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Chennakesavalu S, Manikandan SK, Hu F, Rotskoff GM. Adaptive nonequilibrium design of actin-based metamaterials: Fundamental and practical limits of control. Proc Natl Acad Sci U S A 2024; 121:e2310238121. [PMID: 38359294 PMCID: PMC10895351 DOI: 10.1073/pnas.2310238121] [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: 07/05/2023] [Accepted: 11/13/2023] [Indexed: 02/17/2024] Open
Abstract
The adaptive and surprising emergent properties of biological materials self-assembled in far-from-equilibrium environments serve as an inspiration for efforts to design nanomaterials. In particular, controlling the conditions of self-assembly can modulate material properties, but there is no systematic understanding of either how to parameterize external control or how controllable a given material can be. Here, we demonstrate that branched actin networks can be encoded with metamaterial properties by dynamically controlling the applied force under which they grow and that the protocols can be selected using multi-task reinforcement learning. These actin networks have tunable responses over a large dynamic range depending on the chosen external protocol, providing a pathway to encoding "memory" within these structures. Interestingly, we obtain a bound that relates the dissipation rate and the rate of "encoding" that gives insight into the constraints on control-both physical and information theoretical. Taken together, these results emphasize the utility and necessity of nonequilibrium control for designing self-assembled nanostructures.
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Affiliation(s)
| | | | - Frank Hu
- Department of Chemistry, Stanford University, Stanford, CA94305
| | - Grant M. Rotskoff
- Department of Chemistry, Stanford University, Stanford, CA94305
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA94305
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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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Bashirzadeh Y, Redford SA, Lorpaiboon C, Groaz A, Moghimianavval H, Litschel T, Schwille P, Hocky GM, Dinner AR, Liu AP. Actin crosslinker competition and sorting drive emergent GUV size-dependent actin network architecture. Commun Biol 2021. [PMID: 34584211 DOI: 10.1101/2020.10.03.322354v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
The proteins that make up the actin cytoskeleton can self-assemble into a variety of structures. In vitro experiments and coarse-grained simulations have shown that the actin crosslinking proteins α-actinin and fascin segregate into distinct domains in single actin bundles with a molecular size-dependent competition-based mechanism. Here, by encapsulating actin, α-actinin, and fascin in giant unilamellar vesicles (GUVs), we show that physical confinement can cause these proteins to form much more complex structures, including rings and asters at GUV peripheries and centers; the prevalence of different structures depends on GUV size. Strikingly, we found that α-actinin and fascin self-sort into separate domains in the aster structures with actin bundles whose apparent stiffness depends on the ratio of the relative concentrations of α-actinin and fascin. The observed boundary-imposed effect on protein sorting may be a general mechanism for creating emergent structures in biopolymer networks with multiple crosslinkers.
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Affiliation(s)
- Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Steven A Redford
- James Franck Institute, University of Chicago, Chicago, IL, 60637, USA
- The graduate program in Biophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | | | - Alessandro Groaz
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Thomas Litschel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Glen M Hocky
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Aaron R Dinner
- James Franck Institute, University of Chicago, Chicago, IL, 60637, USA.
- Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA.
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA.
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Bashirzadeh Y, Redford SA, Lorpaiboon C, Groaz A, Moghimianavval H, Litschel T, Schwille P, Hocky GM, Dinner AR, Liu AP. Actin crosslinker competition and sorting drive emergent GUV size-dependent actin network architecture. Commun Biol 2021; 4:1136. [PMID: 34584211 PMCID: PMC8478941 DOI: 10.1038/s42003-021-02653-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023] Open
Abstract
The proteins that make up the actin cytoskeleton can self-assemble into a variety of structures. In vitro experiments and coarse-grained simulations have shown that the actin crosslinking proteins α-actinin and fascin segregate into distinct domains in single actin bundles with a molecular size-dependent competition-based mechanism. Here, by encapsulating actin, α-actinin, and fascin in giant unilamellar vesicles (GUVs), we show that physical confinement can cause these proteins to form much more complex structures, including rings and asters at GUV peripheries and centers; the prevalence of different structures depends on GUV size. Strikingly, we found that α-actinin and fascin self-sort into separate domains in the aster structures with actin bundles whose apparent stiffness depends on the ratio of the relative concentrations of α-actinin and fascin. The observed boundary-imposed effect on protein sorting may be a general mechanism for creating emergent structures in biopolymer networks with multiple crosslinkers. By encapsulating proteins in giant unilamellar vesicles, Bashirzadeh et al find that actin crosslinkers, α-actinin and fascin, can self-assemble with actin into complex structures that depend on the degree of confinement. Further analysis and modeling show that α-actinin and fascin sort to separate domains of these structures. These insights may be generalizable to other biopolymer networks containing crosslinkers.
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Affiliation(s)
- Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Steven A Redford
- James Franck Institute, University of Chicago, Chicago, IL, 60637, USA.,The graduate program in Biophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | | | - Alessandro Groaz
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Thomas Litschel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.,John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Glen M Hocky
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Aaron R Dinner
- James Franck Institute, University of Chicago, Chicago, IL, 60637, USA. .,Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA.
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA. .,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA. .,Department of Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA. .,Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA.
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