane. In cells with conventional lysosomes, this motif is not recognised and FasL is expressed at the plasma membrane. The FasL PRD is not required for endocytosis in any cell type, as deletion mutants lacking this motif are endocytosed efficiently to the lysosomal compartment. Endogenous FasL cannot internalise extracellular antibody, demonstrating that FasL does not transit the plasma membrane en route to the secretory lysosomes. We propose that an interaction of the PRD of FasL with an SH3-domain-containing protein, enables direct sorting of FasL from the Golgi to secretory lysosomes.

scholarly journals Cross-talk between Hippo and Wnt signalling pathways in intestinal crypts: Insights from an agent-based model

2020 ◽  
Vol 18 ◽  
pp. 230-240 ◽  
Author(s):  
Daniel Ward ◽  
Sandra Montes Olivas ◽  
Alexander Fletcher ◽  
Martin Homer ◽  
Lucia Marucci
Keyword(s):  
Cross Talk ◽  
Wnt Signalling ◽  
Signalling Pathways ◽  
Agent Based Model ◽  
Agent Based

scholarly journals Accurate and efficient discretizations for stochastic models providing near agent-based spatial resolution at low computational cost

2019 ◽  
Vol 16 (159) ◽  
pp. 20190421 ◽  
Author(s):  
Nabil T. Fadai ◽  
Ruth E. Baker ◽  
Matthew J. Simpson
Keyword(s):  
Single Cell ◽  
Cell Biology ◽  
Computational Cost ◽  
Kolmogorov Equation ◽  
Single Cell Level ◽  
Agent Based Model ◽  
Computationally Efficient ◽  
Agent Based Models ◽  
Cell Level ◽  
Agent Based

Understanding how cells proliferate, migrate and die in various environments is essential in determining how organisms develop and repair themselves. Continuum mathematical models, such as the logistic equation and the Fisher–Kolmogorov equation, can describe the global characteristics observed in commonly used cell biology assays, such as proliferation and scratch assays. However, these continuum models do not account for single-cell-level mechanics observed in high-throughput experiments. Mathematical modelling frameworks that represent individual cells, often called agent-based models, can successfully describe key single-cell-level features of these assays but are computationally infeasible when dealing with large populations. In this work, we propose an agent-based model with crowding effects that is computationally efficient and matches the logistic and Fisher–Kolmogorov equations in parameter regimes relevant to proliferation and scratch assays, respectively. This stochastic agent-based model allows multiple agents to be contained within compartments on an underlying lattice, thereby reducing the computational storage compared to existing agent-based models that allow one agent per site only. We propose a systematic method to determine a suitable compartment size. Implementing this compartment-based model with this compartment size provides a balance between computational storage, local resolution of agent behaviour and agreement with classical continuum descriptions.

scholarly journals Expansion microscopy facilitates quantitative super-resolution studies of cytoskeletal structures in kinetoplastid parasites

2021 ◽  
Author(s):  
Peter Gorilak ◽  
Martina Pružincová ◽  
Hana Vachova ◽  
Marie Olšinová ◽  
Vladimir Varga
Keyword(s):  
3D Reconstruction ◽  
Trypanosoma Brucei ◽  
Mitotic Spindle ◽  
Cell Biology ◽  
Leishmania Major ◽  
Super Resolution ◽  
Cell Types ◽  
Cleavage Furrow ◽  
Resolution Method ◽  
Entire Volume

AbstractExpansion microscopy (ExM) has become a powerful super-resolution method in cell biology. It is a simple, yet robust approach, which does not require any instrumentation or reagents beyond those present in a standard microscopy facility. In this study, we used kinetoplastid parasites Trypanosoma brucei and Leishmania major, which possess a complex, yet well-defined microtubule-based cytoskeleton, to demonstrate that this method recapitulates faithfully morphology of structures as previously revealed by a combination of sophisticated electron microscopy (EM) approaches. Importantly, we also show that due to rapidness of image acquisition and 3D reconstruction of cellular volumes ExM is capable of complementing EM approaches by providing more quantitative data. This is demonstrated on examples of less well-appreciated microtubule structures, such as the neck microtubule of T. brucei or the pocket, cytosolic, and multivesicular tubule-associated microtubules of L. major. We further demonstrate that ExM enables identifying cell types rare in a population, such as cells in mitosis and cytokinesis. 3D reconstruction of an entire volume of these cells provided details on morphology of the mitotic spindle and the cleavage furrow. Finally, we show that established antibody markers of major cytoskeletal structures function well in ExM, which together with the ability to visualize proteins tagged with small epitope tags will facilitate studies of the kinetoplastid cytoskeleton.

scholarly journals Learning differential equation models from stochastic agent-based model simulations

2021 ◽  
Vol 18 (176) ◽  
Author(s):  
John T. Nardini ◽  
Ruth E. Baker ◽  
Matthew J. Simpson ◽  
Kevin B. Flores
Keyword(s):  
Differential Equation ◽  
Cell Biology ◽  
Coarse Grained ◽  
Disease Spread ◽  
Agent Based Model ◽  
Agent Based Models ◽  
Agent Based ◽  
Model Simulations ◽  
Differential Equation Models ◽  
Model Dynamics

Agent-based models provide a flexible framework that is frequently used for modelling many biological systems, including cell migration, molecular dynamics, ecology and epidemiology. Analysis of the model dynamics can be challenging due to their inherent stochasticity and heavy computational requirements. Common approaches to the analysis of agent-based models include extensive Monte Carlo simulation of the model or the derivation of coarse-grained differential equation models to predict the expected or averaged output from the agent-based model. Both of these approaches have limitations, however, as extensive computation of complex agent-based models may be infeasible, and coarse-grained differential equation models can fail to accurately describe model dynamics in certain parameter regimes. We propose that methods from the equation learning field provide a promising, novel and unifying approach for agent-based model analysis. Equation learning is a recent field of research from data science that aims to infer differential equation models directly from data. We use this tutorial to review how methods from equation learning can be used to learn differential equation models from agent-based model simulations. We demonstrate that this framework is easy to use, requires few model simulations, and accurately predicts model dynamics in parameter regions where coarse-grained differential equation models fail to do so. We highlight these advantages through several case studies involving two agent-based models that are broadly applicable to biological phenomena: a birth–death–migration model commonly used to explore cell biology experiments and a susceptible–infected–recovered model of infectious disease spread.

scholarly journals Expansion microscopy facilitates quantitative super-resolution studies of cytoskeletal structures in kinetoplastid parasites

Open Biology ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 210131 ◽  
Author(s):  
Peter Gorilak ◽  
Martina Pružincová ◽  
Hana Vachova ◽  
Marie Olšinová ◽  
Marketa Schmidt Cernohorska ◽  
...  
Keyword(s):  
Mitotic Spindle ◽  
Cell Biology ◽  
Leishmania Major ◽  
Three Dimensional ◽  
Super Resolution ◽  
Cell Types ◽  
Three Dimensional Reconstruction ◽  
Resolution Method ◽  
Entire Volume ◽  
Dimensional Reconstruction

Expansion microscopy (ExM) has become a powerful super-resolution method in cell biology. It is a simple, yet robust approach, which does not require any instrumentation or reagents beyond those present in a standard microscopy facility. In this study, we used kinetoplastid parasites Trypanosoma brucei and Leishmania major , which possess a complex, yet well-defined microtubule-based cytoskeleton, to demonstrate that this method recapitulates faithfully morphology of structures as previously revealed by a combination of sophisticated electron microscopy (EM) approaches. Importantly, we also show that due to the rapidness of image acquisition and three-dimensional reconstruction of cellular volumes ExM is capable of complementing EM approaches by providing more quantitative data. This is demonstrated on examples of less well-appreciated microtubule structures, such as the neck microtubule of T. brucei or the pocket, cytosolic and multivesicular tubule-associated microtubules of L. major . We further demonstrate that ExM enables identifying cell types rare in a population, such as cells in mitosis and cytokinesis. Three-dimensional reconstruction of an entire volume of these cells provided details on the morphology of the mitotic spindle and the cleavage furrow. Finally, we show that established antibody markers of major cytoskeletal structures function well in ExM, which together with the ability to visualize proteins tagged with small epitope tags will facilitate studies of the kinetoplastid cytoskeleton.

Reversible - through calmodulin - electrostatic interactions between basic residues on proteins and acidic lipids in the plasma membrane.

2005 ◽  
Vol 72 ◽  
pp. 189-198 ◽  
Author(s):  
Stuart McLaughlin ◽  
Gyöngyi Hangyás-Mihályné ◽  
Irina Zaitseva ◽  
Urszula Golebiewska
Keyword(s):  
Plasma Membrane ◽  
Cell Biology ◽  
Electrostatic Interactions ◽  
Theoretical Calculations ◽  
Cell Types ◽  
Kinase Substrate ◽  
Poisson Boltzmann ◽  
Pkc Protein Kinase C ◽  
Poisson Boltzmann Equation ◽  
Acidic Lipids

The inner leaflet of a typical mammalian plasma membrane contains 20-30% univalent PS (phosphatidylserine) and 1% multivalent PtdIns(4,5)P2. Numerous proteins have clusters of basic (or basic/hydrophobic) residues that bind to these acidic lipids. The intracellular effector CaM (calmodulin) can reverse this binding on a wide variety of proteins, including MARCKS (myristoylated alanine-rich C kinase substrate), GAP43 (growth-associated protein 43, also known as neuromodulin), gravin, GRK5 (G-protein-coupled receptor kinase 5), the NMDA (N-methyl-d-aspartate) receptor and the ErbB family. We used the first principles of physics, incorporating atomic models and the Poisson-Boltzmann equation, to describe how the basic effector domain of MARCKS binds electrostatically to acidic lipids on the plasma membrane. The theoretical calculations show the basic cluster produces a local positive electrostatic potential that should laterally sequester PtdInsP2, even when univalent acidic lipids are present at a physiologically relevant 100-fold excess; four independent experimental measurements confirm this prediction. Ca2+/CaM binds with high affinity (Kd approximately 10nM) to this domain and releases the PtdIns(4,5)P2. MARCKS, a major PKC (protein kinase C) substrate, is present at concentrations comparable with those of PtdIns(4,5)P2 (approx. 10 μM) in many cell types. Thus MARCKS can act as a reversible PtdIns(4,5)P2 buffer, binding PtdIns(4,5)P2 in a quiescent cell, and releasing it locally when the intracellular Ca2+ concentration increases. This reversible sequestration is important because PtdIns(4,5)P2 plays many roles in cell biology. Less is known about the role of CaM-mediated reversible membrane binding of basic/hydrophobic clusters for the other proteins.

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