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Wu X, Li D, Chen Y, Wang L, Xu LY, Li EM, Dong G. Fascin - F-actin interaction studied by molecular dynamics simulation and protein network analysis. J Biomol Struct Dyn 2024; 42:435-444. [PMID: 37029713 DOI: 10.1080/07391102.2023.2199083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/14/2023] [Indexed: 04/09/2023]
Abstract
Actin bundles are an important component of cellular cytoskeleton and participate in the movement of cells. The formation of actin bundles requires the participation of many actin binding proteins (ABPs). Fascin is a member of ABPs, which plays a key role in bundling filamentous actin (F-actin) to bundles. However, the detailed interactions between fascin and F-actin are unclear. In this study, we construct an atomic-level structure of fascin - F-actin complex based on a rather poor cryo-EM data with resolution of 20 nm. We first optimized the geometries of the complex by molecular dynamics (MD) simulation and analyzed the binding site and pose of fascin which bundles two F-actin chains. Next, binding free energy of fascin was calculated by MM/GBSA method. Finally, protein structure network analysis (PSNs) was performed to analyze the key residues for fascin binding. Our results show that residues of K22, E27, E29, K41, K43, R110, R149, K358, R408 and K471 on fascin are important for its bundling, which are in good agreement with the experimental data. On the other hand, the consistent results indicate that the atomic-level model of fascin - F-actin complex is reliable. In short, this model can be used to understand the detailed interactions between fascin and F-actin, and to develop novel potential drugs targeting fascin.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xiaodong Wu
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, PR China
| | - Dajia Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, PR China
| | - Yang Chen
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, PR China
- Department of Pathology, The First People's Hospital of Yunnan Province, Kunming, Yunnan Province, China
| | - Liangdong Wang
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, PR China
| | - Li-Yan Xu
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, PR China
- Cancer Research Center, Shantou University Medical College, Shantou, PR China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, PR China
| | - En-Min Li
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, PR China
- Key Laboratory of Molecular Biology in High Cancer Incidence Coastal Area of Guangdong Higher Education Institutes, Shantou University Medical College, Shantou, PR China
| | - Geng Dong
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, PR China
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, PR China
- Medical Informatics Research Center, Shantou University Medical College, Shantou, PR China
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Grill MJ, Kernes J, Slepukhin VM, Wall WA, Levine AJ. Directed force propagation in semiflexible networks. SOFT MATTER 2021; 17:10223-10241. [PMID: 33367438 DOI: 10.1039/d0sm01177k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We consider the propagation of tension along specific filaments of a semiflexible filament network in response to the application of a point force using a combination of numerical simulations and analytic theory. We find the distribution of force within the network is highly heterogeneous, with a small number of fibers supporting a significant fraction of the applied load over distances of multiple mesh sizes surrounding the point of force application. We suggest that these structures may be thought of as tensile force chains, whose structure we explore via simulation. We develop self-consistent calculations of the point-force response function and introduce a transfer matrix approach to explore the decay of tension (into bending) energy and the branching of tensile force chains in the network.
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Affiliation(s)
- Maximilian J Grill
- Institute for Computational Mechanics, Technical University of Munich, 85748 Garching, Germany
| | - Jonathan Kernes
- Department of Physics & Astronomy, University of California, Los Angeles, 90095, USA.
| | - Valentin M Slepukhin
- Department of Physics & Astronomy, University of California, Los Angeles, 90095, USA.
| | - Wolfgang A Wall
- Institute for Computational Mechanics, Technical University of Munich, 85748 Garching, Germany
| | - Alex J Levine
- Department of Physics & Astronomy, University of California, Los Angeles, 90095, USA.
- Department of Chemistry & Biochemistry, University of California, Los Angeles, 90095, USA
- Department of Computational Medicine, University of California, Los Angeles, 90095, USA
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Wei X, Fang C, Gong B, Yao J, Qian J, Lin Y. Viscoelasticity of 3D actin networks dictated by the mechanochemical characteristics of cross-linkers. SOFT MATTER 2021; 17:10177-10185. [PMID: 33646227 DOI: 10.1039/d0sm01558j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In this study, we report a computational investigation on how the mechanochemical characteristics of crosslinking molecules influence the viscoelasticity of three dimensional F-actin networks, an issue of key interest in analyzing the behavior of living cells and biological gels. In particular, it was found that the continuous breakage and rebinding of cross-linkers result in a locally peaked loss modulus in the rheology spectrum of the network, reflecting the fact that maximum energy dissipation is achieved when the driving frequency of the applied oscillating shear becomes comparable to the dissociation/association rate of crosslinking molecules. In addition, we showed that when subjected to constant rate of shear, an actin network can exhibit either strain hardening or softening depending on the ratio between the loading rate and unbinding speed of cross-linkers. A criterion for predicting the transition from softening to hardening was also obtained, in agreement with recent experiments. Finally, significant structural evolution was found to occur in random networks undergoing mechanical "training" (i.e. under a constant applied shear stress over a period of time), eventually leading to a pronounced anisotropic response of the network afterward which again is consistent with experimental observations.
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Affiliation(s)
- X Wei
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China.
- HKU-Shenzhen Institute of Research and Innovation (HKU-SIRI), Guangdong, China
| | - C Fang
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China.
- HKU-Shenzhen Institute of Research and Innovation (HKU-SIRI), Guangdong, China
| | - B Gong
- Department of Engineering Mechanics, Key Laboratory of Soft Machines and Smart Devices of Zhejiang Province, Zhejiang University, Hangzhou, Zhejiang, China.
| | - J Yao
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China.
- HKU-Shenzhen Institute of Research and Innovation (HKU-SIRI), Guangdong, China
| | - J Qian
- Department of Engineering Mechanics, Key Laboratory of Soft Machines and Smart Devices of Zhejiang Province, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Y Lin
- Department of Mechanical Engineering, The University of Hong Kong, Hong Kong, China.
- HKU-Shenzhen Institute of Research and Innovation (HKU-SIRI), Guangdong, China
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Slepukhin VM, Grill MJ, Hu Q, Botvinick EL, Wall WA, Levine AJ. Topological defects produce kinks in biopolymer filament bundles. Proc Natl Acad Sci U S A 2021; 118:e2024362118. [PMID: 33876768 PMCID: PMC8053966 DOI: 10.1073/pnas.2024362118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Bundles of stiff filaments are ubiquitous in the living world, found both in the cytoskeleton and in the extracellular medium. These bundles are typically held together by smaller cross-linking molecules. We demonstrate, analytically, numerically, and experimentally, that such bundles can be kinked, that is, have localized regions of high curvature that are long-lived metastable states. We propose three possible mechanisms of kink stabilization: a difference in trapped length of the filament segments between two cross-links, a dislocation where the endpoint of a filament occurs within the bundle, and the braiding of the filaments in the bundle. At a high concentration of cross-links, the last two effects lead to the topologically protected kinked states. Finally, we explore, numerically and analytically, the transition of the metastable kinked state to the stable straight bundle.
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Affiliation(s)
- Valentin M Slepukhin
- Department of Physics and Astronomy, University of California, Los Angeles, CA 90095-1596;
| | - Maximilian J Grill
- Institute for Computational Mechanics, Technical University of Munich, 80333 Munich, Germany
| | - Qingda Hu
- Department of Biomedical Engineering, University of California, Irvine, CA 92697-2730
- Center for Complex Biological Systems, University of California, Irvine, CA 92697-2280
| | - Elliot L Botvinick
- Department of Biomedical Engineering, University of California, Irvine, CA 92697-2730
- Center for Complex Biological Systems, University of California, Irvine, CA 92697-2280
- Beckman Laser Institute, University of California, Irvine, CA 92697-2730
| | - Wolfgang A Wall
- Institute for Computational Mechanics, Technical University of Munich, 80333 Munich, Germany
| | - Alex J Levine
- Department of Physics and Astronomy, University of California, Los Angeles, CA 90095-1596
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095-1596
- Department of Biomathematics, University of California, Los Angeles, CA 90095-1596
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Mulla Y, Wierenga H, Alkemade C, Ten Wolde PR, Koenderink GH. Frustrated binding of biopolymer crosslinkers. SOFT MATTER 2019; 15:3036-3042. [PMID: 30900710 DOI: 10.1039/c8sm02429d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Transiently crosslinked actin filament networks allow cells to combine elastic rigidity with the ability to deform viscoelastically. Theoretical models of semiflexible polymer networks predict that the crosslinker unbinding rate governs the timescale beyond which viscoelastic flow occurs. However a direct comparison between network and crosslinker dynamics is lacking. Here we measure the network's stress relaxation timescale using rheology and the lifetime of bound crosslinkers using fluorescence recovery after photobleaching (FRAP). Intriguingly, we observe that the crosslinker unbinding rate measured by FRAP is more than an order of magnitude slower than the rate measured by rheology. We rationalize this difference with a three-state model where crosslinkers are bound to either 0, 1 or 2 filaments, which allows us to extract crosslinker transition rates that are otherwise difficult to access. We find that the unbinding rate of singly bound crosslinkers is nearly two orders of magnitude slower than for doubly bound ones. We attribute the increased unbinding rate of doubly bound crosslinkers to the high stiffness of biopolymers, which frustrates crosslinker binding.
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Affiliation(s)
- Yuval Mulla
- Living Matter Department, AMOLF, Science Park 104, 1098 XG Amsterdam, The Netherlands.
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Alvarado J, Sheinman M, Sharma A, MacKintosh FC, Koenderink GH. Force percolation of contractile active gels. SOFT MATTER 2017; 13:5624-5644. [PMID: 28812094 DOI: 10.1039/c7sm00834a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Living systems provide a paradigmatic example of active soft matter. Cells and tissues comprise viscoelastic materials that exert forces and can actively change shape. This strikingly autonomous behavior is powered by the cytoskeleton, an active gel of semiflexible filaments, crosslinks, and molecular motors inside cells. Although individual motors are only a few nm in size and exert minute forces of a few pN, cells spatially integrate the activity of an ensemble of motors to produce larger contractile forces (∼nN and greater) on cellular, tissue, and organismal length scales. Here we review experimental and theoretical studies on contractile active gels composed of actin filaments and myosin motors. Unlike other active soft matter systems, which tend to form ordered patterns, actin-myosin systems exhibit a generic tendency to contract. Experimental studies of reconstituted actin-myosin model systems have long suggested that a mechanical interplay between motor activity and the network's connectivity governs this contractile behavior. Recent theoretical models indicate that this interplay can be understood in terms of percolation models, extended to include effects of motor activity on the network connectivity. Based on concepts from percolation theory, we propose a state diagram that unites a large body of experimental observations. This framework provides valuable insights into the mechanisms that drive cellular shape changes and also provides design principles for synthetic active materials.
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Affiliation(s)
- José Alvarado
- Systems Biophysics Department, AMOLF, 1098 XG Amsterdam, The Netherlands.
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Plagge J, Fischer A, Heussinger C. Viscoelasticity of reversibly crosslinked networks of semiflexible polymers. Phys Rev E 2016; 93:062502. [PMID: 27415312 DOI: 10.1103/physreve.93.062502] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 11/07/2022]
Abstract
We present a theoretical framework for the linear and nonlinear viscoelastic properties of reversibly crosslinked networks of semiflexible polymers. In contrast to affine models where network strain couples to the polymer end-to-end distance, in our model strain rather serves to locally distort the network structure. This induces bending modes in the polymer filaments, the properties of which are slaved to the surrounding network structure. Specifically, we investigate the frequency-dependent linear rheology, in particular in combination with crosslink binding-unbinding processes. We also develop schematic extensions to describe the nonlinear response during creep measurements as well as during constant strain-rate ramps.
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Affiliation(s)
- Jan Plagge
- Institute for Theoretical Physics, Georg-August University of Göttingen, Friedrich-Hund Platz 1, 37077 Göttingen, Germany
| | - Andreas Fischer
- Institute for Theoretical Physics, Georg-August University of Göttingen, Friedrich-Hund Platz 1, 37077 Göttingen, Germany
| | - Claus Heussinger
- Institute for Theoretical Physics, Georg-August University of Göttingen, Friedrich-Hund Platz 1, 37077 Göttingen, Germany
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