1
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Banerjee DS, Freedman SL, Murrell MP, Banerjee S. Growth-induced collective bending and kinetic trapping of cytoskeletal filaments. Cytoskeleton (Hoboken) 2024. [PMID: 38775207 DOI: 10.1002/cm.21877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/30/2024] [Accepted: 05/06/2024] [Indexed: 06/04/2024]
Abstract
Growth and turnover of actin filaments play a crucial role in the construction and maintenance of actin networks within cells. Actin filament growth occurs within limited space and finite subunit resources in the actin cortex. To understand how filament growth shapes the emergent architecture of actin networks, we developed a minimal agent-based model coupling filament mechanics and growth in a limiting subunit pool. We find that rapid filament growth induces kinetic trapping of highly bent actin filaments. Such collective bending patterns are long-lived, organized around nematic defects, and arise from competition between filament polymerization and bending elasticity. The stability of nematic defects and the extent of kinetic trapping are amplified by an increase in the abundance of the actin pool and by crosslinking the network. These findings suggest that kinetic trapping is a robust consequence of growth in crowded environments, providing a route to program shape memory in actin networks.
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Affiliation(s)
- Deb Sankar Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
- James Franck Institute, University of Chicago, Chicago, Illinois, USA
| | | | - Michael P Murrell
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, USA
- Systems Biology Institute, West Haven, Connecticut, USA
- Department of Physics, Yale University, New Haven, Connecticut, USA
| | - Shiladitya Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA
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2
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Singh C, Chaudhuri A. Anomalous dynamics of a passive droplet in active turbulence. Nat Commun 2024; 15:3704. [PMID: 38697961 PMCID: PMC11066042 DOI: 10.1038/s41467-024-47727-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 04/09/2024] [Indexed: 05/05/2024] Open
Abstract
Motion of a passive deformable object in an active environment serves as a representative of both in-vivo systems such as intracellular particle motion in Acanthamoeba castellanii, or in-vitro systems such as suspension of beads inside dense swarms of Escherichia coli. Theoretical modeling of such systems is challenging due to the requirement of well resolved hydrodynamics which can explore the spatiotemporal correlations around the suspended passive object in the active fluid. We address this critical lack of understanding using coupled hydrodynamic equations for nematic liquid crystals with finite active stress to model the active bath, and a suspended nematic droplet with zero activity. The droplet undergoes deformation fluctuations and its movement shows periods of "runs" and "stays". At relatively low interfacial tension, the droplet begins to break and mix with the outer active bath. We establish that the motion of the droplet is influenced by the interplay of spatial correlations of the flow and the size of the droplet. The mean square displacement shows a transition from ballistic to normal diffusion which depends on the droplet size. We discuss this transition in relation to spatiotemporal scales associated with velocity correlations of the active bath and the droplet.
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Affiliation(s)
- Chamkor Singh
- Department of Physics, Central University of Punjab, Bathinda, India.
| | - Abhishek Chaudhuri
- Department of Physical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India.
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3
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Chandrasekaran A, Graham K, Stachowiak JC, Rangamani P. Kinetic trapping organizes actin filaments within liquid-like protein droplets. Nat Commun 2024; 15:3139. [PMID: 38605007 PMCID: PMC11009352 DOI: 10.1038/s41467-024-46726-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 03/07/2024] [Indexed: 04/13/2024] Open
Abstract
Several actin-binding proteins (ABPs) phase separate to form condensates capable of curating the actin network shapes. Here, we use computational modeling to understand the principles of actin network organization within VASP condensate droplets. Our simulations reveal that the different actin shapes, namely shells, rings, and mixture states are highly dependent on the kinetics of VASP-actin interactions, suggesting that they arise from kinetic trapping. Specifically, we show that reducing the residence time of VASP on actin filaments reduces degree of bundling, thereby promoting assembly of shells rather than rings. We validate the model predictions experimentally using a VASP-mutant with decreased bundling capability. Finally, we investigate the ring opening within deformed droplets and found that the sphere-to-ellipsoid transition is favored under a wide range of filament lengths while the ellipsoid-to-rod transition is only permitted when filaments have a specific range of lengths. Our findings highlight key mechanisms of actin organization within phase-separated ABPs.
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Affiliation(s)
- Aravind Chandrasekaran
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, 92093-0411, USA
| | - Kristin Graham
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA
| | - Jeanne C Stachowiak
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
- Department of Chemical Engineering, University of Texas at Austin, Austin, TX, 78712, USA.
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, 92093-0411, USA.
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4
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Chauhan P, Lee HB, Goodbee N, Martin S, Branch R, Sahu S, Schwarz JM, Ross JL. Ionic strength alters crosslinker-driven self-organization of microtubules. Cytoskeleton (Hoboken) 2024. [PMID: 38385864 DOI: 10.1002/cm.21839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/23/2024]
Abstract
The microtubule cytoskeleton is a major structural element inside cells that directs self-organization using microtubule-associated proteins and motors. It has been shown that finite-sized, spindle-like microtubule organizations, called "tactoids," can form in vitro spontaneously from mixtures of tubulin and the antiparallel crosslinker, MAP65, from the MAP65/PRC1/Ase family. Here, we probe the ability of MAP65 to form tactoids as a function of the ionic strength of the buffer to attempt to break the electrostatic interactions binding MAP65 to microtubules and inter-MAP65 binding. We observe that, with increasing monovalent salts, the organizations change from finite tactoids to unbounded length bundles, yet the MAP65 binding and crosslinking appear to stay intact. We further explore the effects of ionic strength on the dissociation constant of MAP65 using both microtubule pelleting and single-molecule binding assays. We find that salt can reduce the binding, yet salt never negates it. Instead, we believe that the salt is affecting the ability of the MAP65 to form phase-separated droplets, which cause the nucleation and growth of tactoids, as recently demonstrated.
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Affiliation(s)
- Prashali Chauhan
- Physics Department, Syracuse University, Syracuse, New York, USA
| | - Hong Beom Lee
- Physics Department, Syracuse University, Syracuse, New York, USA
| | - Niaz Goodbee
- Physics Department, Syracuse University, Syracuse, New York, USA
| | - Sophia Martin
- Physics Department, Syracuse University, Syracuse, New York, USA
| | - Ruell Branch
- Physics Department, Syracuse University, Syracuse, New York, USA
| | - Sumon Sahu
- Department of Physics, New York University, New York, New York, USA
| | | | - Jennifer L Ross
- Physics Department, Syracuse University, Syracuse, New York, USA
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5
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Banerjee DS, Freedman SL, Murrell MP, Banerjee S. Growth-induced collective bending and kinetic trapping of cytoskeletal filaments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574885. [PMID: 38260433 PMCID: PMC10802417 DOI: 10.1101/2024.01.09.574885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Growth and turnover of actin filaments play a crucial role in the construction and maintenance of actin networks within cells. Actin filament growth occurs within limited space and finite subunit resources in the actin cortex. To understand how filament growth shapes the emergent architecture of actin networks, we developed a minimal agent-based model coupling filament mechanics and growth in a limiting subunit pool. We find that rapid filament growth induces kinetic trapping of highly bent actin filaments. Such collective bending patterns are long-lived, organized around nematic defects, and arises from competition between filament polymerization and bending elasticity. The stability of nematic defects and the extent of kinetic trapping are amplified by an increase in the abundance of the actin pool and by crosslinking the network. These findings suggest that kinetic trapping is a robust consequence of growth in crowded environments, providing a route to program shape memory in actin networks.
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Affiliation(s)
- Deb Sankar Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA
| | | | - Michael P Murrell
- Department of Biomedical Engineering, Yale University, 10 Hillhouse Avenue, New Haven, CT, USA
- Systems Biology Institute, 850 West Campus Drive, West Haven, CT, USA
- Department of Physics, Yale University, 217 Prospect Street, New Haven, CT, USA
| | - Shiladitya Banerjee
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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6
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Hallatschek O, Datta SS, Drescher K, Dunkel J, Elgeti J, Waclaw B, Wingreen NS. Proliferating active matter. NATURE REVIEWS. PHYSICS 2023; 5:1-13. [PMID: 37360681 PMCID: PMC10230499 DOI: 10.1038/s42254-023-00593-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 06/28/2023]
Abstract
The fascinating patterns of collective motion created by autonomously driven particles have fuelled active-matter research for over two decades. So far, theoretical active-matter research has often focused on systems with a fixed number of particles. This constraint imposes strict limitations on what behaviours can and cannot emerge. However, a hallmark of life is the breaking of local cell number conservation by replication and death. Birth and death processes must be taken into account, for example, to predict the growth and evolution of a microbial biofilm, the expansion of a tumour, or the development from a fertilized egg into an embryo and beyond. In this Perspective, we argue that unique features emerge in these systems because proliferation represents a distinct form of activity: not only do the proliferating entities consume and dissipate energy, they also inject biomass and degrees of freedom capable of further self-proliferation, leading to myriad dynamic scenarios. Despite this complexity, a growing number of studies document common collective phenomena in various proliferating soft-matter systems. This generality leads us to propose proliferation as another direction of active-matter physics, worthy of a dedicated search for new dynamical universality classes. Conceptual challenges abound, from identifying control parameters and understanding large fluctuations and nonlinear feedback mechanisms to exploring the dynamics and limits of information flow in self-replicating systems. We believe that, by extending the rich conceptual framework developed for conventional active matter to proliferating active matter, researchers can have a profound impact on quantitative biology and reveal fascinating emergent physics along the way.
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Affiliation(s)
- Oskar Hallatschek
- Departments of Physics and Integrative Biology, University of California, Berkeley, CA US
- Peter Debye Institute for Soft Matter Physics, Leipzig University, Leipzig, Germany
| | - Sujit S. Datta
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ USA
| | | | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA USA
| | - Jens Elgeti
- Theoretical Physics of Living Matter, Institute of Biological Information Processing, Forschungszentrum Jülich, Jülich, Germany
| | - Bartek Waclaw
- Dioscuri Centre for Physics and Chemistry of Bacteria, Institute of Physical Chemistry PAN, Warsaw, Poland
- School of Physics and Astronomy, The University of Edinburgh, JCMB, Edinburgh, UK
| | - Ned S. Wingreen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
- Department of Molecular Biology, Princeton University, Princeton, NJ USA
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7
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Sakuta H, Nakatani N, Torisawa T, Sumino Y, Tsumoto K, Oiwa K, Yoshikawa K. Self-emergent vortex flow of microtubule and kinesin in cell-sized droplets under water/water phase separation. Commun Chem 2023; 6:80. [PMID: 37100870 PMCID: PMC10133263 DOI: 10.1038/s42004-023-00879-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 04/11/2023] [Indexed: 04/28/2023] Open
Abstract
By facilitating a water/water phase separation (w/wPS), crowded biopolymers in cells form droplets that contribute to the spatial localization of biological components and their biochemical reactions. However, their influence on mechanical processes driven by protein motors has not been well studied. Here, we show that the w/wPS droplet spontaneously entraps kinesins as well as microtubules (MTs) and generates a micrometre-scale vortex flow inside the droplet. Active droplets with a size of 10-100 µm are generated through w/wPS of dextran and polyethylene glycol mixed with MTs, molecular-engineered chimeric four-headed kinesins and ATP after mechanical mixing. MTs and kinesin rapidly created contractile network accumulated at the interface of the droplet and gradually generated vortical flow, which can drive translational motion of a droplet. Our work reveals that the interface of w/wPS contributes not only to chemical processes but also produces mechanical motion by assembling species of protein motors in a functioning manner.
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Affiliation(s)
- Hiroki Sakuta
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto, 610-0394, Japan
- Organization for Research Initiatives and Development, Doshisha University, Kyotanabe, Kyoto, 610-0394, Japan
- Center for Complex Systems Biology, Universal Biology Institute, The University of Tokyo, Meguro, Tokyo, 153-8902, Japan
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro, Tokyo, 153-8902, Japan
| | - Naoki Nakatani
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto, 610-0394, Japan
| | - Takayuki Torisawa
- Cell Architecture Laboratory, Structural Biology Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Yutaka Sumino
- Department of Applied Physics, Faculty of Advanced Engineering, WaTUS and DCIS, Tokyo University of Science, Katsushika, Tokyo, 125-8585, Japan.
| | - Kanta Tsumoto
- Division of Chemistry for Materials, Graduate School of Engineering, Mie University, Tsu, Mie, 514-8507, Japan
| | - Kazuhiro Oiwa
- Advanced ICT Research Institute, National Institute of Information and Communications Technology, Kobe, Hyogo, 651-2492, Japan.
- Department of Life Science, Graduate School of Science, University of Hyogo, Ako, Hyogo, 678-1297, Japan.
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Kyoto, 610-0394, Japan
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto, Kyoto, 606-8501, Japan
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8
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Jiang J, Wang X, Akomolafe OI, Tang W, Asilehan Z, Ranabhat K, Zhang R, Peng C. Collective transport and reconfigurable assembly of nematic colloids by light-driven cooperative molecular reorientations. Proc Natl Acad Sci U S A 2023; 120:e2221718120. [PMID: 37040402 PMCID: PMC10119998 DOI: 10.1073/pnas.2221718120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/09/2023] [Indexed: 04/12/2023] Open
Abstract
Nanomotors in nature have inspired scientists to design synthetic molecular motors to drive the motion of microscale objects by cooperative action. Light-driven molecular motors have been synthesized, but using their cooperative reorganization to control the collective transport of colloids and to realize the reconfiguration of colloidal assembly remains a challenge. In this work, topological vortices are imprinted in the monolayers of azobenzene molecules which further interface with nematic liquid crystals (LCs). The light-driven cooperative reorientations of the azobenzene molecules induce the collective motion of LC molecules and thus the spatiotemporal evolutions of the nematic disclination networks which are defined by the controlled patterns of vortices. Continuum simulations provide physical insight into the morphology change of the disclination networks. When microcolloids are dispersed in the LC medium, the colloidal assembly is not only transported and reconfigured by the collective change of the disclination lines but also controlled by the elastic energy landscape defined by the predesigned orientational patterns. The collective transport and reconfiguration of colloidal assemblies can also be programmed by manipulating the irradiated polarization. This work opens opportunities to design programmable colloidal machines and smart composite materials.
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Affiliation(s)
- Jinghua Jiang
- Department of Physics, University of Science and Technology of China, Hefei, Anhui230026, China
| | - Xinyu Wang
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong99999, China
| | | | - Wentao Tang
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong99999, China
| | - Zhawure Asilehan
- Department of Physics, University of Science and Technology of China, Hefei, Anhui230026, China
| | - Kamal Ranabhat
- Department of Physics and Materials Science, The University of Memphis, Memphis, TN38152
| | - Rui Zhang
- Department of Physics, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong99999, China
| | - Chenhui Peng
- Department of Physics, University of Science and Technology of China, Hefei, Anhui230026, China
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9
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Slootbeek AD, van Haren MHI, Smokers IBA, Spruijt E. Growth, replication and division enable evolution of coacervate protocells. Chem Commun (Camb) 2022; 58:11183-11200. [PMID: 36128910 PMCID: PMC9536485 DOI: 10.1039/d2cc03541c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/13/2022] [Indexed: 11/21/2022]
Abstract
Living and proliferating cells undergo repeated cycles of growth, replication and division, all orchestrated by complex molecular networks. How a minimal cell cycle emerged and helped primitive cells to evolve remains one of the biggest mysteries in modern science, and is an active area of research in chemistry. Protocells are cell-like compartments that recapitulate features of living cells and may be seen as the chemical ancestors of modern life. While compartmentalization is not strictly required for primitive, open-ended evolution of self-replicating systems, it gives such systems a clear identity by setting the boundaries and it can help them overcome three major obstacles of dilution, parasitism and compatibility. Compartmentalization is therefore widely considered to be a central hallmark of primitive life, and various types of protocells are actively investigated, with the ultimate goal of developing a protocell capable of autonomous proliferation by mimicking the well-known cell cycle of growth, replication and division. We and others have found that coacervates are promising protocell candidates in which chemical building blocks required for life are naturally concentrated, and chemical reactions can be selectively enhanced or suppressed. This feature article provides an overview of how growth, replication and division can be realized with coacervates as protocells and what the bottlenecks are. Considerations are given for designing chemical networks in coacervates that can lead to sustained growth, selective replication and controlled division, in a way that they are linked together like in the cell cycle. Ultimately, such a system may undergo evolution by natural selection of certain phenotypes, leading to adaptation and the gain of new functions, and we end with a brief discussion of the opportunities for coacervates to facilitate this.
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Affiliation(s)
- Annemiek D Slootbeek
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Merlijn H I van Haren
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Iris B A Smokers
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
| | - Evan Spruijt
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands.
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10
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Iyer P, Gompper G, Fedosov DA. Non-equilibrium shapes and dynamics of active vesicles. SOFT MATTER 2022; 18:6868-6881. [PMID: 36043635 DOI: 10.1039/d2sm00622g] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Active vesicles, constructed through the confinement of self-propelled particles (SPPs) inside a lipid membrane shell, exhibit a large variety of non-equilibrium shapes, ranging from the formation of local tethers and dendritic conformations, to prolate and bola-like structures. To better understand the behavior of active vesicles, we perform simulations of membranes modelled as dynamically triangulated surfaces enclosing active Brownian particles. A systematic analysis of membrane deformations and SPP clustering, as a function of SPP activity and volume fraction inside the vesicle is carried out. Distributions of membrane local curvature, and the clustering and mobility of SPPs obtained from simulations of active vesicles are analysed. There exists a feedback mechanism between the enhancement of membrane curvature, the formation of clusters of active particles, and local or global changes in vesicle shape. The emergence of active tension due to the activity of SPPs can well be captured by the Young-Laplace equation. Furthermore, a simple numerical method for tether detection is presented and used to determine correlations between the number of tethers, their length, and local curvature. We also provide several geometrical arguments to explain different tether characteristics for various conditions. These results contribute to the future development of steerable active vesicles or soft micro-robots whose behaviour can be controlled and used for potential applications.
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Affiliation(s)
- Priyanka Iyer
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany.
| | - Gerhard Gompper
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany.
| | - Dmitry A Fedosov
- Theoretical Physics of Living Matter, Institute of Biological Information Processing and Institute for Advanced Simulation, Forschungszentrum Jülich, 52425 Jülich, Germany.
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11
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Lamtyugina A, Qiu Y, Fodor É, Dinner AR, Vaikuntanathan S. Thermodynamic Control of Activity Patterns in Cytoskeletal Networks. PHYSICAL REVIEW LETTERS 2022; 129:128002. [PMID: 36179154 PMCID: PMC10014041 DOI: 10.1103/physrevlett.129.128002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 07/26/2022] [Indexed: 06/16/2023]
Abstract
Biological materials, such as the actin cytoskeleton, exhibit remarkable structural adaptability to various external stimuli by consuming different amounts of energy. In this Letter, we use methods from large deviation theory to identify a thermodynamic control principle for structural transitions in a model cytoskeletal network. Specifically, we demonstrate that biasing the dynamics with respect to the work done by nonequilibrium components effectively renormalizes the interaction strength between such components, which can eventually result in a morphological transition. Our work demonstrates how a thermodynamic quantity can be used to renormalize effective interactions, which in turn can tune structure in a predictable manner, suggesting a thermodynamic principle for the control of cytoskeletal structure and dynamics.
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Affiliation(s)
| | - Yuqing Qiu
- Department of Chemistry, University of Chicago, Chicago, IL 60637
- James Franck Institute, University of Chicago, Chicago, IL 60637
| | - Étienne Fodor
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg
| | - Aaron R. Dinner
- Department of Chemistry, University of Chicago, Chicago, IL 60637
- James Franck Institute, University of Chicago, Chicago, IL 60637
| | - Suriyanarayanan Vaikuntanathan
- Department of Chemistry, University of Chicago, Chicago, IL 60637
- James Franck Institute, University of Chicago, Chicago, IL 60637
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12
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Chandrasekaran A, Giniger E, Papoian GA. Nucleation causes an actin network to fragment into multiple high-density domains. Biophys J 2022; 121:3200-3212. [PMID: 35927959 PMCID: PMC9463697 DOI: 10.1016/j.bpj.2022.07.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/20/2021] [Accepted: 07/28/2022] [Indexed: 11/02/2022] Open
Abstract
Actin networks rely on nucleation mechanisms to generate new filaments because spontaneous nucleation is kinetically disfavored. Branching nucleation of actin filaments by actin-related protein (Arp2/3), in particular, is critical for actin self-organization. In this study, we use the simulation platform for active matter MEDYAN to generate 2000 s long stochastic trajectories of actin networks, under varying Arp2/3 concentrations, in reaction volumes of biologically meaningful size (>20 μm3). We find that the dynamics of Arp2/3 increase the abundance of short filaments and increases network treadmilling rate. By analyzing the density fields of F-actin, we find that at low Arp2/3 concentrations, F-actin is organized into a single connected and contractile domain, while at elevated Arp2/3 levels (10 nM and above), such high-density actin domains fragment into smaller domains spanning a wide range of volumes. These fragmented domains are extremely dynamic, continuously merging and splitting, owing to the high treadmilling rate of the underlying actin network. Treating the domain dynamics as a drift-diffusion process, we find that the fragmented state is stochastically favored, and the network state slowly drifts toward the fragmented state with considerable diffusion (variability) in the number of domains. We suggest that tuning the Arp2/3 concentration enables cells to transition from a globally coherent cytoskeleton, whose response involves the entire cytoplasmic network, to a fragmented cytoskeleton, where domains can respond independently to locally varying signals.
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Affiliation(s)
- Aravind Chandrasekaran
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland; National Institutes of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Edward Giniger
- National Institutes of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Garegin A Papoian
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland; Institute for Physical Science and Technology, University of Maryland, College Park, Maryland.
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13
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Duraivel S, Subramaniam V, Chisolm S, Scheutz GM, Sumerlin BS, Bhattacharjee T, Angelini TE. Leveraging ultra-low interfacial tension and liquid-liquid phase separation in embedded 3D bioprinting. BIOPHYSICS REVIEWS 2022; 3:031307. [PMID: 38505275 PMCID: PMC10903370 DOI: 10.1063/5.0087387] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 08/23/2022] [Indexed: 03/21/2024]
Abstract
Many recently developed 3D bioprinting strategies operate by extruding aqueous biopolymer solutions directly into a variety of different support materials constituted from swollen, solvated, aqueous, polymer assemblies. In developing these 3D printing methods and materials, great care is often taken to tune the rheological behaviors of both inks and 3D support media. By contrast, much less attention has been given to the physics of the interfaces created when structuring one polymer phase into another in embedded 3D printing applications. For example, it is currently unclear whether a dynamic interfacial tension between miscible phases stabilizes embedded 3D bioprinted structures as they are shaped while in a liquid state. Interest in the physics of interfaces between complex fluids has grown dramatically since the discovery of liquid-liquid phase separation (LLPS) in living cells. We believe that many new insights coming from this burst of investigation into LLPS within biological contexts can be leveraged to develop new materials and methods for improved 3D bioprinting that leverage LLPS in mixtures of biopolymers, biocompatible synthetic polymers, and proteins. Thus, in this review article, we highlight work at the interface between recent LLPS research and embedded 3D bioprinting methods and materials, and we introduce a 3D bioprinting method that leverages LLPS to stabilize printed biopolymer inks embedded in a bioprinting support material.
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Affiliation(s)
- Senthilkumar Duraivel
- Department of Materials Science and Engineering, University of Florida, Gainesville, Florida 32611, USA
| | - Vignesh Subramaniam
- Department of Mechanical & Aerospace Engineering, University of Florida, Gainesville, Florida 32611, USA
| | - Steven Chisolm
- Department of Mechanical & Aerospace Engineering, University of Florida, Gainesville, Florida 32611, USA
| | - Georg M. Scheutz
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
| | - Brent. S. Sumerlin
- George & Josephine Butler Polymer Research Laboratory, Center for Macromolecular Science & Engineering, Department of Chemistry, University of Florida, Gainesville, Florida 32611, USA
| | - Tapomoy Bhattacharjee
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bellary Road, Bangalore 560065, Karnataka, India
| | - Thomas E. Angelini
- Department of Mechanical & Aerospace Engineering, University of Florida, Gainesville, Florida 32611, USA
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14
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Gouveia B, Kim Y, Shaevitz JW, Petry S, Stone HA, Brangwynne CP. Capillary forces generated by biomolecular condensates. Nature 2022; 609:255-264. [PMID: 36071192 DOI: 10.1038/s41586-022-05138-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 07/25/2022] [Indexed: 12/21/2022]
Abstract
Liquid-liquid phase separation and related phase transitions have emerged as generic mechanisms in living cells for the formation of membraneless compartments or biomolecular condensates. The surface between two immiscible phases has an interfacial tension, generating capillary forces that can perform work on the surrounding environment. Here we present the physical principles of capillarity, including examples of how capillary forces structure multiphase condensates and remodel biological substrates. As with other mechanisms of intracellular force generation, for example, molecular motors, capillary forces can influence biological processes. Identifying the biomolecular determinants of condensate capillarity represents an exciting frontier, bridging soft matter physics and cell biology.
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Affiliation(s)
- Bernardo Gouveia
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA
| | - Yoonji Kim
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | | | - Sabine Petry
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, NJ, USA.
| | - Clifford P Brangwynne
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ, USA. .,The Howard Hughes Medical Institute, Princeton, NJ, USA.
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15
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Yan VT, Narayanan A, Wiegand T, Jülicher F, Grill SW. A condensate dynamic instability orchestrates actomyosin cortex activation. Nature 2022; 609:597-604. [PMID: 35978196 PMCID: PMC9477739 DOI: 10.1038/s41586-022-05084-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 07/07/2022] [Indexed: 11/17/2022]
Abstract
A key event at the onset of development is the activation of a contractile actomyosin cortex during the oocyte-to-embryo transition1-3. Here we report on the discovery that, in Caenorhabditis elegans oocytes, actomyosin cortex activation is supported by the emergence of thousands of short-lived protein condensates rich in F-actin, N-WASP and the ARP2/3 complex4-8 that form an active micro-emulsion. A phase portrait analysis of the dynamics of individual cortical condensates reveals that condensates initially grow and then transition to disassembly before dissolving completely. We find that, in contrast to condensate growth through diffusion9, the growth dynamics of cortical condensates are chemically driven. Notably, the associated chemical reactions obey mass action kinetics that govern both composition and size. We suggest that the resultant condensate dynamic instability10 suppresses coarsening of the active micro-emulsion11, ensures reaction kinetics that are independent of condensate size and prevents runaway F-actin nucleation during the formation of the first cortical actin meshwork.
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Affiliation(s)
- Victoria Tianjing Yan
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.,Biotechnology Center, TU Dresden, Dresden, Germany
| | - Arjun Narayanan
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany. .,Biotechnology Center, TU Dresden, Dresden, Germany. .,Max Planck Institute for the Physics of Complex Systems (MPI-PKS), Dresden, Germany. .,Center for Systems Biology Dresden (CSBD), Dresden, Germany.
| | - Tina Wiegand
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems (MPI-PKS), Dresden, Germany.,Center for Systems Biology Dresden (CSBD), Dresden, Germany
| | - Frank Jülicher
- Max Planck Institute for the Physics of Complex Systems (MPI-PKS), Dresden, Germany. .,Center for Systems Biology Dresden (CSBD), Dresden, Germany. .,Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
| | - Stephan W Grill
- Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany. .,Center for Systems Biology Dresden (CSBD), Dresden, Germany. .,Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
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16
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Ansari S, Yan W, Lamson A, Shelley MJ, Glaser MA, Betterton MD. Active condensation of filaments under spatial confinement. FRONTIERS IN PHYSICS 2022; 10:897255. [PMID: 38116396 PMCID: PMC10730113 DOI: 10.3389/fphy.2022.897255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Living systems exhibit self-organization, a phenomenon that enables organisms to perform functions essential for life. The interior of living cells is a crowded environment in which the self-assembly of cytoskeletal networks is spatially constrained by membranes and organelles. Cytoskeletal filaments undergo active condensation in the presence of crosslinking motor proteins. In past studies, confinement has been shown to alter the morphology of active condensates. Here, we perform simulations to explore systems of filaments and crosslinking motors in a variety of confining geometries. We simulate spatial confinement imposed by hard spherical, cylindrical, and planar boundaries. These systems exhibit non-equilibrium condensation behavior where crosslinking motors condense a fraction of the overall filament population, leading to coexistence of vapor and condensed states. We find that the confinement lengthscale modifies the dynamics and condensate morphology. With end-pausing crosslinking motors, filaments self-organize into half asters and fully-symmetric asters under spherical confinement, polarity-sorted bilayers and bottle-brush-like states under cylindrical confinement, and flattened asters under planar confinement. The number of crosslinking motors controls the size and shape of condensates, with flattened asters becoming hollow and ring-like for larger motor number. End pausing plays a key role affecting condensate morphology: systems with end-pausing motors evolve into aster-like condensates while those with non-end-pausing crosslinking motor proteins evolve into disordered clusters and polarity-sorted bundles.
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Affiliation(s)
- Saad Ansari
- Department of Physics, University of Colorado Boulder, Colorado, USA
| | - Wen Yan
- Center for Computational Biology, Flatiron Institute, New York, USA
| | - Adam Lamson
- Center for Computational Biology, Flatiron Institute, New York, USA
| | - Michael J. Shelley
- Center for Computational Biology, Flatiron Institute, New York, USA
- Courant Institute, New York University, New York, USA
| | - Matthew A. Glaser
- Department of Physics, University of Colorado Boulder, Colorado, USA
- Center for Computational Biology, Flatiron Institute, New York, USA
| | - Meredith D. Betterton
- Department of Physics, University of Colorado Boulder, Colorado, USA
- Center for Computational Biology, Flatiron Institute, New York, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Colorado, USA
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17
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Li C, Zhang X, Dong M, Han X. Progress on Crowding Effect in Cell-like Structures. MEMBRANES 2022; 12:membranes12060593. [PMID: 35736300 PMCID: PMC9228500 DOI: 10.3390/membranes12060593] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 12/10/2022]
Abstract
Several biological macromolecules, such as proteins, nucleic acids, and polysaccharides, occupy about 30% of the space in cells, resulting in a crowded macromolecule environment. The crowding effect within cells exerts an impact on the functions of biological components, the assembly behavior of biomacromolecules, and the thermodynamics and kinetics of metabolic reactions. Cell-like structures provide confined and independent compartments for studying the working mechanisms of cells, which can be used to study the physiological functions arising from the crowding effect of macromolecules in cells. This article mainly summarizes the progress of research on the macromolecular crowding effects in cell-like structures. It includes the effects of this crowding on actin assembly behavior, tubulin aggregation behavior, and gene expression. The challenges and future trends in this field are presented at the end of the paper.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China; (C.L.); (X.Z.)
| | - Xiangxiang Zhang
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China; (C.L.); (X.Z.)
| | - Mingdong Dong
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, 8000 Aarhus, Denmark
- Correspondence: (M.D.); (X.H.)
| | - Xiaojun Han
- State Key Laboratory of Urban Water Resource and Environment, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, 92 West Da-Zhi Street, Harbin 150001, China; (C.L.); (X.Z.)
- Correspondence: (M.D.); (X.H.)
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18
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Sultan SA, R Nejad M, Doostmohammadi A. Quadrupolar active stress induces exotic patterns of defect motion in compressible active nematics. SOFT MATTER 2022; 18:4118-4126. [PMID: 35579323 DOI: 10.1039/d1sm01683k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A wide range of living and artificial active matter exists in close contact with substrates and under strong confinement, where in addition to dipolar active stresses, quadrupolar active stresses can become important. Here, we numerically investigate the impact of quadrupolar non-equilibrium stresses on the emergent patterns of self-organisation in non-momentum conserving active nematics. Our results reveal that beyond having stabilising effects, the quadrupolar active forces can induce various modes of topological defect motion in active nematics. In particular, we find the emergence of both polar and nematic ordering of the defects, as well as new patterns of self-organisation that comprise topological defect chains and transient topological defect asters. The results contribute to further understanding of emergent patterns of collective motion and non-equilibrium self-organisation in active matter.
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Affiliation(s)
- Salik A Sultan
- The Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Mehrana R Nejad
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, UK
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19
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Kuhnhold A, van der Schoot P. Structure of nematic tactoids of hard rods. J Chem Phys 2022; 156:104501. [DOI: 10.1063/5.0078056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We study by means of Monte Carlo simulations the internal structure of nematic droplets or tactoids formed by hard, rod-like particles in a gas of spherical ghost particles that act as depletion agents for the rods. We find that the shape and internal structure of tactoids are strongly affected by the size of the droplets. The monotonically increasing degree of nematic order with increasing particle density that characterizes the bulk nematic phase is locally violated and more so the smaller the tactoid. We also investigate the impact of an external quadrupolar alignment field on tactoids and find that this tends to make the director field more uniform, but not to very significantly increase the tactoid’s aspect ratio. This agrees with recent theoretical predictions yet is at variance with experimental observations and dynamical simulations. We explain this discrepancy in terms of competing relaxation times.
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Affiliation(s)
- Anja Kuhnhold
- Institute of Physics, University of Freiburg, 79104 Freiburg (Breisgau), Germany
| | - Paul van der Schoot
- Department of Applied Physics, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
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20
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Ganar KA, Honaker LW, Deshpande S. Shaping synthetic cells through cytoskeleton-condensate-membrane interactions. Curr Opin Colloid Interface Sci 2021. [DOI: 10.1016/j.cocis.2021.101459] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Olivi L, Berger M, Creyghton RNP, De Franceschi N, Dekker C, Mulder BM, Claassens NJ, Ten Wolde PR, van der Oost J. Towards a synthetic cell cycle. Nat Commun 2021; 12:4531. [PMID: 34312383 PMCID: PMC8313558 DOI: 10.1038/s41467-021-24772-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/29/2021] [Indexed: 02/08/2023] Open
Abstract
Recent developments in synthetic biology may bring the bottom-up generation of a synthetic cell within reach. A key feature of a living synthetic cell is a functional cell cycle, in which DNA replication and segregation as well as cell growth and division are well integrated. Here, we describe different approaches to recreate these processes in a synthetic cell, based on natural systems and/or synthetic alternatives. Although some individual machineries have recently been established, their integration and control in a synthetic cell cycle remain to be addressed. In this Perspective, we discuss potential paths towards an integrated synthetic cell cycle.
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Affiliation(s)
- Lorenzo Olivi
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | | | | | - Nicola De Franceschi
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | | | - Nico J Claassens
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | | | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
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22
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Safdari M, Zandi R, van der Schoot P. Effect of electric fields on the director field and shape of nematic tactoids. Phys Rev E 2021; 103:062703. [PMID: 34271629 DOI: 10.1103/physreve.103.062703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 04/06/2021] [Indexed: 01/30/2023]
Abstract
Tactoids are spindle-shaped droplets of a uniaxial nematic phase suspended in the coexisting isotropic phase. They are found in dispersions of a wide variety of elongated colloidal particles, including actin, fd virus, carbon nanotubes, vanadium peroxide, and chitin nanocrystals. Recent experiments on tactoids of chitin nanocrystals in water show that electric fields can very strongly elongate tactoids even though the dielectric properties of the coexisting isotropic and nematic phases differ only subtly. We develop a model for partially bipolar tactoids, where the degree of bipolarness of the director field is free to adjust to optimize the sum of the elastic, surface, and Coulomb energies of the system. By means of a combination of a scaling analysis and a numerical study, we investigate the elongation and director field's behavior of the tactoids as a function of their size, the strength of the electric field, the surface tension, anchoring strength, the elastic constants, and the electric susceptibility anisotropy. We find that tactoids cannot elongate significantly due to an external electric field, unless the director field is bipolar or quasibipolar and somehow frozen in the field-free configuration. Presuming that this is the case, we find reasonable agreement with experimental data.
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Affiliation(s)
- Mohammadamin Safdari
- Department of Physics, University of California, Riverside, California 92521, USA
| | - Roya Zandi
- Department of Physics, University of California, Riverside, California 92521, USA
| | - Paul van der Schoot
- Department of Applied Physics, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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23
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Sahu S, Herbst L, Quinn R, Ross JL. Crowder and surface effects on self-organization of microtubules. Phys Rev E 2021; 103:062408. [PMID: 34271669 DOI: 10.1103/physreve.103.062408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 05/14/2021] [Indexed: 12/30/2022]
Abstract
Microtubules are an essential physical building block of cellular systems. They are organized using specific crosslinkers, motors, and influencers of nucleation and growth. With the addition of antiparallel crosslinkers, microtubule self-organization patterns go through a transition from fanlike structures to homogeneous tactoid condensates in vitro. Tactoids are reminiscent of biological mitotic spindles, the cell division machinery. To create these organizations, we previously used polymer crowding agents. Here we study how altering the properties of the crowders, such as type, size, and molecular weight, affects microtubule organization. Comparing simulations with experiments, we observe a scaling law associated with the fanlike patterns in the absence of crosslinkers. Tactoids formed in the presence of crosslinkers show variable length, depending on the crowders. We correlate the subtle differences to filament contour length changes, affected by nucleation and growth rate changes induced by the polymers in solution. Using quantitative image analysis, we deduce that the tactoids differ from traditional liquid crystal organization, as they are limited in width irrespective of crowders and surfaces, and behave as solidlike condensates.
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Affiliation(s)
- Sumon Sahu
- Department of Physics, Syracuse University, Syracuse, New York 13244, USA
| | - Lena Herbst
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - Ryan Quinn
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
| | - Jennifer L Ross
- Department of Physics, Syracuse University, Syracuse, New York 13244, USA
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24
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Lamson AR, Moore JM, Fang F, Glaser MA, Shelley MJ, Betterton MD. Comparison of explicit and mean-field models of cytoskeletal filaments with crosslinking motors. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:45. [PMID: 33779863 PMCID: PMC8220871 DOI: 10.1140/epje/s10189-021-00042-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/20/2021] [Indexed: 05/17/2023]
Abstract
In cells, cytoskeletal filament networks are responsible for cell movement, growth, and division. Filaments in the cytoskeleton are driven and organized by crosslinking molecular motors. In reconstituted cytoskeletal systems, motor activity is responsible for far-from-equilibrium phenomena such as active stress, self-organized flow, and spontaneous nematic defect generation. How microscopic interactions between motors and filaments lead to larger-scale dynamics remains incompletely understood. To build from motor-filament interactions to predict bulk behavior of cytoskeletal systems, more computationally efficient techniques for modeling motor-filament interactions are needed. Here, we derive a coarse-graining hierarchy of explicit and continuum models for crosslinking motors that bind to and walk on filament pairs. We compare the steady-state motor distribution and motor-induced filament motion for the different models and analyze their computational cost. All three models agree well in the limit of fast motor binding kinetics. Evolving a truncated moment expansion of motor density speeds the computation by [Formula: see text]-[Formula: see text] compared to the explicit or continuous-density simulations, suggesting an approach for more efficient simulation of large networks. These tools facilitate further study of motor-filament networks on micrometer to millimeter length scales.
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Affiliation(s)
- Adam R Lamson
- Department of Physics, University of Colorado Boulder, Boulder, USA.
| | - Jeffrey M Moore
- Department of Physics, University of Colorado Boulder, Boulder, USA
| | - Fang Fang
- Courant Institute, New York University, New York, USA
| | - Matthew A Glaser
- Department of Physics, University of Colorado Boulder, Boulder, USA
| | - Michael J Shelley
- Courant Institute, New York University, New York, USA
- Center for Computational Biology, Flatiron Institute, New York, USA
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25
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Lehmann K, Shayegan M, Blab GA, Forde NR. Optical Tweezers Approaches for Probing Multiscale Protein Mechanics and Assembly. Front Mol Biosci 2020; 7:577314. [PMID: 33134316 PMCID: PMC7573139 DOI: 10.3389/fmolb.2020.577314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/27/2020] [Indexed: 01/09/2023] Open
Abstract
Multi-step assembly of individual protein building blocks is key to the formation of essential higher-order structures inside and outside of cells. Optical tweezers is a technique well suited to investigate the mechanics and dynamics of these structures at a variety of size scales. In this mini-review, we highlight experiments that have used optical tweezers to investigate protein assembly and mechanics, with a focus on the extracellular matrix protein collagen. These examples demonstrate how optical tweezers can be used to study mechanics across length scales, ranging from the single-molecule level to fibrils to protein networks. We discuss challenges in experimental design and interpretation, opportunities for integration with other experimental modalities, and applications of optical tweezers to current questions in protein mechanics and assembly.
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Affiliation(s)
- Kathrin Lehmann
- Department of Physics, Simon Fraser University, Burnaby, BC, Canada.,Soft Condensed Matter and Biophysics, Utrecht University, Utrecht, Netherlands
| | - Marjan Shayegan
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States
| | - Gerhard A Blab
- Soft Condensed Matter and Biophysics, Utrecht University, Utrecht, Netherlands
| | - Nancy R Forde
- Department of Physics, Simon Fraser University, Burnaby, BC, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Department of Chemistry, Simon Fraser University, Burnaby, BC, Canada.,Centre for Cell Biology, Development and Disease (C2D2), Simon Fraser University, Burnaby, BC, Canada
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26
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Active forces shape the metaphase spindle through a mechanical instability. Proc Natl Acad Sci U S A 2020; 117:16154-16159. [PMID: 32601228 DOI: 10.1073/pnas.2002446117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The metaphase spindle is a dynamic structure orchestrating chromosome segregation during cell division. Recently, soft matter approaches have shown that the spindle behaves as an active liquid crystal. Still, it remains unclear how active force generation contributes to its characteristic spindle-like shape. Here we combine theory and experiments to show that molecular motor-driven forces shape the structure through a barreling-type instability. We test our physical model by titrating dynein activity in Xenopus egg extract spindles and quantifying the shape and microtubule orientation. We conclude that spindles are shaped by the interplay between surface tension, nematic elasticity, and motor-driven active forces. Our study reveals how motor proteins can mold liquid crystalline droplets and has implications for the design of active soft materials.
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27
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Scheff DR, Weirich KL, Dasbiswas K, Patel A, Vaikuntanathan S, Gardel ML. Tuning shape and internal structure of protein droplets via biopolymer filaments. SOFT MATTER 2020; 16:5659-5668. [PMID: 32519715 DOI: 10.1039/c9sm02462j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Macromolecules can phase separate to form liquid condensates, which are emerging as critical compartments in fields as diverse as intracellular organization and soft materials design. A myriad of macromolecules, including the protein FUS, form condensates which behave as isotropic liquids. Here, we investigate the influence of filament dopants on the material properties of protein liquids. We find that the short, biopolymer filaments of actin spontaneously partition into FUS droplets to form composite liquid droplets. As the concentration of the filament dopants increases, the coalescence time decreases, indicating that the dopants control viscosity relative to surface tension. The droplet shape is tunable and ranges from spherical to tactoid as the filament length or concentration is increased. We find that the tactoids are well described by a model of a quasi bipolar liquid crystal droplet, where nematic order from the anisotropic actin filaments competes with isotropic interfacial energy from the FUS, controlling droplet shape in a size-dependent manner. Our results demonstrate a versatile approach to construct tunable, anisotropic macromolecular liquids.
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Affiliation(s)
- Danielle R Scheff
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA. and Department of Physics, University of Chicago, Chicago, IL 60637, USA
| | - Kimberly L Weirich
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA. and HHMI HCIA Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA and Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Kinjal Dasbiswas
- Department of Physics, University of California, Merced, CA 95343, USA
| | - Avinash Patel
- HHMI HCIA Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA and Dewpoint Therapeutics GmbH, Pfotenhauer Strasse 108, Dresden 01307, USA
| | - Suriyanarayanan Vaikuntanathan
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA. and Department of Chemistry, University of Chicago, Chicago, IL 60637, USA
| | - Margaret L Gardel
- James Franck Institute, University of Chicago, Chicago, IL 60637, USA. and Department of Physics, University of Chicago, Chicago, IL 60637, USA and HHMI HCIA Summer Institute, Marine Biological Laboratory, Woods Hole, MA 02543, USA and Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
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28
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Morozov M. Adsorption inhibition by swollen micelles may cause multistability in active droplets. SOFT MATTER 2020; 16:5624-5632. [PMID: 32530002 DOI: 10.1039/d0sm00662a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Experiments indicate that microdroplets undergoing micellar solubilization in the bulk of surfactant solution may excite Marangoni flows and self-propel spontaneously. Surprisingly, self-propulsion emerges even when the critical micelle concentration is exceeded and the Marangoni effect should be saturated. To explain this, we propose a novel model of a dissolving active droplet that is based on two fundamental assumptions: (a) products of the solubilization may inhibit surfactant adsorption; (b) solubilization prevents the formation of a monolayer of surfactant molecules at the droplet interface. We use numerical simulations and asymptotic methods to demonstrate that our model indeed features spontaneous droplet self-propulsion. Our key finding is that in the case of axisymmetric flow and concentration fields, two qualitatively different types of droplet behavior may be stable for the same values of the physical parameters: steady self-propulsion and steady symmetric pumping. Although stability of these steady regimes is not guaranteed in the absence of axial symmetry, we argue that they will retain their respective stable manifolds in the phase space of a fully 3D problem.
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Affiliation(s)
- Matvey Morozov
- Nonlinear Physical Chemistry Unit, Faculté des Sciences, Université libre de Bruxelles (ULB), CP231, 1050 Brussels, Belgium.
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29
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Ludwig NB, Weirch KL, Alster E, Witten TA, Gardel ML, Dasbiswas K, Vaikuntanathan S. Nucleation and shape dynamics of model nematic tactoids around adhesive colloids. J Chem Phys 2020; 152:084901. [PMID: 32113348 DOI: 10.1063/1.5141997] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recent experiments have shown how nematically ordered tactoid shaped actin droplets can be reorganized and divided by the action of myosin molecular motors. In this paper, we consider how similar morphological changes can potentially be achieved under equilibrium conditions. Using simulations, both atomistic and continuum, and a simple macroscopic model, we explore how the nucleation dynamics, shape changes, and the final steady state of a nematic tactoid droplet can be modified by interactions with model adhesive colloids that mimic a myosin motor cluster. We show how tactoid reorganization may occur in an equilibrium colloidal-nematic setting. We then suggest based on the simple macroscopic model how the simulation models may be extended to potentially stabilize divided tactoids.
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Affiliation(s)
- Nicholas B Ludwig
- Department of Chemistry and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Kimberly L Weirch
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
| | - Eli Alster
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Thomas A Witten
- Department of Physics and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Margaret L Gardel
- Department of Physics and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA
| | - Kinjal Dasbiswas
- Department of Physics, University of California, Merced, Merced, California 95343, USA
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30
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Metselaar L, Yeomans JM, Doostmohammadi A. Topology and Morphology of Self-Deforming Active Shells. PHYSICAL REVIEW LETTERS 2019; 123:208001. [PMID: 31809098 DOI: 10.1103/physrevlett.123.208001] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Indexed: 06/10/2023]
Abstract
We present a generic framework for modeling three-dimensional deformable shells of active matter that captures the orientational dynamics of the active particles and hydrodynamic interactions on the shell and with the surrounding environment. We find that the cross talk between the self-induced flows of active particles and dynamic reshaping of the shell can result in conformations that are tunable by varying the form and magnitude of active stresses. We further demonstrate and explain how self-induced topological defects in the active layer can direct the morphodynamics of the shell. These findings are relevant to understanding morphological changes during organ development and the design of bioinspired materials that are capable of self-organization.
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Affiliation(s)
- Luuk Metselaar
- Rudolf Peierls Centre for Theoretical Physics, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Julia M Yeomans
- Rudolf Peierls Centre for Theoretical Physics, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Amin Doostmohammadi
- Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen, Denmark
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31
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Division in synthetic cells. Emerg Top Life Sci 2019; 3:551-558. [PMID: 33523162 DOI: 10.1042/etls20190023] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 12/13/2022]
Abstract
Cell division is one of the most fundamental processes of life, and so far the only known way of how living systems can come into existence at all. Consequently, its reconstitution in any artificial cell system that will have to be built from the bottom-up is a notoriously complex but an important task. In this short review, I discuss several approaches how to realize division of cell-like compartments, from simply relying on the physical principles of destabilization by growth, or applying external forces, to the design of self-assembling and self-organizing machineries that may autonomously accomplish this task in response to external or internal cues.
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