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  1. Article ; Online: Ultrasensitivity of microtubule severing due to damage repair.

    Shiff, Chloe E / Kondev, Jane / Mohapatra, Lishibanya

    iScience

    2024  Volume 27, Issue 2, Page(s) 108874

    Abstract: Microtubule-based cytoskeletal structures aid in cell motility, cell polarization, and intracellular transport. These functions require a coordinated effort of regulatory proteins which interact with microtubule cytoskeleton distinctively. ...

    Abstract Microtubule-based cytoskeletal structures aid in cell motility, cell polarization, and intracellular transport. These functions require a coordinated effort of regulatory proteins which interact with microtubule cytoskeleton distinctively.
    Language English
    Publishing date 2024-01-11
    Publishing country United States
    Document type Journal Article
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2024.108874
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  2. Article ; Online: Length regulation of multiple flagella that self-assemble from a shared pool of components.

    Fai, Thomas G / Mohapatra, Lishibanya / Kar, Prathitha / Kondev, Jane / Amir, Ariel

    eLife

    2019  Volume 8

    Abstract: The single-celled green ... ...

    Abstract The single-celled green algae
    MeSH term(s) Chlamydomonas reinhardtii/metabolism ; Flagella/metabolism ; Kinesins/metabolism ; Microtubules/metabolism ; Polymerization ; Protein Transport ; Tubulin/metabolism
    Chemical Substances Tubulin ; Kinesins (EC 3.6.4.4)
    Language English
    Publishing date 2019-10-09
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.42599
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  3. Article ; Online: Length regulation of multiple flagella that self-assemble from a shared pool of components

    Thomas G Fai / Lishibanya Mohapatra / Prathitha Kar / Jane Kondev / Ariel Amir

    eLife, Vol

    2019  Volume 8

    Abstract: The single-celled green algae Chlamydomonas reinhardtii with its two flagella—microtubule-based structures of equal and constant lengths—is the canonical model organism for studying size control of organelles. Experiments have identified motor-driven ... ...

    Abstract The single-celled green algae Chlamydomonas reinhardtii with its two flagella—microtubule-based structures of equal and constant lengths—is the canonical model organism for studying size control of organelles. Experiments have identified motor-driven transport of tubulin to the flagella tips as a key component of their length control. Here we consider a class of models whose key assumption is that proteins responsible for the intraflagellar transport (IFT) of tubulin are present in limiting amounts. We show that the limiting-pool assumption is insufficient to describe the results of severing experiments, in which a flagellum is regenerated after it has been severed. Next, we consider an extension of the limiting-pool model that incorporates proteins that depolymerize microtubules. We show that this ‘active disassembly’ model of flagellar length control explains in quantitative detail the results of severing experiments and use it to make predictions that can be tested in experiments.
    Keywords length control ; flagella ; diffusion ; depolymerization ; molecular motors ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2019-10-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
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  4. Article ; Online: Antenna Mechanism of Length Control of Actin Cables.

    Lishibanya Mohapatra / Bruce L Goode / Jane Kondev

    PLoS Computational Biology, Vol 11, Iss 6, p e

    2015  Volume 1004160

    Abstract: Actin cables are linear cytoskeletal structures that serve as tracks for myosin-based intracellular transport of vesicles and organelles in both yeast and mammalian cells. In a yeast cell undergoing budding, cables are in constant dynamic turnover yet ... ...

    Abstract Actin cables are linear cytoskeletal structures that serve as tracks for myosin-based intracellular transport of vesicles and organelles in both yeast and mammalian cells. In a yeast cell undergoing budding, cables are in constant dynamic turnover yet some cables grow from the bud neck toward the back of the mother cell until their length roughly equals the diameter of the mother cell. This raises the question: how is the length of these cables controlled? Here we describe a novel molecular mechanism for cable length control inspired by recent experimental observations in cells. This "antenna mechanism" involves three key proteins: formins, which polymerize actin, Smy1 proteins, which bind formins and inhibit actin polymerization, and myosin motors, which deliver Smy1 to formins, leading to a length-dependent actin polymerization rate. We compute the probability distribution of cable lengths as a function of several experimentally tuneable parameters such as the formin-binding affinity of Smy1 and the concentration of myosin motors delivering Smy1. These results provide testable predictions of the antenna mechanism of actin-cable length control.
    Keywords Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2015-06-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
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  5. Article ; Online: Antenna Mechanism of Length Control of Actin Cables.

    Mohapatra, Lishibanya / Goode, Bruce L / Kondev, Jane

    PLoS computational biology

    2015  Volume 11, Issue 6, Page(s) e1004160

    Abstract: Actin cables are linear cytoskeletal structures that serve as tracks for myosin-based intracellular transport of vesicles and organelles in both yeast and mammalian cells. In a yeast cell undergoing budding, cables are in constant dynamic turnover yet ... ...

    Abstract Actin cables are linear cytoskeletal structures that serve as tracks for myosin-based intracellular transport of vesicles and organelles in both yeast and mammalian cells. In a yeast cell undergoing budding, cables are in constant dynamic turnover yet some cables grow from the bud neck toward the back of the mother cell until their length roughly equals the diameter of the mother cell. This raises the question: how is the length of these cables controlled? Here we describe a novel molecular mechanism for cable length control inspired by recent experimental observations in cells. This "antenna mechanism" involves three key proteins: formins, which polymerize actin, Smy1 proteins, which bind formins and inhibit actin polymerization, and myosin motors, which deliver Smy1 to formins, leading to a length-dependent actin polymerization rate. We compute the probability distribution of cable lengths as a function of several experimentally tuneable parameters such as the formin-binding affinity of Smy1 and the concentration of myosin motors delivering Smy1. These results provide testable predictions of the antenna mechanism of actin-cable length control.
    MeSH term(s) Actins/chemistry ; Actins/metabolism ; Computational Biology ; Microtubule-Associated Proteins/chemistry ; Microtubule-Associated Proteins/metabolism ; Models, Molecular ; Myosins/chemistry ; Myosins/metabolism ; Polymerization ; Saccharomyces cerevisiae/cytology ; Saccharomyces cerevisiae/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/metabolism
    Chemical Substances Actins ; Microtubule-Associated Proteins ; Saccharomyces cerevisiae Proteins ; Myosins (EC 3.6.4.1)
    Language English
    Publishing date 2015-06-24
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1004160
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  6. Article: The Limiting-Pool Mechanism Fails to Control the Size of Multiple Organelles.

    Mohapatra, Lishibanya / Lagny, Thibaut J / Harbage, David / Jelenkovic, Predrag R / Kondev, Jane

    Cell systems

    2017  Volume 4, Issue 5, Page(s) 559–567.e14

    Abstract: How the size of micrometer-scale cellular structures such as the mitotic spindle, cytoskeletal filaments, the nucleus, the nucleolus, and other non-membrane bound organelles is controlled despite a constant turnover of their constituent parts is a ... ...

    Abstract How the size of micrometer-scale cellular structures such as the mitotic spindle, cytoskeletal filaments, the nucleus, the nucleolus, and other non-membrane bound organelles is controlled despite a constant turnover of their constituent parts is a central problem in biology. Experiments have implicated the limiting-pool mechanism: structures grow by stochastic addition of molecular subunits from a finite pool until the rates of subunit addition and removal are balanced, producing a structure of well-defined size. Here, we consider these dynamics when multiple filamentous structures are assembled stochastically from a shared pool of subunits. Using analytical calculations and computer simulations, we show that robust size control can be achieved only when a single filament is assembled. When multiple filaments compete for monomers, filament lengths exhibit large fluctuations. These results extend to three-dimensional structures and reveal the physical limitations of the limiting-pool mechanism of size control when multiple organelles are assembled from a shared pool of subunits.
    MeSH term(s) Actin Cytoskeleton/chemistry ; Actins/analysis ; Biophysical Phenomena ; Cell Size ; Computational Biology/methods ; Computer Simulation ; Cytoskeleton/chemistry ; Models, Biological ; Organelles/metabolism ; Systems Biology/methods
    Chemical Substances Actins
    Language English
    Publishing date 2017-05-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ISSN 2405-4712
    ISSN 2405-4712
    DOI 10.1016/j.cels.2017.04.011
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  7. Article ; Online: Design Principles of Length Control of Cytoskeletal Structures.

    Mohapatra, Lishibanya / Goode, Bruce L / Jelenkovic, Predrag / Phillips, Rob / Kondev, Jane

    Annual review of biophysics

    2016  Volume 45, Page(s) 85–116

    Abstract: Cells contain elaborate and interconnected networks of protein polymers, which make up the cytoskeleton. The cytoskeleton governs the internal positioning and movement of vesicles and organelles and controls dynamic changes in cell polarity, shape, and ... ...

    Abstract Cells contain elaborate and interconnected networks of protein polymers, which make up the cytoskeleton. The cytoskeleton governs the internal positioning and movement of vesicles and organelles and controls dynamic changes in cell polarity, shape, and movement. Many of these processes require tight control of the size and shape of cytoskeletal structures, which is achieved despite rapid turnover of their molecular components. Here we review mechanisms by which cells control the size of filamentous cytoskeletal structures, from the point of view of simple quantitative models that take into account stochastic dynamics of their assembly and disassembly. Significantly, these models make experimentally testable predictions that distinguish different mechanisms of length control. Although the primary focus of this review is on cytoskeletal structures, we believe that the broader principles and mechanisms discussed herein will apply to a range of other subcellular structures whose sizes are tightly controlled and are linked to their functions.
    MeSH term(s) Actin Cytoskeleton/chemistry ; Actin Cytoskeleton/physiology ; Actin Cytoskeleton/ultrastructure ; Animals ; Cytoskeleton/chemistry ; Cytoskeleton/physiology ; Cytoskeleton/ultrastructure ; Microtubules/chemistry ; Microtubules/physiology ; Microtubules/ultrastructure
    Language English
    Publishing date 2016-07-05
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 2434725-5
    ISSN 1936-1238 ; 1936-122X
    ISSN (online) 1936-1238
    ISSN 1936-122X
    DOI 10.1146/annurev-biophys-070915-094206
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  8. Book ; Online: Antenna mechanism of length control of actin cables

    Mohapatra, Lishibanya / Goode, Bruce L. / Kondev, Jane

    2014  

    Abstract: Actin cables are linear cytoskeletal structures that serve as tracks for myosin-based intracellular transport of vesicles and organelles in both yeast and mammalian cells. In a yeast cell undergoing budding, cables are in constant dynamic turnover yet ... ...

    Abstract Actin cables are linear cytoskeletal structures that serve as tracks for myosin-based intracellular transport of vesicles and organelles in both yeast and mammalian cells. In a yeast cell undergoing budding, cables are in constant dynamic turnover yet some cables grow from the bud neck toward the back of the mother cell until their length roughly equals the diameter of the mother cell. This raises the question: how is the length of these cables controlled? Here we describe a novel molecular mechanism for cable length control inspired by recent experimental observations in cells. This antenna mechanism involves three key proteins: formins, which polymerize actin, Smy1 proteins, which bind formins and inhibit actin polymerization, and myosin motors, which deliver Smy1 to formins, leading to a length-dependent actin polymerization rate. We compute the probability distribution of cable lengths as a function of several experimentally tuneable parameters such as the formin-binding affinity of Smy1 and the concentration of myosin motors delivering Smy1. These results provide testable predictions of the antenna mechanism of actin-cable length control.
    Keywords Physics - Biological Physics ; Quantitative Biology - Subcellular Processes
    Subject code 612
    Publishing date 2014-11-14
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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