Cell Cytoskeleton

2015 ◽  
Author(s):  
Matthieu Piel ◽  
Raphael Voituriez
Keyword(s):  
Cell Wall ◽  
Cell Polarity ◽  
Molecular Motors ◽  
Actin Filaments ◽  
Soft Matter ◽  
Coarse Grained ◽  
Cellular Functions ◽  
Cell Cytoskeleton ◽  
Matter Model ◽  
Soft Matter Physics

This article examines the ‘active’ part of the cell cytoskeleton — which mostly corresponds to actin and tubulin polymers and associated molecular motors — using theoretical tools derived from a soft matter physics coarse-grained approach. It begins with an overview of the cytoskeleton and its components, which include actin filaments and gels, microtubules and specialized microtubule-based organelles, molecular motors, intermediate filaments, the plasma membrane and glycocalix, the cell wall, and the extracellular matrix. It then describes coarse-grained models of the cytoskeleton and gives two examples of models for important cellular functions, namely cell migration and cell polarity. It also proposes a new kind of soft matter model providing a coarse-grained description of cytoskeletal polymers and associated molecular motors.

Introduction to molecular simulations in soft matter

2017 ◽  
Author(s):  
J.-L. Barrat ◽  
J. J. de Pablo
Keyword(s):  
Phase Space ◽  
Numerical Methods ◽  
Theoretical Basis ◽  
Soft Matter ◽  
Relevant Literature ◽  
Coarse Grained ◽  
Soft Interfaces ◽  
Molecular Scale ◽  
Soft Matter Physics ◽  
The Continuum

We describe the main features of the coarse-grained models that are typically useful in modelling soft interfaces, from force fields to the continuum descriptions involving density fields. We explain the theoretical basis of the main numerical methods that are used to explore the phase space associated with these models. Finally, three recent examples, illustrating the spirit in which relatively simple simulations can contribute to solving pending problems in soft matter physics, are briefly described. Clearly, a short series of lectures can offer, at best, a biased and restricted view of the available approaches. Our aim here will be to provide the reader with such an overview, with a focus on methods and descriptions that ‘bridge the scale’ between the molecular scale and the continuum or quasi-continuum one. The objective to present a guide to the relevant literature—which has now to a large extent appeared in the form of textbooks.

scholarly journals Coarse-grained simulations of actomyosin rings point to a nodeless model involving both unipolar and bipolar myosins

2018 ◽  
Vol 29 (11) ◽  
pp. 1318-1331 ◽  
Author(s):  
Lam T. Nguyen ◽  
Matthew T. Swulius ◽  
Samya Aich ◽  
Mithilesh Mishra ◽  
Grant J. Jensen
Keyword(s):  
Cell Wall ◽  
Actin Filaments ◽  
Three Dimensional ◽  
Coarse Grained ◽  
Eukaryotic Cells ◽  
Ring Assembly ◽  
Assembly Result ◽  
Microscope Images ◽  
Coarse Grained Simulations ◽  
Electron Cryotomography

Cytokinesis in many eukaryotic cells is orchestrated by a contractile actomyosin ring. While many of the proteins involved are known, the mechanism of constriction remains unclear. Informed by the existing literature and new three-dimensional (3D) molecular details from electron cryotomography, here we develop 3D coarse-grained models of actin filaments, unipolar and bipolar myosins, actin cross-linkers, and membranes and simulate their interactions. Assuming that local force on the membrane results in inward growth of the cell wall, we explored a matrix of possible actomyosin configurations and found that node-based architectures like those presently described for ring assembly result in membrane puckers not seen in electron microscope images of real cells. Instead, the model that best matches data from fluorescence microscopy, electron cryotomography, and biochemical experiments is one in which actin filaments transmit force to the membrane through evenly distributed, membrane-attached, unipolar myosins, with bipolar myosins in the ring driving contraction. While at this point this model is only favored (not proven), the work highlights the power of coarse-grained biophysical simulations to compare complex mechanistic hypotheses.

Actin filaments regulate the adhesion between the plasma membrane and the cell wall of tobacco guard cells

PROTOPLASMA ◽  
2017 ◽  
Vol 255 (1) ◽  
pp. 235-245 ◽  
Author(s):  
Qin Yu ◽  
Jing-Jing Ren ◽  
Lan-Jing Kong ◽  
Xiu-Ling Wang
Keyword(s):  
Cell Wall ◽  
Plasma Membrane ◽  
Actin Filaments ◽  
Guard Cells

Application of video microscopy in experimental soft matter physics

2018 ◽  
Vol 32 (18) ◽  
pp. 1840012
Author(s):  
Hao Feng ◽  
Huaguang Wang ◽  
Zexin Zhang
Keyword(s):  
Video Processing ◽  
Soft Matter ◽  
Colloidal Suspensions ◽  
Real Space ◽  
Video Microscopy ◽  
Quantitative Image ◽  
Soft Matter Physics ◽  
Microscopic World ◽  
The One ◽  
Microscopic Measurement

Combining precise microscopic measurement with quantitative image analysis, video microscopy has become one of the most important, real-space experiment techniques to study the microscopic properties of soft matter systems. On the one hand, it provides a basic tool to observe and record the microscopic world. On the other hand, it offers a powerful experiment method to study the underlying physics of the microscopic world. In this paper, we review the development of the video microscopy, introduce the corresponding hardware and video processing software, and summarize the typical applications and recent progresses of video microscopy in colloidal suspensions. The future of the video microscopy in the soft condensed matter physics and interdisciplinary research is discussed.

scholarly journals Parts list for a microtubule depolymerising kinesin

2018 ◽  
Vol 46 (6) ◽  
pp. 1665-1672 ◽  
Author(s):  
Claire T. Friel ◽  
Julie P. Welburn
Keyword(s):  
Chromosome Segregation ◽  
Molecular Motors ◽  
Neuronal Development ◽  
Current Understanding ◽  
Cellular Functions ◽  
Microtubule Cytoskeleton ◽  
Microtubule Binding ◽  
Large Group ◽  
Kinesin Superfamily ◽  
Different Parts

The Kinesin superfamily is a large group of molecular motors that use the turnover of ATP to regulate their interaction with the microtubule cytoskeleton. The coupled relationship between nucleotide turnover and microtubule binding is harnessed in various ways by these motors allowing them to carry out a variety of cellular functions. The Kinesin-13 family is a group of specialist microtubule depolymerising motors. Members of this family use their microtubule destabilising activity to regulate processes such as chromosome segregation, maintenance of cilia and neuronal development. Here, we describe the current understanding of the structure of this family of kinesins and the role different parts of these proteins play in their microtubule depolymerisation activity and in the wider function of this family of kinesins.

scholarly journals Recent Advances in Conservation–Dissipation Formalism for Irreversible Processes

Entropy ◽  
2021 ◽  
Vol 23 (11) ◽  
pp. 1447
Author(s):  
Liangrong Peng ◽  
Liu Hong
Keyword(s):  
Soft Matter ◽  
Irreversible Processes ◽  
Recent Advances ◽  
Classical Models ◽  
Fourier Heat Conduction ◽  
Soft Matter Physics ◽  
Novel Applications ◽  
Fokker Planck Equations ◽  
Mathematical Foundations ◽  
Well Posed

The main purpose of this review is to summarize the recent advances of the Conservation–Dissipation Formalism (CDF), a new way for constructing both thermodynamically compatible and mathematically stable and well-posed models for irreversible processes. The contents include but are not restricted to the CDF’s physical motivations, mathematical foundations, formulations of several classical models in mathematical physics from master equations and Fokker–Planck equations to Boltzmann equations and quasi-linear Maxwell equations, as well as novel applications in the fields of non-Fourier heat conduction, non-Newtonian viscoelastic fluids, wave propagation/transportation in geophysics and neural science, soft matter physics, etc. Connections with other popular theories in the field of non-equilibrium thermodynamics are examined too.

scholarly journals Elasticity of dense actin networks produces nanonewton protrusive forces

2021 ◽  
Author(s):  
Marion Jasnin ◽  
Jordan Hervy ◽  
Stéphanie Balor ◽  
Anais Bouissou ◽  
Amsha Proag ◽  
...  
Keyword(s):  
Actin Filaments ◽  
Actin Polymerization ◽  
Electron Tomography ◽  
Force Production ◽  
Basal Membrane ◽  
Theoretical Modelling ◽  
Elastic Behavior ◽  
Integrative Approach ◽  
Cellular Functions ◽  
Actin Networks

AbstractActin filaments assemble into force-generating systems involved in diverse cellular functions, including cell motility, adhesion, contractility and division. It remains unclear how networks of actin filaments, which individually generate piconewton forces, can produce forces reaching tens of nanonewtons. Here we use in situ cryo-electron tomography to unveil how the nanoscale architecture of macrophage podosomes enables basal membrane protrusion. We show that the sum of the actin polymerization forces at the membrane is not sufficient to explain podosome protrusive forces. Quantitative analysis of podosome organization demonstrates that the core is composed of a dense network of bent actin filaments storing elastic energy. Theoretical modelling of the network as a spring-loaded elastic material reveals that it exerts forces of up to tens of nanonewtons, similar to those evaluated experimentally. Thus, taking into account not only the interface with the membrane but also the bulk of the network, is crucial to understand force generation by actin machineries. Our integrative approach sheds light on the elastic behavior of dense actin networks and opens new avenues to understand force production inside cells.

scholarly journals Paraspeckles are constructed as block copolymer micelles through microphase separation

2020 ◽  
Author(s):  
Tomohiro Yamazaki ◽  
Tetsuya Yamamoto ◽  
Hyura Yoshino ◽  
Sylvie Souquere ◽  
Shinichi Nakagawa ◽  
...  
Keyword(s):  
Block Copolymer ◽  
Soft Matter ◽  
Microphase Separation ◽  
Theoretical Framework ◽  
Internal Organization ◽  
Ribonucleoprotein Complexes ◽  
Block Copolymer Micelles ◽  
Copolymer Micelles ◽  
Rna Domains ◽  
Soft Matter Physics

SummaryParaspeckles are constructed by NEAT1_2 architectural long noncoding RNAs and possess characteristic cylindrical shapes with highly ordered internal organization, distinct from typical liquid–liquid phase-separated condensates. We experimentally and theoretically investigated how the shape and organization of paraspeckles are determined. We identified the NEAT1_2 RNA domains responsible for shell localization of the NEAT1_2 ends, which determine the characteristic internal organization. We then applied a theoretical framework using soft matter physics to understand the principles that determine the NEAT1_2 organization, shape, number, and size of paraspeckles. By treating paraspeckles as amphipathic block copolymer micelles, we could explain and predict the experimentally observed behaviors of paraspeckles upon NEAT1_2 domain deletions or transcriptional modulation. Thus, we propose that paraspeckles are block copolymer micelles assembled through microphase separation. This work provides an experimentally-based theoretical framework for the concept that ribonucleoprotein complexes (RNPs) can act as block copolymers to form RNA-scaffolding microphase-separated condensates in cells.

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