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Shiff CE, Kondev J, Mohapatra L. Ultrasensitivity of microtubule severing due to damage repair. iScience 2024; 27:108874. [PMID: 38327774 PMCID: PMC10847648 DOI: 10.1016/j.isci.2024.108874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 01/01/2024] [Accepted: 01/08/2024] [Indexed: 02/09/2024] Open
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. In-vitro experiments have shown that free tubulin can repair nanoscale damages of microtubules created by severing proteins. Based on this observation, we theoretically analyze microtubule severing as a competition between the processes of damage spreading and tubulin-induced repair. We demonstrate that this model is in quantitative agreement with in-vitro experiments and predict the existence of a critical tubulin concentration above which severing becomes rare, fast, and sensitive to concentration of free tubulin. We show that this sensitivity leads to a dramatic increase in the dynamic range of steady-state microtubule lengths when the free tubulin concentration is varied, and microtubule lengths are controlled by severing. Our work demonstrates how synergy between tubulin and microtubule-associated proteins can bring about specific dynamical properties of microtubules.
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Affiliation(s)
- Chloe E. Shiff
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Jane Kondev
- Department of Physics, Brandeis University, Waltham, MA 02454, USA
| | - Lishibanya Mohapatra
- School of Physics and Astronomy, College of Science, Rochester Institute of Technology, Rochester, NY 14623, USA
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Surendiran P, Meinecke CR, Salhotra A, Heldt G, Zhu J, Månsson A, Diez S, Reuter D, Kugler H, Linke H, Korten T. Solving Exact Cover Instances with Molecular-Motor-Powered Network-Based Biocomputation. ACS NANOSCIENCE AU 2022; 2:396-403. [PMID: 36281252 PMCID: PMC9585575 DOI: 10.1021/acsnanoscienceau.2c00013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Information processing
by traditional, serial electronic processors
consumes an ever-increasing part of the global electricity supply.
An alternative, highly energy efficient, parallel computing paradigm
is network-based biocomputation (NBC). In NBC a given combinatorial
problem is encoded into a nanofabricated, modular network. Parallel
exploration of the network by a very large number of independent molecular-motor-propelled
protein filaments solves the encoded problem. Here we demonstrate
a significant scale-up of this technology by solving four instances
of Exact Cover, a nondeterministic polynomial time (NP) complete problem
with applications in resource scheduling. The difficulty of the largest
instances solved here is 128 times greater in comparison to the current
state of the art for NBC.
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Affiliation(s)
| | | | - Aseem Salhotra
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar SE-39231, Sweden
| | - Georg Heldt
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar SE-39231, Sweden
| | - Jingyuan Zhu
- NanoLund and Solid State Physics, Lund University, Box 118, Lund SE-22100, Sweden
| | - Alf Månsson
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Kalmar SE-39231, Sweden
| | - Stefan Diez
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden D-01307, Germany
- Cluster of Excellence Physics of Life, Technische Universität Dresden, Dresden D-01307, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden D-01307, Germany
| | - Danny Reuter
- Center for Microtechnologies, Technische Universität Chemnitz, Chemnitz D-09126, Germany
- Fraunhofer Institute for Electronic Nano Systems ENAS, Chemnitz, D-09126, Germany
| | - Hillel Kugler
- Faculty of Engineering, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Heiner Linke
- NanoLund and Solid State Physics, Lund University, Box 118, Lund SE-22100, Sweden
| | - Till Korten
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden D-01307, Germany
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