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Clarke J, Melcher L, Crowell AD, Cavanna F, Houser JR, Graham K, Green AM, Stachowiak JC, Truskett TM, Milliron DJ, Rosales AM, Das M, Alvarado J. Morphological control of bundled actin networks subject to fixed-mass depletion. J Chem Phys 2024; 161:074905. [PMID: 39166892 DOI: 10.1063/5.0197269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 07/10/2024] [Indexed: 08/23/2024] Open
Abstract
Depletion interactions are thought to significantly contribute to the organization of intracellular structures in the crowded cytosol. The strength of depletion interactions depends on physical parameters such as the depletant number density and the depletant size ratio. Cells are known to dynamically regulate these two parameters by varying the copy number of proteins of a wide distribution of sizes. However, mammalian cells are also known to keep the total protein mass density remarkably constant, to within 0.5% throughout the cell cycle. We thus ask how the strength of depletion interactions varies when the total depletant mass is held fixed, a.k.a. fixed-mass depletion. We answer this question via scaling arguments, as well as by studying depletion effects on networks of reconstituted semiflexible actin in silico and in vitro. We examine the maximum strength of the depletion interaction potential U∗ as a function of q, the size ratio between the depletant and the matter being depleted. We uncover a scaling relation U∗ ∼ qζ for two cases: fixed volume fraction φ and fixed mass density ρ. For fixed volume fraction, we report ζ < 0. For the fixed mass density case, we report ζ > 0, which suggests that the depletion interaction strength increases as the depletant size ratio is increased. To test this prediction, we prepared our filament networks at fixed mass concentrations with varying sizes of the depletant molecule poly(ethylene glycol) (PEG). We characterize the depletion interaction strength in our simulations via the mesh size. In experiments, we observe two distinct actin network morphologies, which we call weakly bundled and strongly bundled. We identify a mass concentration where different PEG depletant sizes lead to weakly bundled or strongly bundled morphologies. For these conditions, we find that the mesh size and intra-bundle spacing between filaments across the different morphologies do not show significant differences, while the dynamic light scattering relaxation time and storage modulus between the two states do show significant differences. Our results demonstrate the ability to tune actin network morphology and mechanics by controlling depletant size and give insights into depletion interaction mechanisms under the fixed-depletant-mass constraint relevant to living cells.
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Affiliation(s)
- James Clarke
- UT Austin Department of Physics, 2515 Speedway, Austin, Texas 78712, USA
| | - Lauren Melcher
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, New York 14623, USA
| | - Anne D Crowell
- UT Austin McKetta Department of Chemical Engineering, E 24th St., Austin, Texas 78712, USA
| | - Francis Cavanna
- UT Austin Department of Physics, 2515 Speedway, Austin, Texas 78712, USA
| | - Justin R Houser
- UT Austin Department of Biomedical Engineering, Austin, Texas 78712, USA
| | - Kristin Graham
- UT Austin Department of Biomedical Engineering, Austin, Texas 78712, USA
| | - Allison M Green
- UT Austin McKetta Department of Chemical Engineering, E 24th St., Austin, Texas 78712, USA
| | - Jeanne C Stachowiak
- UT Austin McKetta Department of Chemical Engineering, E 24th St., Austin, Texas 78712, USA
- UT Austin Department of Biomedical Engineering, Austin, Texas 78712, USA
| | - Thomas M Truskett
- UT Austin McKetta Department of Chemical Engineering, E 24th St., Austin, Texas 78712, USA
| | - Delia J Milliron
- UT Austin McKetta Department of Chemical Engineering, E 24th St., Austin, Texas 78712, USA
| | - Adrianne M Rosales
- UT Austin McKetta Department of Chemical Engineering, E 24th St., Austin, Texas 78712, USA
| | - Moumita Das
- School of Mathematical Sciences, Rochester Institute of Technology, Rochester, New York 14623, USA
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, New York 14623, USA
| | - José Alvarado
- UT Austin Department of Physics, 2515 Speedway, Austin, Texas 78712, USA
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Sheung JY, Garamella J, Kahl SK, Lee BY, McGorty RJ, Robertson-Anderson RM. Motor-driven advection competes with crowding to drive spatiotemporally heterogeneous transport in cytoskeleton composites. FRONTIERS IN PHYSICS 2022; 10:1055441. [PMID: 37547053 PMCID: PMC10403238 DOI: 10.3389/fphy.2022.1055441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The cytoskeleton-a composite network of biopolymers, molecular motors, and associated binding proteins-is a paradigmatic example of active matter. Particle transport through the cytoskeleton can range from anomalous and heterogeneous subdiffusion to superdiffusion and advection. Yet, recapitulating and understanding these properties-ubiquitous to the cytoskeleton and other out-of-equilibrium soft matter systems-remains challenging. Here, we combine light sheet microscopy with differential dynamic microscopy and single-particle tracking to elucidate anomalous and advective transport in actomyosin-microtubule composites. We show that particles exhibit multi-mode transport that transitions from pronounced subdiffusion to superdiffusion at tunable crossover timescales. Surprisingly, while higher actomyosin content increases the range of timescales over which transport is superdiffusive, it also markedly increases the degree of subdiffusion at short timescales and generally slows transport. Corresponding displacement distributions display unique combinations of non-Gaussianity, asymmetry, and non-zero modes, indicative of directed advection coupled with caged diffusion and hopping. At larger spatiotemporal scales, particles in active composites exhibit superdiffusive dynamics with scaling exponents that are robust to changing actomyosin fractions, in contrast to normal, yet faster, diffusion in networks without actomyosin. Our specific results shed important new light on the interplay between non-equilibrium processes, crowding and heterogeneity in active cytoskeletal systems. More generally, our approach is broadly applicable to active matter systems to elucidate transport and dynamics across scales.
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Affiliation(s)
- Janet Y. Sheung
- W. M. Keck Science Department, Scripps College, Claremont, CA, United States
- W. M. Keck Science Department, Pitzer College, Claremont, CA, United States
| | - Jonathan Garamella
- Physics and Biophysics Department, University of San Diego, San Diego, CA, United States
| | - Stella K. Kahl
- W. M. Keck Science Department, Scripps College, Claremont, CA, United States
| | - Brian Y. Lee
- W. M. Keck Science Department, Pitzer College, Claremont, CA, United States
| | - Ryan J. McGorty
- Physics and Biophysics Department, University of San Diego, San Diego, CA, United States
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Berezney J, Goode BL, Fraden S, Dogic Z. Extensile to contractile transition in active microtubule-actin composites generates layered asters with programmable lifetimes. Proc Natl Acad Sci U S A 2022; 119:e2115895119. [PMID: 35086931 PMCID: PMC8812548 DOI: 10.1073/pnas.2115895119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/21/2021] [Indexed: 12/15/2022] Open
Abstract
We study a reconstituted composite system consisting of an active microtubule network interdigitated with a passive network of entangled F-actin filaments. Increasing the concentration of filamentous actin controls the emergent dynamics, inducing a transition from turbulent-like flows to bulk contractions. At intermediate concentrations, where the active stresses change their symmetry from anisotropic extensile to isotropic contracting, the composite separates into layered asters that coexist with the background turbulent fluid. Contracted onion-like asters have a radially extending microtubule-rich cortex that envelops alternating layers of microtubules and F-actin. These self-regulating structures undergo internal reorganization, which appears to minimize the surface area and maintain the ordered layering, even when undergoing aster merging events. Finally, the layered asters are metastable structures. Their lifetime, which ranges from minutes to hours, is encoded in the material properties of the composite. These results challenge the current models of active matter. They demonstrate self-organized dynamical states and patterns evocative of those observed in the cytoskeleton do not require precise biochemical regulation, but can arise from purely mechanical interactions of actively driven filamentous materials.
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Affiliation(s)
- John Berezney
- Department of Physics, Brandeis University, Waltham, MA 02454
| | - Bruce L Goode
- Department of Biology, Brandeis University, Waltham, MA 02454
| | - Seth Fraden
- Department of Physics, Brandeis University, Waltham, MA 02454
| | - Zvonimir Dogic
- Department of Physics, Brandeis University, Waltham, MA 02454;
- Department of Physics, University of California, Santa Barbara, CA 93106
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106
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Lee G, Leech G, Rust MJ, Das M, McGorty RJ, Ross JL, Robertson-Anderson RM. Myosin-driven actin-microtubule networks exhibit self-organized contractile dynamics. SCIENCE ADVANCES 2021; 7:7/6/eabe4334. [PMID: 33547082 PMCID: PMC7864579 DOI: 10.1126/sciadv.abe4334] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/21/2020] [Indexed: 06/02/2023]
Abstract
The cytoskeleton is a dynamic network of proteins, including actin, microtubules, and their associated motor proteins, that enables essential cellular processes such as motility, division, and growth. While actomyosin networks are extensively studied, how interactions between actin and microtubules, ubiquitous in the cytoskeleton, influence actomyosin activity remains an open question. Here, we create a network of co-entangled actin and microtubules driven by myosin II. We combine dynamic differential microscopy, particle image velocimetry, and particle tracking to show that both actin and microtubules undergo ballistic contraction with unexpectedly indistinguishable characteristics. This contractility is distinct from faster disordered motion and rupturing that active actin networks exhibit. Our results suggest that microtubules enable self-organized myosin-driven contraction by providing flexural rigidity and enhanced connectivity to actin networks. Beyond the immediate relevance to cytoskeletal dynamics, our results shed light on the design of active materials that can be precisely tuned by the network composition.
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Affiliation(s)
- Gloria Lee
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92110, USA
| | - Gregor Leech
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92110, USA
| | - Michael J Rust
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Moumita Das
- School of Physics and Astronomy, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Ryan J McGorty
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92110, USA
| | - Jennifer L Ross
- Department of Physics, Syracuse University, Syracuse, NY 13244, USA
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Cipelletti L, Martens K, Ramos L. Microscopic precursors of failure in soft matter. SOFT MATTER 2020; 16:82-93. [PMID: 31720666 DOI: 10.1039/c9sm01730e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The mechanical properties of soft matter are of great importance in countless applications, in addition of being an active field of academic research. Given the relative ease with which soft materials can be deformed, their non-linear behavior is of particular relevance. Large loads eventually result in material failure. In this Perspective article, we discuss recent work aiming at detecting precursors of failure by scrutinizing the microscopic structure and dynamics of soft systems under various conditions of loading. In particular, we show that the microscopic dynamics is a powerful indicator of the ultimate fate of soft materials, capable of unveiling precursors of failure up to thousands of seconds before any macroscopic sign of weakening.
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