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Cubuk J, Greenberg L, Greenberg AE, Emenecker RJ, Stuchell-Brereton MD, Holehouse AS, Soranno A, Greenberg MJ. Structural dynamics of the intrinsically disordered linker region of cardiac troponin T. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596451. [PMID: 38853835 PMCID: PMC11160775 DOI: 10.1101/2024.05.30.596451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The cardiac troponin complex, composed of troponins I, T, and C, plays a central role in regulating the calcium-dependent interactions between myosin and the thin filament. Mutations in troponin can cause cardiomyopathies; however, it is still a major challenge for the field to connect how changes in sequence affect troponin's function. Recent high-resolution structures of the thin filament revealed critical insights into the structure-function relationship of the troponin complex, but there remain large, unresolved segments of troponin, including the troponin-T linker region that is a hotspot for several cardiomyopathy mutations. This unresolved yet functionally-significant linker region has been proposed to be intrinsically disordered, with behaviors that are not well described by traditional structural approaches; however, this proposal has not been experimentally verified. Here, we used a combination of single-molecule Förster resonance energy transfer (FRET), molecular dynamics simulations, and functional reconstitution assays to investigate the troponin-T linker region. We experimentally and computationally show that in the context of both isolated troponin and the fully regulated troponin complex, the linker behaves as a dynamic, intrinsically disordered region. This region undergoes polyampholyte expansion in the presence of high salt and distinct conformational changes during the assembly of the troponin complex. We also examine the ΔE160 hypertrophic cardiomyopathy mutation in the linker, and we demonstrate that this mutation does not affect the conformational dynamics of the linker, rather it allosterically affects interactions with other subunits of the troponin complex, leading to increased molecular contractility. Taken together, our data clearly demonstrate the importance of disorder within the troponin-T linker and provide new insights into the molecular mechanisms controlling the pathogenesis of cardiomyopathies.
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Affiliation(s)
- Jasmine Cubuk
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 Euclid Ave, 63110, Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130, Saint Louis, MO, USA
| | - Lina Greenberg
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 Euclid Ave, 63110, Saint Louis, MO, USA
| | - Akiva E. Greenberg
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 Euclid Ave, 63110, Saint Louis, MO, USA
| | - Ryan J. Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 Euclid Ave, 63110, Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130, Saint Louis, MO, USA
| | - Melissa D. Stuchell-Brereton
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 Euclid Ave, 63110, Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130, Saint Louis, MO, USA
| | - Alex S. Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 Euclid Ave, 63110, Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130, Saint Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 Euclid Ave, 63110, Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130, Saint Louis, MO, USA
| | - Michael J. Greenberg
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 Euclid Ave, 63110, Saint Louis, MO, USA
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2
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Spudich JA. One must reconstitute the functions of interest from purified proteins. Front Physiol 2024; 15:1390186. [PMID: 38827995 PMCID: PMC11140241 DOI: 10.3389/fphys.2024.1390186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 04/01/2024] [Indexed: 06/05/2024] Open
Abstract
I am often asked by students and younger colleagues and now by the editors of this issue to tell the history of the development of the in vitro motility assay and the dual-beam single-molecule laser trap assay for myosin-driven actin filament movement, used widely as key assays for understanding how both muscle and nonmuscle myosin molecular motors work. As for all discoveries, the history of the development of the myosin assays involves many people who are not authors of the final publications, but without whom the assays would not have been developed as they are. Also, early experiences shape how one develops ideas and experiments, and influence future discoveries in major ways. I am pleased here to trace my own path and acknowledge the many individuals involved and my early science experiences that led to the work I and my students, postdoctoral fellows, and sabbatical visitors did to develop these assays. Mentors are too often overlooked in historical descriptions of discoveries, and my story starts with those who mentored me.
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Affiliation(s)
- James A. Spudich
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, United States
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3
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Aydin F, Katkar HH, Morganthaler A, Harker AJ, Kovar DR, Voth GA. Prediction of the essential intermolecular contacts for side-binding of VASP on F-actin. Cytoskeleton (Hoboken) 2024. [PMID: 38647032 DOI: 10.1002/cm.21864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/25/2024]
Abstract
Vasodilator-stimulated phosphoprotein (VASP) family proteins play a crucial role in mediating the actin network architecture in the cytoskeleton. The Ena/VASP homology 2 (EVH2) domain in each of the four identical arms of the tetrameric VASP consists of a loading poly-Pro region, a G-actin-binding domain (GAB), and an F-actin-binding domain (FAB). Together, the poly-Pro, GAB, and FAB domains allow VASP to bind to sides of actin filaments in a bundle, and recruit profilin-G-actin to processively elongate the filaments. The atomic resolution structure of the ternary complex, consisting of the loading poly-Pro region and GAB domain of VASP with profilin-actin, has been solved over a decade ago; however, a detailed structure of the FAB-F-actin complex has not been resolved to date. Experimental insights, based on homology of the FAB domain with the C region of WASP, have been used to hypothesize that the FAB domain binds to the cleft between subdomains 1 and 3 of F-actin. Here, in order to develop our understanding of the VASP-actin complex, we first augment known structural information about the GAB domain binding to actin with the missing FAB domain-actin structure, which we predict using homology modeling and docking simulations. In earlier work, we used mutagenesis and kinetic modeling to study the role of domain-level binding-unbinding kinetics of Ena/VASP on actin filaments in a bundle, specifically on the side of actin filaments. We further look at the nature of the side-binding of the FAB domain of VASP at the atomistic level using our predicted structure, and tabulate effective mutation sites on the FAB domain that would disrupt the VASP-actin complex. We test the binding affinity of Ena with mutated FAB domain using total internal reflection fluorescence microscopy experiments. The binding affinity of VASP is affected significantly for the mutant, providing additional support for our predicted structure.
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Affiliation(s)
- Fikret Aydin
- Department of Chemistry, The James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Harshwardhan H Katkar
- Department of Chemistry, The James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
| | - Alisha Morganthaler
- Department of Biochemistry and Molecular Biology and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, USA
| | - Alyssa J Harker
- Department of Biochemistry and Molecular Biology and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, USA
| | - David R Kovar
- Department of Biochemistry and Molecular Biology and Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, USA
| | - Gregory A Voth
- Department of Chemistry, The James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois, USA
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4
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Chen J, Wang Z, Yao B, Geng Y, Wang C, Xu J, Chen T, Jing J, Fu J. Ultra-Highly Stiff and Tough Shape Memory Polyurea with Unprecedented Energy Density by Precise Slight Cross-Linking. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2401178. [PMID: 38648568 DOI: 10.1002/adma.202401178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Indexed: 04/25/2024]
Abstract
Shape memory polymers (SMPs) have attracted significant attention and hold vast potential for diverse applications. Nevertheless, conventional SMPs suffer from notable shortcomings in terms of mechanical properties, environmental stability, and energy density, significantly constraining their practical utility. Here, inspired by the structure of muscle fibers, an innovative approach that involves the precise incorporation of subtle, permanent cross-linking within a hierarchical hydrogen bonding supramolecular network is reported. This novel strategy has culminated in the development of covalent and supramolecular shape memory polyurea, which exhibits exceptional mechanical properties, including high stiffness (1347 MPa), strength (82.4 MPa), and toughness (312.7 MJ m-3), ensuring its suitability for a wide range of applications. Furthermore, it boasts remarkable recyclability and repairability, along with excellent resistance to moisture, heat, and solvents. Moreover, the polymer demonstrates outstanding shape memory effects characterized by a high energy density (24.5 MJ m-3), facilitated by the formation of strain-induced oriented nanostructures that can store substantial amounts of entropic energy. Simultaneously, it maintains a remarkable 96% shape fixity and 99% shape recovery. This delicate interplay of covalent and supramolecular bonds opens up a promising pathway to the creation of high-performance SMPs, expanding their applicability across various domains.
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Affiliation(s)
- Jiaoyang Chen
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Zhifeng Wang
- Testing Center, Yangzhou University, Yangzhou, 225002, P. R. China
| | - Bowen Yao
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Yuhao Geng
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Cheng Wang
- Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P. R. China
| | - Jianhua Xu
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Tao Chen
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Jiajie Jing
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
| | - Jiajun Fu
- School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing, 210094, P. R. China
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Oosterheert W, Boiero Sanders M, Funk J, Prumbaum D, Raunser S, Bieling P. Molecular mechanism of actin filament elongation by formins. Science 2024; 384:eadn9560. [PMID: 38603491 DOI: 10.1126/science.adn9560] [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: 01/09/2024] [Accepted: 03/05/2024] [Indexed: 04/13/2024]
Abstract
Formins control the assembly of actin filaments (F-actin) that drive cell morphogenesis and motility in eukaryotes. However, their molecular interaction with F-actin and their mechanism of action remain unclear. In this work, we present high-resolution cryo-electron microscopy structures of F-actin barbed ends bound by three distinct formins, revealing a common asymmetric formin conformation imposed by the filament. Formation of new intersubunit contacts during actin polymerization sterically displaces formin and triggers its translocation. This "undock-and-lock" mechanism explains how actin-filament growth is coordinated with formin movement. Filament elongation speeds are controlled by the positioning and stability of actin-formin interfaces, which distinguish fast and slow formins. Furthermore, we provide a structure of the actin-formin-profilin ring complex, which resolves how profilin is rapidly released from the barbed end during filament elongation.
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Affiliation(s)
- Wout Oosterheert
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Micaela Boiero Sanders
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Johanna Funk
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Daniel Prumbaum
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
| | - Peter Bieling
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany
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6
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Dhar A, Bagyashree VT, Biswas S, Kumari J, Sridhara A, Jeevan Subodh B, Shekhar S, Palani S. Functional redundancy and formin-independent localization of tropomyosin isoforms in Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.587703. [PMID: 38617342 PMCID: PMC11014519 DOI: 10.1101/2024.04.04.587703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Tropomyosin is an actin binding protein which protects actin filaments from cofilin-mediated disassembly. Distinct tropomyosin isoforms have long been hypothesized to differentially sort to subcellular actin networks and impart distinct functionalities. Nevertheless, a mechanistic understanding of the interplay between Tpm isoforms and their functional contributions to actin dynamics has been lacking. In this study, we present acetylation-mimic engineered mNeonGreen-Tpm fusion proteins that exhibit complete functionality as a sole copy, surpassing limitations of existing probes and enabling real-time dynamic tracking of Tpm-actin filaments in vivo. Using these functional Tpm fusion proteins, we find that both Tpm1 and Tpm2 indiscriminately bind to actin filaments nucleated by either formin isoform- Bnr1 and Bni1 in vivo, in contrast to the long-held paradigm of Tpm-formin pairing. We also show that Tpm2 can protect and organize functional actin cables in absence of Tpm1. Overall, our work supports a concentration-dependent and formin-independent model of Tpm-actin binding and demonstrates for the first time, the functional redundancy of the paralog Tpm2 in actin cable maintenance in S. cerevisiae.
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Affiliation(s)
- Anubhav Dhar
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka 560012, India
- equal contribution
| | - VT Bagyashree
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka 560012, India
- equal contribution
| | - Sudipta Biswas
- Departments of Physics, Cell Biology and Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Jayanti Kumari
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Amruta Sridhara
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - B Jeevan Subodh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka 560012, India
| | - Shashank Shekhar
- Departments of Physics, Cell Biology and Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Saravanan Palani
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka 560012, India
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7
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Kengyel A, Palarz PM, Krohn J, Marquardt A, Greve JN, Heiringhoff R, Jörns A, Manstein DJ. Motor properties of Myosin 5c are modulated by tropomyosin isoforms and inhibited by pentabromopseudilin. Front Physiol 2024; 15:1394040. [PMID: 38606007 PMCID: PMC11008601 DOI: 10.3389/fphys.2024.1394040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
Myosin 5c (Myo5c) is a motor protein that is produced in epithelial and glandular tissues, where it plays an important role in secretory processes. Myo5c is composed of two heavy chains, each containing a generic motor domain, an elongated neck domain consisting of a single α-helix with six IQ motifs, each of which binds to a calmodulin (CaM) or a myosin light chain from the EF-hand protein family, a coiled-coil dimer-forming region and a carboxyl-terminal globular tail domain. Although Myo5c is a low duty cycle motor, when two or more Myo5c-heavy meromyosin (HMM) molecules are linked together, they move processively along actin filaments. We describe the purification and functional characterization of human Myo5c-HMM co-produced either with CaM alone or with CaM and the essential and regulatory light chains Myl6 and Myl12b. We describe the extent to which cofilaments of actin and Tpm1.6, Tpm1.8 or Tpm3.1 alter the maximum actin-activated ATPase and motile activity of the recombinant Myo5c constructs. The small allosteric effector pentabromopseudilin (PBP), which is predicted to bind in a groove close to the actin and nucleotide binding site with a calculated ΔG of -18.44 kcal/mol, inhibits the motor function of Myo5c with a half-maximal concentration of 280 nM. Using immunohistochemical staining, we determined the distribution and exact localization of Myo5c in endothelial and endocrine cells from rat and human tissue. Particular high levels of Myo5c were observed in insulin-producing β-cells located within the pancreatic islets of Langerhans.
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Affiliation(s)
- András Kengyel
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
- Department of Biophysics, University of Pécs Medical School, Pécs, Hungary
| | - Philip M. Palarz
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Jacqueline Krohn
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Anja Marquardt
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Johannes N. Greve
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Robin Heiringhoff
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
| | - Anne Jörns
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Dietmar J. Manstein
- Institute for Biophysical Chemistry, Hannover Medical School, Hannover, Germany
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8
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Kumari R, Ven K, Chastney M, Kokate SB, Peränen J, Aaron J, Kogan K, Almeida-Souza L, Kremneva E, Poincloux R, Chew TL, Gunning PW, Ivaska J, Lappalainen P. Focal adhesions contain three specialized actin nanoscale layers. Nat Commun 2024; 15:2547. [PMID: 38514695 PMCID: PMC10957975 DOI: 10.1038/s41467-024-46868-7] [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: 01/25/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024] Open
Abstract
Focal adhesions (FAs) connect inner workings of cell to the extracellular matrix to control cell adhesion, migration and mechanosensing. Previous studies demonstrated that FAs contain three vertical layers, which connect extracellular matrix to the cytoskeleton. By using super-resolution iPALM microscopy, we identify two additional nanoscale layers within FAs, specified by actin filaments bound to tropomyosin isoforms Tpm1.6 and Tpm3.2. The Tpm1.6-actin filaments, beneath the previously identified α-actinin cross-linked actin filaments, appear critical for adhesion maturation and controlled cell motility, whereas the adjacent Tpm3.2-actin filament layer beneath seems to facilitate adhesion disassembly. Mechanistically, Tpm3.2 stabilizes ACF-7/MACF1 and KANK-family proteins at adhesions, and hence targets microtubule plus-ends to FAs to catalyse their disassembly. Tpm3.2 depletion leads to disorganized microtubule network, abnormally stable FAs, and defects in tail retraction during migration. Thus, FAs are composed of distinct actin filament layers, and each may have specific roles in coupling adhesions to the cytoskeleton, or in controlling adhesion dynamics.
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Affiliation(s)
- Reena Kumari
- HiLIFE Institute of Biotechnology, University of Helsinki, FI-00014, Helsinki, Finland
| | - Katharina Ven
- HiLIFE Institute of Biotechnology, University of Helsinki, FI-00014, Helsinki, Finland
| | - Megan Chastney
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
| | - Shrikant B Kokate
- HiLIFE Institute of Biotechnology, University of Helsinki, FI-00014, Helsinki, Finland
| | - Johan Peränen
- HiLIFE Institute of Biotechnology, University of Helsinki, FI-00014, Helsinki, Finland
| | - Jesse Aaron
- Advanced Imaging Center, HHMI Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Konstantin Kogan
- HiLIFE Institute of Biotechnology, University of Helsinki, FI-00014, Helsinki, Finland
| | - Leonardo Almeida-Souza
- HiLIFE Institute of Biotechnology, University of Helsinki, FI-00014, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Elena Kremneva
- HiLIFE Institute of Biotechnology, University of Helsinki, FI-00014, Helsinki, Finland
| | - Renaud Poincloux
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Teng-Leong Chew
- Advanced Imaging Center, HHMI Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Peter W Gunning
- School of Biomedical Sciences, UNSW Sydney, Wallace Wurth Building, Sydney, NSW 2052, Australia
| | - Johanna Ivaska
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, FI-20520, Turku, Finland
- Department of Life Technologies, University of Turku, FI-20520, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
- Foundation for the Finnish Cancer Institute, Tukholmankatu 8, FI-00014, Helsinki, Finland
| | - Pekka Lappalainen
- HiLIFE Institute of Biotechnology, University of Helsinki, FI-00014, Helsinki, Finland.
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.
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9
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Garg A, Jansen S, Zhang R, Lavine KJ, Greenberg MJ. Dilated cardiomyopathy-associated skeletal muscle actin (ACTA1) mutation R256H disrupts actin structure and function and causes cardiomyocyte hypocontractility. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.10.583979. [PMID: 38559046 PMCID: PMC10979883 DOI: 10.1101/2024.03.10.583979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Skeletal muscle actin (ACTA1) mutations are a prevalent cause of skeletal myopathies consistent with ACTA1's high expression in skeletal muscle. Rare de novo mutations in ACTA1 associated with combined cardiac and skeletal myopathies have been reported, but ACTA1 represents only ~20% of the total actin pool in cardiomyocytes, making its role in cardiomyopathy controversial. Here we demonstrate how a mutation in an actin isoform expressed at low levels in cardiomyocytes can cause cardiomyopathy by focusing on a unique ACTA1 mutation, R256H. We previously identified this mutation in multiple family members with dilated cardiomyopathy (DCM), who had reduced systolic function without clinical skeletal myopathy. Using a battery of multiscale biophysical tools, we show that R256H has potent functional effects on ACTA1 function at the molecular scale and in human cardiomyocytes. Importantly, we demonstrate that R256H acts in a dominant manner, where the incorporation of small amounts of mutant protein into thin filaments is sufficient to disrupt molecular contractility, and that this effect is dependent on the presence of troponin and tropomyosin. To understand the structural basis of this change in regulation, we resolved a structure of R256H filaments using Cryo-EM, and we see alterations in actin's structure that have the potential to disrupt interactions with tropomyosin. Finally, we show that ACTA1R256H/+ human induced pluripotent stem cell cardiomyocytes demonstrate reduced contractility and sarcomeric disorganization. Taken together, we demonstrate that R256H has multiple effects on ACTA1 function that are sufficient to cause reduced contractility and establish a likely causative relationship between ACTA1 R256H and clinical cardiomyopathy.
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Affiliation(s)
- Ankit Garg
- Division of Cardiology, Department of Medicine Johns Hopkins University Baltimore MD USA
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Silvia Jansen
- Department of Cell Biology and Physiology, Washington University in St. Louis, St. Louis, MO, United States
| | - Rui Zhang
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kory J. Lavine
- Cardiovascular Division, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Michael J. Greenberg
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, USA
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10
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Xia Y, Wu K, Liu C, Zhao X, Wang J, Cao J, Chen Z, Fang M, Yu J, Zhu C, Zhang X, Wang Z. Filamentous-Actin-Mimicking Nanoplatform for Enhanced Cytosolic Protein Delivery. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305600. [PMID: 38152963 PMCID: PMC10933650 DOI: 10.1002/advs.202305600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/29/2023] [Indexed: 12/29/2023]
Abstract
Despite the potential of protein therapeutics, the cytosolic delivery of proteins with high efficiency and bioactivity remains a significant challenge owing to exocytosis and lysosomal degradation after endocytosis. Therefore, it is important to develop a safe and efficient strategy to bypass endocytosis. Inspired by the extraordinary capability of filamentous-actin (F-actin) to promote cell membrane fusion, a cyanine dye assembly-containing nanoplatform mimicking the structure of natural F-actin is developed. The nanoplatform exhibits fast membrane fusion to cell membrane mimics and thus enters live cells through membrane fusion and bypasses endocytosis. Moreover, it is found to efficiently deliver protein cargos into live cells and quickly release them into the cytosol, leading to high protein cargo transfection efficiency and bioactivity. The nanoplatform also results in the superior inhibition of tumor cells when loaded with anti-tumor proteins. These results demonstrate that this fusogenic nanoplatform can be valuable for cytosolic protein delivery and tumor treatment.
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Affiliation(s)
- Yuqiong Xia
- Lab of Molecular Imaging and Translational Medicine (MITM)Engineering Research Center of Molecular & NeuroimagingMinistry of EducationSchool of Life Science and TechnologyXidian University & International Joint Research Center for Advanced Medical Imaging and Intelligent Diagnosis and TreatmentXi'anShaanxi710126P. R. China
- Guangzhou Institute of TechnologyXidian UniversityGuangzhouGuangdong510555P. R. China
| | - Keyun Wu
- Lab of Molecular Imaging and Translational Medicine (MITM)Engineering Research Center of Molecular & NeuroimagingMinistry of EducationSchool of Life Science and TechnologyXidian University & International Joint Research Center for Advanced Medical Imaging and Intelligent Diagnosis and TreatmentXi'anShaanxi710126P. R. China
- Guangzhou Institute of TechnologyXidian UniversityGuangzhouGuangdong510555P. R. China
| | - Chang Liu
- Lab of Molecular Imaging and Translational Medicine (MITM)Engineering Research Center of Molecular & NeuroimagingMinistry of EducationSchool of Life Science and TechnologyXidian University & International Joint Research Center for Advanced Medical Imaging and Intelligent Diagnosis and TreatmentXi'anShaanxi710126P. R. China
- Guangzhou Institute of TechnologyXidian UniversityGuangzhouGuangdong510555P. R. China
| | - Xuejuan Zhao
- Lab of Molecular Imaging and Translational Medicine (MITM)Engineering Research Center of Molecular & NeuroimagingMinistry of EducationSchool of Life Science and TechnologyXidian University & International Joint Research Center for Advanced Medical Imaging and Intelligent Diagnosis and TreatmentXi'anShaanxi710126P. R. China
- Guangzhou Institute of TechnologyXidian UniversityGuangzhouGuangdong510555P. R. China
| | - Jun Wang
- Lab of Molecular Imaging and Translational Medicine (MITM)Engineering Research Center of Molecular & NeuroimagingMinistry of EducationSchool of Life Science and TechnologyXidian University & International Joint Research Center for Advanced Medical Imaging and Intelligent Diagnosis and TreatmentXi'anShaanxi710126P. R. China
| | - Jianxia Cao
- Lab of Molecular Imaging and Translational Medicine (MITM)Engineering Research Center of Molecular & NeuroimagingMinistry of EducationSchool of Life Science and TechnologyXidian University & International Joint Research Center for Advanced Medical Imaging and Intelligent Diagnosis and TreatmentXi'anShaanxi710126P. R. China
| | - Zhaoxu Chen
- Lab of Molecular Imaging and Translational Medicine (MITM)Engineering Research Center of Molecular & NeuroimagingMinistry of EducationSchool of Life Science and TechnologyXidian University & International Joint Research Center for Advanced Medical Imaging and Intelligent Diagnosis and TreatmentXi'anShaanxi710126P. R. China
| | - Minchao Fang
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular StructuresSchool of Life SciencesTianjin University92 Weijin Road, Nankai DistrictTianjin300072P. R. China
| | - Jie Yu
- School of Biology and EngineeringGuizhou Medical UniversityGuizhouGuiyang550025P. R. China
| | - Cheng Zhu
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular StructuresSchool of Life SciencesTianjin University92 Weijin Road, Nankai DistrictTianjin300072P. R. China
| | - Xianghan Zhang
- Lab of Molecular Imaging and Translational Medicine (MITM)Engineering Research Center of Molecular & NeuroimagingMinistry of EducationSchool of Life Science and TechnologyXidian University & International Joint Research Center for Advanced Medical Imaging and Intelligent Diagnosis and TreatmentXi'anShaanxi710126P. R. China
- Guangzhou Institute of TechnologyXidian UniversityGuangzhouGuangdong510555P. R. China
| | - Zhongliang Wang
- Lab of Molecular Imaging and Translational Medicine (MITM)Engineering Research Center of Molecular & NeuroimagingMinistry of EducationSchool of Life Science and TechnologyXidian University & International Joint Research Center for Advanced Medical Imaging and Intelligent Diagnosis and TreatmentXi'anShaanxi710126P. R. China
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11
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Qin X, Zeng B, Sooranna SR, Li M. LAMB3 Promotes Myofibrogenesis and Cytoskeletal Reorganization in Endometrial Stromal Cells via the RhoA/ROCK1/MYL9 Pathway. Cell Biochem Biophys 2024; 82:127-137. [PMID: 37801199 PMCID: PMC10867058 DOI: 10.1007/s12013-023-01186-5] [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: 03/26/2023] [Accepted: 09/23/2023] [Indexed: 10/07/2023]
Abstract
LAMB3, a major extracellular matrix and basal membrane component, is involved in wound healing. We aimed to understand its role in Asherman's syndrome (AS), which is associated with infertility, by using bioinformatics analysis and cultured endometrial stromal cells (ESCs). MRNAs extracted from tissues obtained from control subjects and patients with severe intrauterine adhesion were sequenced and subjected to bioinformatics analysis and the RhoA/ROCK1/MYL9 pathway was implicated and this subsequently studied using cultured primary ESCs. The effects of overexpression and knockdown and activation and inhibition of LAMB3 on the mesenchymal to myofibroblastic phenotypic transformation of ECCs were assessed using PCR and western blot analysis. Phalloidin was used to localize the actin cytoskeletal proteins. Silencing of LAMB3 reversed the TGF-β-induced ESC myofibroblast phenotype conversion, whereas overexpression of LAMB3 promoted this process. Activation and silencing of LAMB3 led to remodeling of the ESC cytoskeleton. Overexpression and silencing of LAMB3 caused activation and inhibition of ESCs, respectively. Y-27632 and LPA reversed the activation and inhibition of the RhoA/ROCK1/MYL9 pathway after overexpression and silencing, respectively. These results suggest that LAMB3 can regulate ESC fibrosis transformation and cytoskeleton remodeling via the RhoA/ROCK1/MYL9 pathway. This study provides a potential new target for gene therapy and drug intervention of AS.
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Affiliation(s)
- Xiaomei Qin
- Gynecology Section, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Guangxi Medical University, 530000, Nanning, China
| | - Bin Zeng
- Reproductive Medical Center, The First Affiliated Hospital, Guangxi Medical University, 530000, Nanning, China
| | - Suren R Sooranna
- Department of Metabolism, Digestion and Reproduction Faculty of Medicine Imperial College London Chelsea & Westminster Hospital, London, SW10 9NH, UK
- Life Science and Clinical Research Center, Youjiang Medical University for Nationalities, Baise, China
| | - Mujun Li
- Reproductive Medical Center, The First Affiliated Hospital, Guangxi Medical University, 530000, Nanning, China.
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12
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Yin S, Duan M, Zhang J, Zhang T, Zhao G. Interactions between paramyosin and actin greatly improve their thermostability and gel properties. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:1564-1571. [PMID: 37807842 DOI: 10.1002/jsfa.13035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/20/2023] [Accepted: 10/09/2023] [Indexed: 10/10/2023]
Abstract
BACKGROUND Myofibrillar proteins, the main contributors to the quality of meat products, are the main structural protein component of muscle and have functional properties such as the formation of a 3D protein gel network and water binding. The susceptibility of meat-derived proteins to heat-induced aggregation is the functional constraint that hinders their applications in industry, and so establishing an effective but simple method to improve their thermostability of the proteins is of great importance. RESULTS In the present study, we describe an easy approach to perform high colloidal thermostability of both paramyosin and actin by mixing them at low ionic strength. The improvement in thermal stability was found to be derived from intermolecular interactions between these two different proteins through non-covalent binding with each other. Consequently, such interactions protected each of them from thermal-induced degradation compared to individual components. Notably, this binary native protein mixture rather than single paramyosin or actin component has the ability to form protein hydrogels with a shear-thinning and reversible sol-gel transformation behavior, which is markedly different from most of reported heat-induced, denatured protein hydrogels. CONCLUSION The present study not only presents a facile and effective strategy for improvement of the thermal stability and gel properties of a binary paramyosin and actin mixture, but also enhances our understanding of how mutual interactions of protein components affect their physicochemical and functional properties. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Shuhua Yin
- College of Food Science and Nutritional Engineering, Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, China Agricultural University, Beijing, China
| | - Maoping Duan
- College of Food Science and Nutritional Engineering, Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, China Agricultural University, Beijing, China
| | - Jian Zhang
- School of Food Science and Technology, Shihezi University, Shihezi, China
| | - Tuo Zhang
- College of Food Science and Nutritional Engineering, Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, China Agricultural University, Beijing, China
| | - Guanghua Zhao
- College of Food Science and Nutritional Engineering, Key Laboratory of Precision Nutrition and Food Quality, Ministry of Education, China Agricultural University, Beijing, China
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13
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Shahzadi S, Hassan JU, Oneeb M, Riaz S, Sharif R, Ban D. Pesticide Efficiency of Environment-Friendly Transition Metal-Doped Magnetite Nanoparticles. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:218. [PMID: 38276736 PMCID: PMC10820912 DOI: 10.3390/nano14020218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/25/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024]
Abstract
This study explored the potential of Fe3O4, SnFe2O4, and CoFe2O4 nanoparticles as larvicidal and adulticidal agents against Aedes aegypti (A. aegypti) larvae and adults, which are vectors for various diseases. This research involved the synthesis of these nanoparticles using the coprecipitate method. The results indicate that CoFe2O4 nanoparticles are the most effective in both larvicidal and adulticidal activities, with complete mortality achieved after 96 h of exposure. SnFe2O4 nanoparticles also showed some larvicidal and adulticidal efficacy, although to a lesser extent than the CoFe2O4 nanoparticles. Fe3O4 nanoparticles exhibited minimal larvicidal and adulticidal effects at low concentrations but showed increased efficacy at higher concentrations. The study also revealed the superparamagnetic nature of these nanoparticles, making them potentially suitable for applications in aquatic environments, where A. aegypti larvae often thrive. Additionally, the nanoparticles induced observable damage to the gut structure of the mosquitoes and larvae, which could contribute to their mortality. Overall, this research suggests that CoFe2O4 nanoparticles, in particular, hold promise as environment-friendly and effective agents for controlling A. aegypti mosquitoes, which are responsible for the transmission of diseases such as dengue fever, Zika virus, and Chikungunya. Further studies and field trials are needed to validate their practical use in mosquito control programs.
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Affiliation(s)
- Shamaila Shahzadi
- Waterloo Institute for Nanotechnology & Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada
- Physics Department, University of Engineering & Technology, Lahore 54890, Pakistan; (J.U.H.); (R.S.)
| | - Jalees Ul Hassan
- Physics Department, University of Engineering & Technology, Lahore 54890, Pakistan; (J.U.H.); (R.S.)
| | - Muhammad Oneeb
- Department of Parasitology, University of Veterinary & Animal Sciences, Lahore 54000, Pakistan;
| | - Saira Riaz
- Centre of Solid State Physics, Punjab University, Lahore 54590, Pakistan;
| | - Rehana Sharif
- Physics Department, University of Engineering & Technology, Lahore 54890, Pakistan; (J.U.H.); (R.S.)
| | - Dayan Ban
- Waterloo Institute for Nanotechnology & Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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14
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Farkas D, Szikora S, Jijumon AS, Polgár TF, Patai R, Tóth MÁ, Bugyi B, Gajdos T, Bíró P, Novák T, Erdélyi M, Mihály J. Peripheral thickening of the sarcomeres and pointed end elongation of the thin filaments are both promoted by SALS and its formin interaction partners. PLoS Genet 2024; 20:e1011117. [PMID: 38198522 PMCID: PMC10805286 DOI: 10.1371/journal.pgen.1011117] [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: 06/24/2023] [Revised: 01/23/2024] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
During striated muscle development the first periodically repeated units appear in the premyofibrils, consisting of immature sarcomeres that must undergo a substantial growth both in length and width, to reach their final size. Here we report that, beyond its well established role in sarcomere elongation, the Sarcomere length short (SALS) protein is involved in Z-disc formation and peripheral growth of the sarcomeres. Our protein localization data and loss-of-function studies in the Drosophila indirect flight muscle strongly suggest that radial growth of the sarcomeres is initiated at the Z-disc. As to thin filament elongation, we used a powerful nanoscopy approach to reveal that SALS is subject to a major conformational change during sarcomere development, which might be critical to stop pointed end elongation in the adult muscles. In addition, we demonstrate that the roles of SALS in sarcomere elongation and radial growth are both dependent on formin type of actin assembly factors. Unexpectedly, when SALS is present in excess amounts, it promotes the formation of actin aggregates highly resembling the ones described in nemaline myopathy patients. Collectively, these findings helped to shed light on the complex mechanisms of SALS during the coordinated elongation and thickening of the sarcomeres, and resulted in the discovery of a potential nemaline myopathy model, suitable for the identification of genetic and small molecule inhibitors.
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Affiliation(s)
- Dávid Farkas
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - Szilárd Szikora
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - A S Jijumon
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
| | - Tamás F Polgár
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
- Doctoral School of Theoretical Medicine, University of Szeged, Szeged, Hungary
| | - Roland Patai
- Institute of Biophysics, Biological Research Centre, Szeged, Hungary
| | - Mónika Ágnes Tóth
- University of Pécs, Medical School, Department of Biophysics, Pécs, Hungary
| | - Beáta Bugyi
- University of Pécs, Medical School, Department of Biophysics, Pécs, Hungary
| | - Tamás Gajdos
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Hungary
| | - Péter Bíró
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Hungary
| | - Tibor Novák
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Hungary
| | - Miklós Erdélyi
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Hungary
| | - József Mihály
- Institute of Genetics, Biological Research Centre, Szeged, Hungary
- University of Szeged, Department of Genetics, Szeged, Hungary
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15
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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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16
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Li D, Jiang W. Classification of helical polymers with deep-learning language models. J Struct Biol 2023; 215:108041. [PMID: 37939748 PMCID: PMC10843845 DOI: 10.1016/j.jsb.2023.108041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/11/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
Many macromolecules in biological systems exist in the form of helical polymers. However, the inherent polymorphism and heterogeneity of samples complicate the reconstruction of helical polymers from cryo-EM images. Currently, available 2D classification methods are effective at separating particles of interest from contaminants, but they do not effectively differentiate between polymorphs, resulting in heterogeneity in the 2D classes. As such, it is crucial to develop a method that can computationally divide a dataset of polymorphic helical structures into homogenous subsets. In this work, we utilized deep-learning language models to embed the filaments as vectors in hyperspace and group them into clusters. Tests with both simulated and experimental datasets have demonstrated that our method - HLM (Helical classification with Language Model) can effectively distinguish different types of filaments, in the presence of many contaminants and low signal-to-noise ratios. We also demonstrate that HLM can isolate homogeneous subsets of particles from a publicly available dataset, resulting in the discovery of a previously unreported filament variant with an extra density around the tau filaments.
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Affiliation(s)
- Daoyi Li
- Department of Biological Sciences, Purdue University
| | - Wen Jiang
- Department of Biological Sciences, Purdue University.
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17
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Oosterheert W, Blanc FEC, Roy A, Belyy A, Sanders MB, Hofnagel O, Hummer G, Bieling P, Raunser S. Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments. Nat Struct Mol Biol 2023; 30:1774-1785. [PMID: 37749275 PMCID: PMC10643162 DOI: 10.1038/s41594-023-01101-9] [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: 04/07/2023] [Accepted: 08/18/2023] [Indexed: 09/27/2023]
Abstract
The release of inorganic phosphate (Pi) from actin filaments constitutes a key step in their regulated turnover, which is fundamental to many cellular functions. The mechanisms underlying Pi release from the core and barbed end of actin filaments remain unclear. Here, using human and bovine actin isoforms, we combine cryo-EM with molecular-dynamics simulations and in vitro reconstitution to demonstrate how actin releases Pi through a 'molecular backdoor'. While constantly open at the barbed end, the backdoor is predominantly closed in filament-core subunits and opens only transiently through concerted amino acid rearrangements. This explains why Pi escapes rapidly from the filament end but slowly from internal subunits. In a nemaline-myopathy-associated actin variant, the backdoor is predominantly open in filament-core subunits, resulting in accelerated Pi release and filaments with drastically shortened ADP-Pi caps. Our results provide the molecular basis for Pi release from actin and exemplify how a disease-linked mutation distorts the nucleotide-state distribution and atomic structure of the filament.
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Affiliation(s)
- Wout Oosterheert
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Florian E C Blanc
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Ankit Roy
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Alexander Belyy
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Micaela Boiero Sanders
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Oliver Hofnagel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
- Institute for Biophysics, Goethe University, Frankfurt am Main, Germany.
| | - Peter Bieling
- Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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18
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Bai Y, Zhao F, Wu T, Chen F, Pang X. Actin polymerization and depolymerization in developing vertebrates. Front Physiol 2023; 14:1213668. [PMID: 37745245 PMCID: PMC10515290 DOI: 10.3389/fphys.2023.1213668] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023] Open
Abstract
Development is a complex process that occurs throughout the life cycle. F-actin, a major component of the cytoskeleton, is essential for the morphogenesis of tissues and organs during development. F-actin is formed by the polymerization of G-actin, and the dynamic balance of polymerization and depolymerization ensures proper cellular function. Disruption of this balance results in various abnormalities and defects or even embryonic lethality. Here, we reviewed recent findings on the structure of G-actin and F-actin and the polymerization of G-actin to F-actin. We also focused on the functions of actin isoforms and the underlying mechanisms of actin polymerization/depolymerization in cellular and organic morphogenesis during development. This information will extend our understanding of the role of actin polymerization in the physiologic or pathologic processes during development and may open new avenues for developing therapeutics for embryonic developmental abnormalities or tissue regeneration.
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Affiliation(s)
- Yang Bai
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Feng Zhao
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Tingting Wu
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Fangchun Chen
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
| | - Xiaoxiao Pang
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Chongqing, China
- Chongqing Municipal Key Laboratory of Oral Biomedical Engineering of Higher Education, Chongqing, China
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19
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Ono S, Watabe E, Morisaki K, Ono K, Kuroyanagi H. Alternative splicing of a single exon causes a major impact on the affinity of Caenorhabditis elegans tropomyosin isoforms for actin filaments. Front Cell Dev Biol 2023; 11:1208913. [PMID: 37745299 PMCID: PMC10512467 DOI: 10.3389/fcell.2023.1208913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/29/2023] [Indexed: 09/26/2023] Open
Abstract
Tropomyosin is generally known as an actin-binding protein that regulates actomyosin interaction and actin filament stability. In metazoans, multiple tropomyosin isoforms are expressed, and some of them are involved in generating subpopulations of actin cytoskeleton in an isoform-specific manner. However, functions of many tropomyosin isoforms remain unknown. Here, we report identification of a novel alternative exon in the Caenorhabditis elegans tropomyosin gene and characterization of the effects of alternative splicing on the properties of tropomyosin isoforms. Previous studies have reported six tropomyosin isoforms encoded by the C. elegans lev-11 tropomyosin gene. We identified a seventh isoform, LEV-11U, that contained a novel alternative exon, exon 7c (E7c). LEV-11U is a low-molecular-weight tropomyosin isoform that differs from LEV-11T only at the exon 7-encoded region. In silico analyses indicated that the E7c-encoded peptide sequence was unfavorable for coiled-coil formation and distinct from other tropomyosin isoforms in the pattern of electrostatic surface potentials. In vitro, LEV-11U bound poorly to actin filaments, whereas LEV-11T bound to actin filaments in a saturable manner. When these isoforms were transgenically expressed in the C. elegans striated muscle, LEV-11U was present in the diffuse cytoplasm with tendency to form aggregates, whereas LEV-11T co-localized with sarcomeric actin filaments. Worms with a mutation in E7c showed reduced motility and brood size, suggesting that this exon is important for the optimal health. These results indicate that alternative splicing of a single exon can produce biochemically diverged tropomyosin isoforms and suggest that a tropomyosin isoform with poor actin affinity has a novel biological function.
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Affiliation(s)
- Shoichiro Ono
- Departments of Pathology and Cell Biology, Emory University School of Medicine, Atlanta, GA, United States
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, United States
| | - Eichi Watabe
- Laboratory of Gene Expression, Graduate School of Biomedical Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keita Morisaki
- Departments of Pathology and Cell Biology, Emory University School of Medicine, Atlanta, GA, United States
| | - Kanako Ono
- Departments of Pathology and Cell Biology, Emory University School of Medicine, Atlanta, GA, United States
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, GA, United States
| | - Hidehito Kuroyanagi
- Laboratory of Gene Expression, Graduate School of Biomedical Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Biochemistry, University of the Ryukyus Graduate School of Medicine, Okinawa, Japan
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20
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Parry DAD. 50 Years of the steric-blocking mechanism in vertebrate skeletal muscle: a retrospective. J Muscle Res Cell Motil 2023; 44:133-141. [PMID: 35789471 PMCID: PMC10542282 DOI: 10.1007/s10974-022-09619-z] [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: 04/02/2022] [Accepted: 05/12/2022] [Indexed: 11/27/2022]
Abstract
Fifty years have now passed since Parry and Squire proposed a detailed structural model that explained how tropomyosin, mediated by troponin, played a steric-blocking role in the regulation of vertebrate skeletal muscle. In this Special Issue dedicated to the memory of John Squire it is an opportune time to look back on this research and to appreciate John's key contributions. A review is also presented of a selection of the developments and insights into muscle regulation that have occurred in the years since this proposal was formulated.
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Affiliation(s)
- David A D Parry
- School of Natural Sciences, Massey University, Private Bag 11-222, Palmerston North, 4442, New Zealand.
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21
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Mollenkopf P, Prascevic D, Bayerl TM, Käs JA, Schnauß J. Heavy water induces bundling in entangled actin networks. RSC Adv 2023; 13:24795-24800. [PMID: 37601592 PMCID: PMC10437092 DOI: 10.1039/d3ra03917j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 07/26/2023] [Indexed: 08/22/2023] Open
Abstract
Heavy water is known to affect many different biological systems, with the most striking effects observed at the cellular level. Many dynamic processes, such as migration or invasion, but also central processes of cell proliferation are measurably inhibited by the presence of deuterium oxide (D2O). Furthermore, individual cell deformabilities are significantly decreased upon D2O treatment. In order to understand the origin of these effects, we studied entangled filamentous actin networks, a commonly used model system for the cytoskeleton, which is considered a central functional element for dynamic cellular processes. Using bulk shear rheology to extract rheological signatures of reconstituted actin networks at varying concentrations of D2O, we found a non-monotonic behavior, which is explainable by a drastic change in the actin network architecture. Applying light scattering and fluorescence microscopy, we were able to demonstrate that the presence of deuterium oxide induces bundling in reconstituted entangled networks of filamentous actin. This constitutes an entirely novel and previously undescribed actin bundling mechanism.
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Affiliation(s)
- Paul Mollenkopf
- Department of Physiology, University of Pennsylvania Philadelphia PA 19104 USA
| | - Dusan Prascevic
- Peter-Debye Institute for Soft Matter Physics, Leipzig University 04103 Leipzig Germany
| | - Thomas M Bayerl
- Inventages 16 Northfields Prospect Business Centre, Putney Bridge Rd London SW181PE UK
| | - Josef A Käs
- Peter-Debye Institute for Soft Matter Physics, Leipzig University 04103 Leipzig Germany
| | - Jörg Schnauß
- Peter-Debye Institute for Soft Matter Physics, Leipzig University 04103 Leipzig Germany
- Fraunhofer Institute for Cell Therapy and Immunology 04103 Leipzig Germany
- Unconventional Computing Lab, Department of Computer Science and Creative Technologies, University of the West of England Bristol BS16 1QY UK
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22
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Chong JX, Childers MC, Marvin CT, Marcello AJ, Gonorazky H, Hazrati LN, Dowling JJ, Al Amrani F, Alanay Y, Nieto Y, Gabriel MÁM, Aylsworth AS, Buckingham KJ, Shively KM, Sommers O, Anderson K, Regnier M, Bamshad MJ. Variants in ACTC1 underlie distal arthrogryposis accompanied by congenital heart defects. HGG ADVANCES 2023; 4:100213. [PMID: 37457373 PMCID: PMC10345160 DOI: 10.1016/j.xhgg.2023.100213] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Contraction of the human sarcomere is the result of interactions between myosin cross-bridges and actin filaments. Pathogenic variants in genes such as MYH7, TPM1, and TNNI3 that encode parts of the cardiac sarcomere cause muscle diseases that affect the heart, such as dilated cardiomyopathy and hypertrophic cardiomyopathy. In contrast, pathogenic variants in homologous genes such as MYH2, TPM2, and TNNI2 that encode parts of the skeletal muscle sarcomere cause muscle diseases affecting skeletal muscle, such as distal arthrogryposis (DA) syndromes and skeletal myopathies. To date, there have been few reports of genes (e.g., MYH7) encoding sarcomeric proteins in which the same pathogenic variant affects skeletal and cardiac muscle. Moreover, none of the known genes underlying DA have been found to contain pathogenic variants that also cause cardiac abnormalities. We report five families with DA because of heterozygous missense variants in the gene actin, alpha, cardiac muscle 1 (ACTC1). ACTC1 encodes a highly conserved actin that binds to myosin in cardiac and skeletal muscle. Pathogenic variants in ACTC1 have been found previously to underlie atrial septal defect, dilated cardiomyopathy, hypertrophic cardiomyopathy, and left ventricular noncompaction. Our discovery delineates a new DA condition because of variants in ACTC1 and suggests that some functions of ACTC1 are shared in cardiac and skeletal muscle.
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Affiliation(s)
- Jessica X. Chong
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman-Baty Institute, Seattle, WA 98195, USA
| | - Matthew Carter Childers
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- University of Washington Center for Translational Muscle Research, Seattle, WA 98195, USA
| | - Colby T. Marvin
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Anthony J. Marcello
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Hernan Gonorazky
- Division of Neurology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - Lili-Naz Hazrati
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
| | - James J. Dowling
- Division of Neurology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Departments of Paediatrics and Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
| | - Fatema Al Amrani
- Division of Neurology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Division of Neurology, Department of Pediatrics, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Yasemin Alanay
- Division of Pediatric Genetics, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, 34752 Istanbul, Turkey
| | - Yolanda Nieto
- Department of Basic Bio-Medical Sciences, European University of Madrid, Madrid, Spain
| | - Miguel Á Marín Gabriel
- Department of Pediatrics, Puerta de Hierro-Majadahonda University Hospital, 28221 Madrid, Spain
| | - Arthur S. Aylsworth
- Departments of Pediatrics and Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Kati J. Buckingham
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Kathryn M. Shively
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Olivia Sommers
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Kailyn Anderson
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - University of Washington Center for Mendelian Genomics
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman-Baty Institute, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- University of Washington Center for Translational Muscle Research, Seattle, WA 98195, USA
- Division of Neurology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Departments of Paediatrics and Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
- Division of Neurology, Department of Pediatrics, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Sultanate of Oman
- Division of Pediatric Genetics, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, 34752 Istanbul, Turkey
- Department of Basic Bio-Medical Sciences, European University of Madrid, Madrid, Spain
- Department of Pediatrics, Puerta de Hierro-Majadahonda University Hospital, 28221 Madrid, Spain
- Departments of Pediatrics and Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - University of Washington Center for Rare Disease Research
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman-Baty Institute, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- University of Washington Center for Translational Muscle Research, Seattle, WA 98195, USA
- Division of Neurology, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
- Departments of Paediatrics and Molecular Genetics, University of Toronto, Toronto, ON M5G 0A4, Canada
- Division of Neurology, Department of Pediatrics, Sultan Qaboos University Hospital, Sultan Qaboos University, Muscat, Sultanate of Oman
- Division of Pediatric Genetics, Department of Pediatrics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, 34752 Istanbul, Turkey
- Department of Basic Bio-Medical Sciences, European University of Madrid, Madrid, Spain
- Department of Pediatrics, Puerta de Hierro-Majadahonda University Hospital, 28221 Madrid, Spain
- Departments of Pediatrics and Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Michael Regnier
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
- University of Washington Center for Translational Muscle Research, Seattle, WA 98195, USA
| | - Michael J. Bamshad
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman-Baty Institute, Seattle, WA 98195, USA
- University of Washington Center for Translational Muscle Research, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
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23
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Lehman W, Rynkiewicz MJ. Troponin-I-induced tropomyosin pivoting defines thin-filament function in relaxed and active muscle. J Gen Physiol 2023; 155:e202313387. [PMID: 37249525 PMCID: PMC10227645 DOI: 10.1085/jgp.202313387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/25/2023] [Accepted: 05/15/2023] [Indexed: 05/31/2023] Open
Abstract
Regulation of the crossbridge cycle that drives muscle contraction involves a reconfiguration of the troponin-tropomyosin complex on actin filaments. By comparing atomic models of troponin-tropomyosin fitted to cryo-EM structures of inhibited and Ca2+-activated thin filaments, we find that tropomyosin pivots rather than rolls or slides across actin as generally thought. We propose that pivoting can account for the Ca2+ activation that initiates muscle contraction and then relaxation influenced by troponin-I (TnI). Tropomyosin is well-known to occupy either of three meta-stable configurations on actin, regulating access of myosin motorheads to their actin-binding sites and thus the crossbridge cycle. At low Ca2+ concentrations, tropomyosin is trapped by TnI in an inhibitory B-state that sterically blocks myosin binding to actin, leading to muscle relaxation. Ca2+ binding to TnC draws TnI away from tropomyosin, while tropomyosin moves to a C-state location over actin. This partially relieves the steric inhibition and allows weak binding of myosin heads to actin, which then transition to strong actin-bound configurations, fully activating the thin filament. Nevertheless, the reconfiguration that accompanies the initial Ca2+-sensitive B-state/C-state shift in troponin-tropomyosin on actin remains uncertain and at best is described by moderate-resolution cryo-EM reconstructions. Our recent computational studies indicate that intermolecular residue-to-residue salt-bridge linkage between actin and tropomyosin is indistinguishable in B- and C-state thin filament configurations. We show here that tropomyosin can pivot about relatively fixed points on actin to accompany B-state/C-state structural transitions. We argue that at low Ca2+ concentrations C-terminal TnI domains attract tropomyosin, causing it to bend and then pivot toward the TnI, thus blocking myosin binding and contraction.
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Affiliation(s)
- William Lehman
- Department of Pharmacology, Physiology and Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Michael J. Rynkiewicz
- Department of Pharmacology, Physiology and Biophysics, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
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24
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Dahlstroem C, Paraschiakos T, Sun H, Windhorst S. Cryo-EM structures of actin binding proteins as tool for drug discovery. Biochem Pharmacol 2023:115680. [PMID: 37399949 DOI: 10.1016/j.bcp.2023.115680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/05/2023]
Abstract
Cellular actin dynamic is controlled by a plethora of actin binding proteins (ABPs), including actin nucleating, bundling, cross-linking, capping, and severing proteins. In this review, regulation of actin dynamics by ABPs will be introduced, and the role of the F-actin severing protein cofilin-1 and the F-actin bundling protein L-plastin in actin dynamics discussed in more detail. Since up-regulation of these proteins in different kinds of cancers is associated with malignant progression of cancer cells, we suggest the cryogenic electron microscopy (Cryo-EM) structure of F- actin with the respective ABP as template for in silico drug design to specifically disrupt the interaction of these ABPs with F-actin.
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Affiliation(s)
- Christian Dahlstroem
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246 Hamburg
| | - Themistoklis Paraschiakos
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246 Hamburg
| | - Han Sun
- Structural Chemistry and Computational Biophysics Group, Leipniz-Forschungsinstitut für Moekulare Pharmakologie, Robert-Rössle-Strasse 10, D-13125, Berlin; Institute of Chemistry, Technical University of Berlin, D-10623, Berlin
| | - Sabine Windhorst
- Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, D-20246 Hamburg.
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25
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Li N, Chen S, Xu K, He MT, Dong MQ, Zhang QC, Gao N. Structural basis of membrane skeleton organization in red blood cells. Cell 2023; 186:1912-1929.e18. [PMID: 37044097 DOI: 10.1016/j.cell.2023.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/12/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023]
Abstract
The spectrin-based membrane skeleton is a ubiquitous membrane-associated two-dimensional cytoskeleton underneath the lipid membrane of metazoan cells. Mutations of skeleton proteins impair the mechanical strength and functions of the membrane, leading to several different types of human diseases. Here, we report the cryo-EM structures of the native spectrin-actin junctional complex (from porcine erythrocytes), which is a specialized short F-actin acting as the central organizational unit of the membrane skeleton. While an α-/β-adducin hetero-tetramer binds to the barbed end of F-actin as a flexible cap, tropomodulin and SH3BGRL2 together create an absolute cap at the pointed end. The junctional complex is strengthened by ring-like structures of dematin in the middle actin layers and by patterned periodic interactions with tropomyosin over its entire length. This work serves as a structural framework for understanding the assembly and dynamics of membrane skeleton and offers insights into mechanisms of various ubiquitous F-actin-binding factors in other F-actin systems.
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Affiliation(s)
- Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
| | - Siyi Chen
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China; Changping Laboratory Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Kui Xu
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Meng-Ting He
- National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China; Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China; National Biomedical Imaging Center, Peking University, Beijing 100871, China.
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26
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Frant MP, Trytek M, Deryło K, Kutyła M, Paduch R. Cellular Localization of Selected Porphyrins and Their Effect on the In Vitro Motility of Human Colon Tumors and Normal Cells. Molecules 2023; 28:molecules28072907. [PMID: 37049670 PMCID: PMC10096141 DOI: 10.3390/molecules28072907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/13/2023] [Accepted: 03/22/2023] [Indexed: 04/14/2023] Open
Abstract
Standard therapies for colorectal cancer cannot eliminate or sufficiently reduce the metastasis process. Photodynamic therapy (PDT) may be an alternative to minimizing this problem. Here, we examined the cellular localization of selected porphyrins and determined whether free-base and manganese (III) metallated porphyrins may limit colon cancer cells' (HT29) or normal colon epithelial cells' (CCD 841 CoTr) motility in vitro. White light irradiation was used to initiate the photodynamic effect. Porphyrin uptake by the cells was determined by porphyrin fluorescence measurements through the use of confocal microscopy. Free-base porphyrin was found in cells, where it initially localized at the edge of the cytoplasm and later in the perinuclear area. The concentrations of porphyrins had no effect on cancer cell migration but had a significant effect on normal cell motility. Due to the low concentrations of porphyrins used, no changes in F-actin filaments of the cellular cytoskeleton were detected. Signal transmission via connexons between neighbouring cells was limited to a maximum of 40 µm for HT29 and 30 µm for CCD 841 CoTr cells. The tested porphyrins differed in their activity against the tumor and normal cells' migration capacity. Depending on the porphyrin used and the type of cells, their migration changed in relation to the control sample. The use of white light may change the activity of the porphyrins relative to the migratory capacity of the cells. The aim of the present study was to analyse the intracellular localization of tested porphyrins and their influence on the mobility of cells after irradiation with harmless white light.
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Affiliation(s)
- Maciej P Frant
- Department of Swine Diseases, National Veterinary Research Institute, Al. Partyzantów 57, 24-100 Puławy, Poland
| | - Mariusz Trytek
- Department of Industrial and Environmental Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 20-033 Lublin, Poland
| | - Kamil Deryło
- Department of Molecular Biology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 20-033 Lublin, Poland
| | - Mateusz Kutyła
- Department of Industrial and Environmental Microbiology, Institute of Biological Sciences, Maria Curie-Skłodowska University, 20-033 Lublin, Poland
| | - Roman Paduch
- Department of Virology and Immunology, Institute of Biological Sciences, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
- Department of General and Pediatric Ophthalmology, Medical University of Lublin, Chmielna 1, 20-079 Lublin, Poland
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27
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Chong JX, Childers MC, Marvin CT, Marcello AJ, Gonorazky H, Hazrati LN, Dowling JJ, Amrani FA, Alanay Y, Nieto Y, Marín Gabriel MÁ, Aylsworth AS, Buckingham KJ, Shively KM, Sommers O, Anderson K, Regnier M, Bamshad MJ. Variants in ACTC1 underlie distal arthrogryposis accompanied by congenital heart defects. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023. [PMID: 36945405 PMCID: PMC10029015 DOI: 10.1101/2023.03.07.23286862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
Contraction of the human sarcomere is the result of interactions between myosin cross-bridges and actin filaments. Pathogenic variants in genes such as MYH7 , TPM1 , and TNNI3 that encode parts of the cardiac sarcomere cause muscle diseases that affect the heart, such as dilated cardiomyopathy and hypertrophic cardiomyopathy. In contrast, pathogenic variants in homologous genes MYH2 , TPM2 , and TNNI2 , that encode parts of the skeletal muscle sarcomere, cause muscle diseases affecting skeletal muscle, such as the distal arthrogryposis (DA) syndromes and skeletal myopathies. To date, there have been few reports of genes (e.g., MYH7 ) encoding sarcomeric proteins in which the same pathogenic variant affects both skeletal and cardiac muscle. Moreover, none of the known genes underlying DA have been found to contain mutations that also cause cardiac abnormalities. We report five families with DA due to heterozygous missense variants in the gene actin, alpha, cardiac muscle 1 ( ACTC1 ). ACTC1 encodes a highly conserved actin that binds to myosin in both cardiac and skeletal muscle. Mutations in ACTC1 have previously been found to underlie atrial septal defect, dilated cardiomyopathy, hypertrophic cardiomyopathy, and left ventricular noncompaction. Our discovery delineates a new DA condition due to mutations in ACTC1 and suggests that some functions of actin, alpha, cardiac muscle 1 are shared in cardiac and skeletal muscle.
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28
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Lopez AJ, Andreadaki M, Vahokoski J, Deligianni E, Calder LJ, Camerini S, Freitag A, Bergmann U, Rosenthal PB, Sidén-Kiamos I, Kursula I. Structure and function of Plasmodium actin II in the parasite mosquito stages. PLoS Pathog 2023; 19:e1011174. [PMID: 36877739 PMCID: PMC10019781 DOI: 10.1371/journal.ppat.1011174] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 03/16/2023] [Accepted: 02/03/2023] [Indexed: 03/07/2023] Open
Abstract
Actins are filament-forming, highly-conserved proteins in eukaryotes. They are involved in essential processes in the cytoplasm and also have nuclear functions. Malaria parasites (Plasmodium spp.) have two actin isoforms that differ from each other and from canonical actins in structure and filament-forming properties. Actin I has an essential role in motility and is fairly well characterized. The structure and function of actin II are not as well understood, but mutational analyses have revealed two essential functions in male gametogenesis and in the oocyst. Here, we present expression analysis, high-resolution filament structures, and biochemical characterization of Plasmodium actin II. We confirm expression in male gametocytes and zygotes and show that actin II is associated with the nucleus in both stages in filament-like structures. Unlike actin I, actin II readily forms long filaments in vitro, and near-atomic structures in the presence or absence of jasplakinolide reveal very similar structures. Small but significant differences compared to other actins in the openness and twist, the active site, the D-loop, and the plug region contribute to filament stability. The function of actin II was investigated through mutational analysis, suggesting that long and stable filaments are necessary for male gametogenesis, while a second function in the oocyst stage also requires fine-tuned regulation by methylation of histidine 73. Actin II polymerizes via the classical nucleation-elongation mechanism and has a critical concentration of ~0.1 μM at the steady-state, like actin I and canonical actins. Similarly to actin I, dimers are a stable form of actin II at equilibrium.
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Affiliation(s)
- Andrea J. Lopez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Maria Andreadaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Juha Vahokoski
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Elena Deligianni
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Lesley J. Calder
- Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, London, United Kingdom
| | | | - Anika Freitag
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Ulrich Bergmann
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Peter B. Rosenthal
- Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, London, United Kingdom
| | - Inga Sidén-Kiamos
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
- * E-mail: (ISK); (IK)
| | - Inari Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
- * E-mail: (ISK); (IK)
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29
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Deciphering the molecular mechanisms of actin cytoskeleton regulation in cell migration using cryo-EM. Biochem Soc Trans 2023; 51:87-99. [PMID: 36695514 PMCID: PMC9987995 DOI: 10.1042/bst20220221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/12/2023] [Accepted: 01/12/2023] [Indexed: 01/26/2023]
Abstract
The actin cytoskeleton plays a key role in cell migration and cellular morphodynamics in most eukaryotes. The ability of the actin cytoskeleton to assemble and disassemble in a spatiotemporally controlled manner allows it to form higher-order structures, which can generate forces required for a cell to explore and navigate through its environment. It is regulated not only via a complex synergistic and competitive interplay between actin-binding proteins (ABP), but also by filament biochemistry and filament geometry. The lack of structural insights into how geometry and ABPs regulate the actin cytoskeleton limits our understanding of the molecular mechanisms that define actin cytoskeleton remodeling and, in turn, impact emerging cell migration characteristics. With the advent of cryo-electron microscopy (cryo-EM) and advanced computational methods, it is now possible to define these molecular mechanisms involving actin and its interactors at both atomic and ultra-structural levels in vitro and in cellulo. In this review, we will provide an overview of the available cryo-EM methods, applicable to further our understanding of the actin cytoskeleton, specifically in the context of cell migration. We will discuss how these methods have been employed to elucidate ABP- and geometry-defined regulatory mechanisms in initiating, maintaining, and disassembling cellular actin networks in migratory protrusions.
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30
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Selvaraj M, Kokate SB, Reggiano G, Kogan K, Kotila T, Kremneva E, DiMaio F, Lappalainen P, Huiskonen JT. Structural basis underlying specific biochemical activities of non-muscle tropomyosin isoforms. Cell Rep 2023; 42:111900. [PMID: 36586407 DOI: 10.1016/j.celrep.2022.111900] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 11/03/2022] [Accepted: 12/07/2022] [Indexed: 12/31/2022] Open
Abstract
The actin cytoskeleton is critical for cell migration, morphogenesis, endocytosis, organelle dynamics, and cytokinesis. To support diverse cellular processes, actin filaments form a variety of structures with specific architectures and dynamic properties. Key proteins specifying actin filaments are tropomyosins. Non-muscle cells express several functionally non-redundant tropomyosin isoforms, which differentially control the interactions of other proteins, including myosins and ADF/cofilin, with actin filaments. However, the underlying molecular mechanisms have remained elusive. By determining the cryogenic electron microscopy structures of actin filaments decorated by two functionally distinct non-muscle tropomyosin isoforms, Tpm1.6 and Tpm3.2, we reveal that actin filament conformation remains unaffected upon binding. However, Tpm1.6 and Tpm3.2 follow different paths along the actin filament major groove, providing an explanation for their incapability to co-polymerize on actin filaments. We also elucidate the molecular basis underlying specific roles of Tpm1.6 and Tpm3.2 in myosin II activation and protecting actin filaments from ADF/cofilin-catalyzed severing.
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Affiliation(s)
- Muniyandi Selvaraj
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Shrikant B Kokate
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Gabriella Reggiano
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Konstantin Kogan
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Tommi Kotila
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Elena Kremneva
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Pekka Lappalainen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland.
| | - Juha T Huiskonen
- Institute of Biotechnology, Helsinki Institute of Life Science HiLIFE, University of Helsinki, P.O. Box 56, 00014 Helsinki, Finland.
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31
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Actin cytoskeleton and complex cell architecture in an Asgard archaeon. Nature 2023; 613:332-339. [PMID: 36544020 PMCID: PMC9834061 DOI: 10.1038/s41586-022-05550-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022]
Abstract
Asgard archaea are considered to be the closest known relatives of eukaryotes. Their genomes contain hundreds of eukaryotic signature proteins (ESPs), which inspired hypotheses on the evolution of the eukaryotic cell1-3. A role of ESPs in the formation of an elaborate cytoskeleton and complex cellular structures has been postulated4-6, but never visualized. Here we describe a highly enriched culture of 'Candidatus Lokiarchaeum ossiferum', a member of the Asgard phylum, which thrives anaerobically at 20 °C on organic carbon sources. It divides every 7-14 days, reaches cell densities of up to 5 × 107 cells per ml and has a significantly larger genome compared with the single previously cultivated Asgard strain7. ESPs represent 5% of its protein-coding genes, including four actin homologues. We imaged the enrichment culture using cryo-electron tomography, identifying 'Ca. L. ossiferum' cells on the basis of characteristic expansion segments of their ribosomes. Cells exhibited coccoid cell bodies and a network of branched protrusions with frequent constrictions. The cell envelope consists of a single membrane and complex surface structures. A long-range cytoskeleton extends throughout the cell bodies, protrusions and constrictions. The twisted double-stranded architecture of the filaments is consistent with F-actin. Immunostaining indicates that the filaments comprise Lokiactin-one of the most highly conserved ESPs in Asgard archaea. We propose that a complex actin-based cytoskeleton predated the emergence of the first eukaryotes and was a crucial feature in the evolution of the Asgard phylum by scaffolding elaborate cellular structures.
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Risi CM, Belknap B, White HD, Dryden K, Pinto JR, Chase PB, Galkin VE. High-resolution cryo-EM structure of the junction region of the native cardiac thin filament in relaxed state. PNAS NEXUS 2023; 2:pgac298. [PMID: 36712934 PMCID: PMC9832952 DOI: 10.1093/pnasnexus/pgac298] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
Cardiac contraction depends on molecular interactions among sarcomeric proteins coordinated by the rising and falling intracellular Ca2+ levels. Cardiac thin filament (cTF) consists of two strands composed of actin, tropomyosin (Tm), and equally spaced troponin (Tn) complexes forming regulatory units. Tn binds Ca2+ to move Tm strand away from myosin-binding sites on actin to enable actomyosin cross-bridges required for force generation. The Tn complex has three subunits-Ca2+-binding TnC, inhibitory TnI, and Tm-binding TnT. Tm strand is comprised of adjacent Tm molecules that overlap "head-to-tail" along the actin filament. The N-terminus of TnT (e.g., TnT1) binds to the Tm overlap region to form the cTF junction region-the region that connects adjacent regulatory units and confers to cTF internal cooperativity. Numerous studies have predicted interactions among actin, Tm, and TnT1 within the junction region, although a direct structural description of the cTF junction region awaited completion. Here, we report a 3.8 Å resolution cryo-EM structure of the native cTF junction region at relaxing (pCa 8) Ca2+ conditions. We provide novel insights into the "head-to-tail" interactions between adjacent Tm molecules and interactions between the Tm junction with F-actin. We demonstrate how TnT1 stabilizes the Tm overlap region via its interactions with the Tm C- and N-termini and actin. Our data show that TnT1 works as a joint that anchors the Tm overlap region to actin, which stabilizes the relaxed state of the cTF. Our structure provides insight into the molecular basis of cardiac diseases caused by missense mutations in TnT1.
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Affiliation(s)
- Cristina M Risi
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Betty Belknap
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Howard D White
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Kelly Dryden
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22904, USA
| | - Jose R Pinto
- Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32304, USA
| | - P Bryant Chase
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Vitold E Galkin
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA 23507, USA
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Risi CM, Villanueva E, Belknap B, Sadler RL, Harris SP, White HD, Galkin VE. Cryo-Electron Microscopy Reveals Cardiac Myosin Binding Protein-C M-Domain Interactions with the Thin Filament. J Mol Biol 2022; 434:167879. [PMID: 36370805 PMCID: PMC9771592 DOI: 10.1016/j.jmb.2022.167879] [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: 08/23/2022] [Revised: 10/18/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
Abstract
Cardiac myosin binding protein C (cMyBP-C) modulates cardiac contraction via direct interactions with cardiac thick (myosin) and thin (actin) filaments (cTFs). While its C-terminal domains (e.g. C8-C10) anchor cMyBP-C to the backbone of the thick filament, its N-terminal domains (NTDs) (e.g. C0, C1, M, and C2) bind to both myosin and actin to accomplish its dual roles of inhibiting thick filaments and activating cTFs. While the positions of C0, C1 and C2 on cTF have been reported, the binding site of the M-domain on the surface of the cTF is unknown. Here, we used cryo-EM to reveal that the M-domain interacts with actin via helix 3 of its ordered tri-helix bundle region, while the unstructured part of the M-domain does not maintain extensive interactions with actin. We combined the recently obtained structure of the cTF with the positions of all the four NTDs on its surface to propose a complete model of the NTD binding to the cTF. The model predicts that the interactions of the NTDs with the cTF depend on the activation state of the cTF. At the peak of systole, when bound to the extensively activated cTF, NTDs would inhibit actomyosin interactions. In contrast, at falling Ca2+ levels, NTDs would not compete with the myosin heads for binding to the cTF, but would rather promote formation of active cross-bridges at the adjacent regulatory units located at the opposite cTF strand. Our structural data provides a testable model of the cTF regulation by the cMyBP-C.
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Affiliation(s)
- Cristina M Risi
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Edwin Villanueva
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Betty Belknap
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Rachel L Sadler
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Samantha P Harris
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ 85724, USA
| | - Howard D White
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Vitold E Galkin
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA 23507, USA.
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Liu Y, Chen X, Yin S, Chang X, Lv C, Zang J, Leng X, Zhang T, Zhao G. Directed Self-Assembly of Dimeric Building Blocks into Networklike Protein Origami to Construct Hydrogels. ACS NANO 2022; 16:19472-19481. [PMID: 36315654 DOI: 10.1021/acsnano.2c09391] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Engineering proteins to construct self-assemblies is of crucial significance not only for understanding the sophisticated living systems but also for fabricating advanced materials with unexplored functions. However, due to the inherent chemical heterogeneity and structural complexity of the protein surface, designing complex protein assemblies in an anisotropic fashion remains challenging. Here, we describe a self-assembly approach to fabricating protein origami with a networklike structure by designing dual noncovalent interactions on the different positions of a single protein building block. With dimeric proteins as building blocks, 1D protein filaments were constructed by the designed metal coordination at key protein interfaces. Subsequently, the network superstructures were created by the cross-linking of the 1D protein filaments at branch point linkages through the second designed π-π stacking interactions. Notably, upon increasing the protein concentration, the formed protein networks convert into hydrogels with reversible, injectable, and self-healing properties, which have the ability to promote bone regeneration. This strategy could be used to fabricate other protein-based materials with unexplored functions.
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Affiliation(s)
- Yu Liu
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| | - Xuemin Chen
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| | - Shuhua Yin
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| | - Xiaoxi Chang
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| | - Chenyan Lv
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| | - Jiachen Zang
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| | - Xiaojing Leng
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| | - Tuo Zhang
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
| | - Guanghua Zhao
- College of Food Science & Nutritional Engineering, Beijing Key Laboratory of Functional Food from Plant Resources, China Agricultural University, Beijing 100083, People's Republic of China
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Oosterheert W, Klink BU, Belyy A, Pospich S, Raunser S. Structural basis of actin filament assembly and aging. Nature 2022; 611:374-379. [DOI: 10.1038/s41586-022-05241-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/16/2022] [Indexed: 12/12/2022]
Abstract
AbstractThe dynamic turnover of actin filaments (F-actin) controls cellular motility in eukaryotes and is coupled to changes in the F-actin nucleotide state1–3. It remains unclear how F-actin hydrolyses ATP and subsequently undergoes subtle conformational rearrangements that ultimately lead to filament depolymerization by actin-binding proteins. Here we present cryo-electron microscopy structures of F-actin in all nucleotide states, polymerized in the presence of Mg2+ or Ca2+ at approximately 2.2 Å resolution. The structures show that actin polymerization induces the relocation of water molecules in the nucleotide-binding pocket, activating one of them for the nucleophilic attack of ATP. Unexpectedly, the back door for the subsequent release of inorganic phosphate (Pi) is closed in all structures, indicating that Pi release occurs transiently. The small changes in the nucleotide-binding pocket after ATP hydrolysis and Pi release are sensed by a key amino acid, amplified and transmitted to the filament periphery. Furthermore, differences in the positions of water molecules in the nucleotide-binding pocket explain why Ca2+-actin shows slower polymerization rates than Mg2+-actin. Our work elucidates the solvent-driven rearrangements that govern actin filament assembly and aging and lays the foundation for the rational design of drugs and small molecules for imaging and therapeutic applications.
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Abstract
A variety of cellular functions are driven by actin, which undergoes cyclic transitions between the monomeric G-form and the filamentous F-form. To gain insights into actin dynamics, the mechanism by which the energy is supplied by the ATP hydrolysis reaction in the F-form actin must be elucidated. This has been hampered by the lack of actin filament structures at atomic resolutions. Here, we have crystallized actin molecules trapped in the F-form without forming filaments, and based upon these structures we determined the reaction path by quantum mechanics calculations. The results are consistent with previous biochemical data. Remarkably, the hydrolysis reaction mechanism is essentially identical to those of motor proteins, while the process of Pi release is distinct. The major cytoskeleton protein actin undergoes cyclic transitions between the monomeric G-form and the filamentous F-form, which drive organelle transport and cell motility. This mechanical work is driven by the ATPase activity at the catalytic site in the F-form. For deeper understanding of the actin cellular functions, the reaction mechanism must be elucidated. Here, we show that a single actin molecule is trapped in the F-form by fragmin domain-1 binding and present their crystal structures in the ATP analog-, ADP-Pi-, and ADP-bound forms, at 1.15-Å resolutions. The G-to-F conformational transition shifts the side chains of Gln137 and His161, which relocate four water molecules including W1 (attacking water) and W2 (helping water) to facilitate the hydrolysis. By applying quantum mechanics/molecular mechanics calculations to the structures, we have revealed a consistent and comprehensive reaction path of ATP hydrolysis by the F-form actin. The reaction path consists of four steps: 1) W1 and W2 rotations; 2) PG–O3B bond cleavage; 3) four concomitant events: W1–PO3− formation, OH− and proton cleavage, nucleophilic attack by the OH− against PG, and the abstracted proton transfer; and 4) proton relocation that stabilizes the ADP-Pi–bound F-form actin. The mechanism explains the slow rate of ATP hydrolysis by actin and the irreversibility of the hydrolysis reaction. While the catalytic strategy of actin ATP hydrolysis is essentially the same as those of motor proteins like myosin, the process after the hydrolysis is distinct and discussed in terms of Pi release, F-form destabilization, and global conformational changes.
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Zhao Y, Ding S, Todoh M. Validate the force-velocity relation of the Hill's muscle model from a molecular perspective. Front Bioeng Biotechnol 2022; 10:1006571. [PMID: 36312549 PMCID: PMC9614041 DOI: 10.3389/fbioe.2022.1006571] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/30/2022] [Indexed: 07/30/2023] Open
Affiliation(s)
- Yongkun Zhao
- Division of Human Mechanical Systems and Design, Graduate School of Engineering, Hokkaido University, Sapporo, Japan
- Division of Bioengineering, Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Shihang Ding
- Division of Bioengineering, Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Masahiro Todoh
- Division of Mechanical and Aerospace Engineering, Faculty of Engineering, Hokkaido University, Sapporo, Japan
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Tarrago L, Kaya A, Kim HY, Manta B, Lee BC, Gladyshev VN. The selenoprotein methionine sulfoxide reductase B1 (MSRB1). Free Radic Biol Med 2022; 191:228-240. [PMID: 36084791 DOI: 10.1016/j.freeradbiomed.2022.08.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/11/2022] [Accepted: 08/31/2022] [Indexed: 11/24/2022]
Abstract
Methionine (Met) can be oxidized to methionine sulfoxide (MetO), which exist as R- and S-diastereomers. Present in all three domains of life, methionine sulfoxide reductases (MSR) are the enzymes that reduce MetO back to Met. Most characterized among them are MSRA and MSRB, which are strictly stereospecific for the S- and R-diastereomers of MetO, respectively. While the majority of MSRs use a catalytic Cys to reduce their substrates, some employ selenocysteine. This is the case of mammalian MSRB1, which was initially discovered as selenoprotein SELR or SELX and later was found to exhibit an MSRB activity. Genomic analyses demonstrated its occurrence in most animal lineages, and biochemical and structural analyses uncovered its catalytic mechanism. The use of transgenic mice and mammalian cell culture revealed its physiological importance in the protection against oxidative stress, maintenance of neuronal cells, cognition, cancer cell proliferation, and the immune response. Coincident with the discovery of Met oxidizing MICAL enzymes, recent findings of MSRB1 regulating the innate immunity response through reversible stereospecific Met-R-oxidation of cytoskeletal actin opened up new avenues for biological importance of MSRB1 and its role in disease. In this review, we discuss the current state of research on MSRB1, compare it with other animal Msrs, and offer a perspective on further understanding of biological functions of this selenoprotein.
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Affiliation(s)
- Lionel Tarrago
- UMR 1163, Biodiversité et Biotechnologie Fongiques, INRAE, Aix-Marseille Université, 13009, Marseille, France.
| | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Hwa-Young Kim
- Department of Biochemistry and Molecular Biology, Yeungnam University College of Medicine, Daegu, Republic of Korea
| | - Bruno Manta
- Laboratorio de Genomica Microbiana, Institut Pasteur de Montevideo, Mataojo 2020, 11440, Montevideo, Uruguay; Catedra de Fisiopatología, Facultad de Odontología, Universidad de la República, Las Heras 1925, 11600, Montevideo, Uruguay
| | - Byung-Cheon Lee
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, Republic of Korea.
| | - Vadim N Gladyshev
- Brigham and Women's Hospital, Harvard Medical School, Boston, 02115, USA.
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Yee M, Walther T, Frischknecht F, Douglas RG. Divergent Plasmodium actin residues are essential for filament localization, mosquito salivary gland invasion and malaria transmission. PLoS Pathog 2022; 18:e1010779. [PMID: 35998188 PMCID: PMC9439217 DOI: 10.1371/journal.ppat.1010779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 09/02/2022] [Accepted: 07/29/2022] [Indexed: 11/18/2022] Open
Abstract
Actin is one of the most conserved and ubiquitous proteins in eukaryotes. Its sequence has been highly conserved for its monomers to self-assemble into filaments that mediate essential cell functions such as trafficking, cell shape and motility. The malaria-causing parasite, Plasmodium, expresses a highly sequence divergent actin that is critical for its rapid motility at different stages within its mammalian and mosquito hosts. Each of Plasmodium actin’s four subdomains have divergent regions compared to canonical vertebrate actins. We previously identified subdomains 2 and 3 as providing critical contributions for parasite actin function as these regions could not be replaced by subdomains of vertebrate actins. Here we probed the contributions of individual divergent amino acid residues in these subdomains on parasite motility and progression. Non-lethal changes in these subdomains did not affect parasite development in the mammalian host but strongly affected progression through the mosquito with striking differences in transmission to and through the insect. Live visualization of actin filaments showed that divergent amino acid residues in subdomains 2 and 4 enhanced localization associated with filaments, while those in subdomain 3 negatively affected actin filaments. This suggests that finely tuned actin dynamics are essential for efficient organ entry in the mosquito vector affecting malaria transmission. This work provides residue level insight on the fundamental requirements of actin in highly motile cells. Actin is one of the most abundant and conserved proteins known. Actin monomers can join together to form long filaments. The malaria-causing parasite is transmitted by mosquitoes and needs actin to move very rapidly. An actin from the parasite is different to other actins: its amino acid sequence has relatively high amounts of changes compared to animal species and the actin tends to form only short filaments. We previously identified two large parts of the protein that were critical for the parasite since these large parts could not be exchanged with the equivalent regions of other species. In this study, we focused in on these regions by making more discrete mutations. Most mutations of the actin sequence were tolerated by the parasite in the blood stages. However, these mutants has striking defects in progressing through mosquitoes, especially in invading its salivary glands. We used a new filament labeler to visualize how these mutations affect the actin filaments and found surprisingly different effects. Taken together, small changes to the sequence can have large consequences for the parasite, which ultimately affects its ability to transmit to a new host.
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Affiliation(s)
- Michelle Yee
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
| | - Tobias Walther
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
- German Centre for Infection Research, DZIF, partner site Heidelberg, Heidelberg, Germany
- * E-mail: (FF); (RGD)
| | - Ross G. Douglas
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Heidelberg, Germany
- Biochemistry and Molecular Biology, Interdisciplinary Research Centre and Molecular Infection Biology, Biomedical Research Centre Seltersberg, Justus Liebig University Giessen, Giessen, Germany
- * E-mail: (FF); (RGD)
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Chen Y, Chen X, Zhang H, Sha Y, Meng R, Shao T, Yang X, Jin P, Zhuang Y, Min W, Xu D, Jiang Z, Li Y, Li L, Yue W, Yin C. TBC1D21 is an essential factor for sperm mitochondrial sheath assembly and male fertility‡. Biol Reprod 2022; 107:619-634. [PMID: 35403672 DOI: 10.1093/biolre/ioac069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 02/03/2022] [Accepted: 03/29/2022] [Indexed: 11/12/2022] Open
Abstract
During spermiogenesis, the formation of the mitochondrial sheath is critical for male fertility. The molecular processes that govern the development of the mitochondrial sheath remain unknown. Whether TBC1D21 serves as a GTPase-activating protein (GAP) for GTP hydrolysis in the testis is unclear, despite recent findings indicating that it collaborates with numerous proteins to regulate the formation of the mitochondrial sheath. To thoroughly examine the property of TBC1D21 in spermiogenesis, we applied the CRISPR/Cas9 technology to generate the Tbc1d21-/- mice, Tbc1d21D125A R128K mice with mutation in the GAP catalytic residues (IxxDxxR), and Tbc1d21-3xFlag mice. Male Tbc1d21-/- mice were infertile due to the curved spermatozoa flagella. In vitro fertilization is ineffective for Tbc1d21-/- sperm, although healthy offspring were obtained by intracytoplasmic sperm injection. Electron microscopy revealed aberrant ultrastructural changes in the mitochondrial sheath. Thirty-four Rab vectors were constructed followed by co-immunoprecipitation, which identified RAB13 as a novel TBC1D21 binding protein. Interestingly, infertility was not observed in Tbc1d21D125A R128K mice harboring the catalytic residue, suggesting that TBC1D21 is not a typical GAP for Rab-GTP hydrolysis. Moreover, TBC1D21 was expressed in the sperm mitochondrial sheath in Tbc1d21-3xFlag mice. Immunoprecipitation-mass spectrometry demonstrated the interactions of TBC1D21 with ACTB, TPM3, SPATA19, and VDAC3 to regulate the architecture of the sperm midpiece. The collective findings suggest that TBC1D21 is a scaffold protein required for the organization and stabilization of the mitochondrial sheath morphology.
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Affiliation(s)
- Yongjie Chen
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Xiu Chen
- Department of Pharmacy, Heze University, Heze, Shandong, China
| | - Haihang Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Yanwei Sha
- Department of Andrology, United Diagnostic and Research Center for Clinical Genetics, School of Public Health & Women and Children's Hospital, Xiamen University, Xiamen, China
| | - Ranran Meng
- National Institute of Biological Sciences, Beijing, China
| | - Tianyu Shao
- National Institute of Biological Sciences, Beijing, China
| | - Xiaoyan Yang
- National Institute of Biological Sciences, Beijing, China
| | - Pengpeng Jin
- National Institute of Biological Sciences, Beijing, China
| | - Yinghua Zhuang
- National Institute of Biological Sciences, Beijing, China
| | - Wanping Min
- National Institute of Biological Sciences, Beijing, China
| | - Dan Xu
- National Institute of Biological Sciences, Beijing, China
| | - Zhaodi Jiang
- National Institute of Biological Sciences, Beijing, China
| | - Yuhua Li
- National Institute of Biological Sciences, Beijing, China
| | - Lin Li
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Wentao Yue
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
| | - Chenghong Yin
- Central Laboratory, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing Maternal and Child Health Care Hospital, Beijing, China
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Structural basis of rapid actin dynamics in the evolutionarily divergent Leishmania parasite. Nat Commun 2022; 13:3442. [PMID: 35705539 PMCID: PMC9200798 DOI: 10.1038/s41467-022-31068-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/01/2022] [Indexed: 11/08/2022] Open
Abstract
Actin polymerization generates forces for cellular processes throughout the eukaryotic kingdom, but our understanding of the ‘ancient’ actin turnover machineries is limited. We show that, despite > 1 billion years of evolution, pathogenic Leishmania major parasite and mammalian actins share the same overall fold and co-polymerize with each other. Interestingly, Leishmania harbors a simple actin-regulatory machinery that lacks cofilin ‘cofactors’, which accelerate filament disassembly in higher eukaryotes. By applying single-filament biochemistry we discovered that, compared to mammalian proteins, Leishmania actin filaments depolymerize more rapidly from both ends, and are severed > 100-fold more efficiently by cofilin. Our high-resolution cryo-EM structures of Leishmania ADP-, ADP-Pi- and cofilin-actin filaments identify specific features at actin subunit interfaces and cofilin-actin interactions that explain the unusually rapid dynamics of parasite actin filaments. Our findings reveal how divergent parasites achieve rapid actin dynamics using a remarkably simple set of actin-binding proteins, and elucidate evolution of the actin cytoskeleton. The authors report here the structure-function analysis of highly divergent actin from Leishmania parasite. The study reveals remarkably rapid dynamics of parasite actin as well as the underlying molecular basis, thus providing insight into evolution of the actin cytoskeleton.
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Barth M, Toto Nienguesso A, Navarrete Santos A, Schmidt C. Quantitative proteomics and in-cell cross-linking reveal cellular reorganisation during early neuronal differentiation of SH-SY5Y cells. Commun Biol 2022; 5:551. [PMID: 35672350 PMCID: PMC9174471 DOI: 10.1038/s42003-022-03478-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 05/11/2022] [Indexed: 12/23/2022] Open
Abstract
The neuroblastoma cell line SH-SY5Y is commonly employed to study neuronal function and disease. This includes cells grown under standard conditions or differentiated to neuron-like cells by administration of chemical reagents such as retinoic acid (RA) or phorbol-12-myristate-13-acetate (PMA). Even though SH-SY5Y cells are widely explored, a complete description of the resulting proteomes and cellular reorganisation during differentiation is still missing. Here, we relatively quantify the proteomes of cells grown under standard conditions and obtained from two differentiation protocols employing RA or a combination of RA and PMA. Relative quantification and KEGG pathway analysis of the proteins reveals the presence of early differentiating cells and provides a list of marker proteins for undifferentiated and differentiated cells. For characterisation of neuronal sub-types, we analyse expression of marker genes and find that RA-differentiated cells are acetylcholinergic and cholinergic, while RA/PMA-differentiated cells show high expression of acetylcholinergic and dopaminergic marker genes. In-cell cross-linking further allows capturing protein interactions in different cellular organelles. Specifically, we observe structural reorganisation upon differentiation involving regulating protein factors of the actin cytoskeleton. Quantitative proteomic analyses are employed to explore the changes in the proteome that occur upon neuronal differentiation in the SH-SY5Y cell line.
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Affiliation(s)
- Marie Barth
- Interdisciplinary Research Center HALOmem, Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Alicia Toto Nienguesso
- Institute of Anatomy and Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Anne Navarrete Santos
- Institute of Anatomy and Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Carla Schmidt
- Interdisciplinary Research Center HALOmem, Institute of Biochemistry and Biotechnology, Charles Tanford Protein Center, Martin Luther University Halle-Wittenberg, Halle, Germany.
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Reindl T, Giese S, Greve JN, Reinke PY, Chizhov I, Latham SL, Mulvihill DP, Taft MH, Manstein DJ. Distinct actin–tropomyosin cofilament populations drive the functional diversification of cytoskeletal myosin motor complexes. iScience 2022; 25:104484. [PMID: 35720262 PMCID: PMC9204724 DOI: 10.1016/j.isci.2022.104484] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/02/2022] [Accepted: 05/24/2022] [Indexed: 11/02/2022] Open
Abstract
The effects of N-terminal acetylation of the high molecular weight tropomyosin isoforms Tpm1.6 and Tpm2.1 and the low molecular weight isoforms Tpm1.12, Tpm3.1, and Tpm4.2 on the actin affinity and the thermal stability of actin-tropomyosin cofilaments are described. Furthermore, we show how the exchange of cytoskeletal tropomyosin isoforms and their N-terminal acetylation affects the kinetic and chemomechanical properties of cytoskeletal actin-tropomyosin-myosin complexes. Our results reveal the extent to which the different actin-tropomyosin-myosin complexes differ in their kinetic and functional properties. The maximum sliding velocity of the actin filament as well as the optimal motor density for continuous unidirectional movement, parameters that were previously considered to be unique and invariant properties of each myosin isoform, are shown to be influenced by the exchange of the tropomyosin isoform and the N-terminal acetylation of tropomyosin. Tpm diversity is largely determined by sequences contributing to the overlap region Global sequence differences are of greater importance than variable exon 6 usage Tpm isoforms confer distinctly altered properties to cytoskeletal myosin motors Cytoskeletal myosins are differentially affected by N-terminal acetylation of Tpm
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Hassoun R, Erdmann C, Schmitt S, Fujita-Becker S, Mügge A, Schröder RR, Geyer M, Borbor M, Jaquet K, Hamdani N, Mannherz HG. Functional Characterization of Cardiac Actin Mutants Causing Hypertrophic (p.A295S) and Dilated Cardiomyopathy (p.R312H and p.E361G). Int J Mol Sci 2022; 23:ijms23084465. [PMID: 35457283 PMCID: PMC9024677 DOI: 10.3390/ijms23084465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/15/2022] [Accepted: 04/15/2022] [Indexed: 11/16/2022] Open
Abstract
Human wild type (wt) cardiac α-actin and its mutants p.A295S or p.R312H and p.E361G correlated with hypertrophic or dilated cardiomyopathy, respectively, were expressed by using the baculovirus/Sf21 insect cell system. The c-actin variants inhibited DNase I, indicating maintenance of their native state. Electron microscopy showed the formation of normal appearing actin filaments though they showed mutant specific differences in length and straightness correlating with their polymerization rates. TRITC-phalloidin staining showed that p.A295S and p.R312H exhibited reduced and the p.E361G mutant increased lengths of their formed filaments. Decoration of c-actins with cardiac tropomyosin (cTm) and troponin (cTn) conveyed Ca2+-sensitivity of the myosin-S1 ATPase stimulation, which was higher for the HCM p.A295S mutant and lower for the DCM p.R312H and p.E361G mutants than for wt c-actin. The lower Ca2+-sensitivity of myosin-S1 stimulation by both DCM actin mutants was corrected by the addition of levosimendan. Ca2+-dependency of the movement of pyrene-labeled cTm along polymerized c-actin variants decorated with cTn corresponded to the relations observed for the myosin-S1 ATPase stimulation though shifted to lower Ca2+-concentrations. The N-terminal C0C2 domain of cardiac myosin-binding protein-C increased the Ca2+-sensitivity of the pyrene-cTM movement of bovine, recombinant wt, p.A295S, and p.E361G c-actins, but not of the p.R312H mutant, suggesting decreased affinity to cTm.
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Affiliation(s)
- Roua Hassoun
- Institut für Forschung und Lehre (IFL), Molecular and Experimental Cardiology, Medical Faculty, Ruhr University Bochum, D-44791 Bochum, Germany; (R.H.); (A.M.); (K.J.)
- Department of Cardiology, St. Josef-Hospital, Medical Faculty, Ruhr University Bochum, D-44791 Bochum, Germany
| | - Constanze Erdmann
- Department of Anatomy and Molecular Embryology, Medical Faculty, Ruhr-University Bochum, D-44780 Bochum, Germany;
| | - Sebastian Schmitt
- Institute of Structural Biology, University of Bonn, D-53127 Bonn, Germany; (S.S.); (M.G.)
| | - Setsuko Fujita-Becker
- Cryoelectron Microscopy, BioQuant, Medical Faculty, University of Heidelberg, D-69120 Heidelberg, Germany; (S.F.-B.); (R.R.S.)
| | - Andreas Mügge
- Institut für Forschung und Lehre (IFL), Molecular and Experimental Cardiology, Medical Faculty, Ruhr University Bochum, D-44791 Bochum, Germany; (R.H.); (A.M.); (K.J.)
- Department of Cardiology, St. Josef-Hospital, Medical Faculty, Ruhr University Bochum, D-44791 Bochum, Germany
| | - Rasmus R. Schröder
- Cryoelectron Microscopy, BioQuant, Medical Faculty, University of Heidelberg, D-69120 Heidelberg, Germany; (S.F.-B.); (R.R.S.)
| | - Matthias Geyer
- Institute of Structural Biology, University of Bonn, D-53127 Bonn, Germany; (S.S.); (M.G.)
| | - Mina Borbor
- Department of Neurology, University Hospital Essen, D-45147 Essen, Germany;
| | - Kornelia Jaquet
- Institut für Forschung und Lehre (IFL), Molecular and Experimental Cardiology, Medical Faculty, Ruhr University Bochum, D-44791 Bochum, Germany; (R.H.); (A.M.); (K.J.)
- Department of Cardiology, St. Josef-Hospital, Medical Faculty, Ruhr University Bochum, D-44791 Bochum, Germany
| | - Nazha Hamdani
- Institut für Forschung und Lehre (IFL), Molecular and Experimental Cardiology, Medical Faculty, Ruhr University Bochum, D-44791 Bochum, Germany; (R.H.); (A.M.); (K.J.)
- Department of Cardiology, St. Josef-Hospital, Medical Faculty, Ruhr University Bochum, D-44791 Bochum, Germany
- Correspondence: (N.H.); (H.G.M.); Tel.: +49-234-32-29412 (N.H.); Fax: +49-234-32-14040 (N.H.); +49-234-32-14474 (H.G.M.)
| | - Hans Georg Mannherz
- Institut für Forschung und Lehre (IFL), Molecular and Experimental Cardiology, Medical Faculty, Ruhr University Bochum, D-44791 Bochum, Germany; (R.H.); (A.M.); (K.J.)
- Department of Anatomy and Molecular Embryology, Medical Faculty, Ruhr-University Bochum, D-44780 Bochum, Germany;
- Correspondence: (N.H.); (H.G.M.); Tel.: +49-234-32-29412 (N.H.); Fax: +49-234-32-14040 (N.H.); +49-234-32-14474 (H.G.M.)
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45
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Vahokoski J, Calder LJ, Lopez AJ, Molloy JE, Kursula I, Rosenthal PB. High-resolution structures of malaria parasite actomyosin and actin filaments. PLoS Pathog 2022; 18:e1010408. [PMID: 35377914 PMCID: PMC9037914 DOI: 10.1371/journal.ppat.1010408] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 04/25/2022] [Accepted: 03/01/2022] [Indexed: 12/20/2022] Open
Abstract
Malaria is responsible for half a million deaths annually and poses a huge economic burden on the developing world. The mosquito-borne parasites (Plasmodium spp.) that cause the disease depend upon an unconventional actomyosin motor for both gliding motility and host cell invasion. The motor system, often referred to as the glideosome complex, remains to be understood in molecular terms and is an attractive target for new drugs that might block the infection pathway. Here, we present the high-resolution structure of the actomyosin motor complex from Plasmodium falciparum. The complex includes the malaria parasite actin filament (PfAct1) complexed with the class XIV myosin motor (PfMyoA) and its two associated light-chains. The high-resolution core structure reveals the PfAct1:PfMyoA interface in atomic detail, while at lower-resolution, we visualize the PfMyoA light-chain binding region, including the essential light chain (PfELC) and the myosin tail interacting protein (PfMTIP). Finally, we report a bare PfAct1 filament structure at improved resolution.
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Affiliation(s)
- Juha Vahokoski
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Lesley J. Calder
- Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, London, United Kingdom
| | - Andrea J. Lopez
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Justin E. Molloy
- Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, London, United Kingdom
| | - Inari Kursula
- Department of Biomedicine, University of Bergen, Bergen, Norway
- Biocenter Oulu and Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Peter B. Rosenthal
- Structural Biology of Cells and Viruses Laboratory, Francis Crick Institute, London, United Kingdom
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Ehrlich H, Luczak M, Ziganshin R, Mikšík I, Wysokowski M, Simon P, Baranowska‐Bosiacka I, Kupnicka P, Ereskovsky A, Galli R, Dyshlovoy S, Fischer J, Tabachnick KR, Petrenko I, Jesionowski T, Lubkowska A, Figlerowicz M, Ivanenko VN, Summers AP. Arrested in Glass: Actin within Sophisticated Architectures of Biosilica in Sponges. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105059. [PMID: 35156333 PMCID: PMC9009123 DOI: 10.1002/advs.202105059] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/25/2022] [Indexed: 06/14/2023]
Abstract
Actin is a fundamental member of an ancient superfamily of structural intracellular proteins and plays a crucial role in cytoskeleton dynamics, ciliogenesis, phagocytosis, and force generation in both prokaryotes and eukaryotes. It is shown that actin has another function in metazoans: patterning biosilica deposition, a role that has spanned over 500 million years. Species of glass sponges (Hexactinellida) and demosponges (Demospongiae), representatives of the first metazoans, with a broad diversity of skeletal structures with hierarchical architecture unchanged since the late Precambrian, are studied. By etching their skeletons, organic templates dominated by individual F-actin filaments, including branched fibers and the longest, thickest actin fiber bundles ever reported, are isolated. It is proposed that these actin-rich filaments are not the primary site of biosilicification, but this highly sophisticated and multi-scale form of biomineralization in metazoans is ptterned.
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Affiliation(s)
- Hermann Ehrlich
- Institute of Electronic and Sensor MaterialsTU Bergakademie FreibergFreiberg09599Germany
- Center for Advanced TechnologyAdam Mickiewicz UniversityPoznan61614Poland
| | - Magdalena Luczak
- Institute of Bioorganic ChemistryPolish Academy of SciencesPoznan61704Poland
| | - Rustam Ziganshin
- Institute of Bioorganic ChemistryRussian Academy of SciencesMoscow142290Russian Federation
| | - Ivan Mikšík
- Institute of PhysiologyThe Czech Academy of SciencesPrague142 20Czech Republic
| | - Marcin Wysokowski
- Institute of Electronic and Sensor MaterialsTU Bergakademie FreibergFreiberg09599Germany
- Faculty of Chemical TechnologyInstitute of Chemical Technology and EngineeringPoznan University of TechnologyPoznan60965Poland
| | - Paul Simon
- Max Planck Institute for Chemical Physics of SolidsDresden01187Germany
| | - Irena Baranowska‐Bosiacka
- Department of Biochemistry and Medical ChemistryPomeranian Medical University in SzczecinSzczecin70111Poland
| | - Patrycja Kupnicka
- Department of Biochemistry and Medical ChemistryPomeranian Medical University in SzczecinSzczecin70111Poland
| | - Alexander Ereskovsky
- Institut Méditerranéen de Biodiversité et d'Ecologie (IMBE)CNRSIRDAix Marseille UniversitéMarseille13003France
- Biological FacultySt. Petersburg State UniversitySt. Petersburg199034Russian Federation
- Koltzov Institute of Developmental Biology of Russian Academy of SciencesMoscow119334Russian Federation
| | - Roberta Galli
- Clinical Sensoring and MonitoringDepartment of Anesthesiology and Intensive Care MedicineTU DresdenDresden01307Germany
| | - Sergey Dyshlovoy
- Laboratory of Experimental OncologyUniversity Medical Center Hamburg‐EppendorfHamburg20251Germany
- Laboratory of PharmacologyA.V. Zhirmunsky National Scientific Center of Marine BiologyFar Eastern BranchRussian Academy of SciencesVladivostok690041Russian Federation
| | - Jonas Fischer
- Institute of Electronic and Sensor MaterialsTU Bergakademie FreibergFreiberg09599Germany
| | | | - Iaroslav Petrenko
- Institute of Electronic and Sensor MaterialsTU Bergakademie FreibergFreiberg09599Germany
| | - Teofil Jesionowski
- Faculty of Chemical TechnologyInstitute of Chemical Technology and EngineeringPoznan University of TechnologyPoznan60965Poland
| | - Anna Lubkowska
- Department of Functional Diagnostics and Physical MedicineFaculty of Health SciencesPomeranian Medical University in SzczecinSzczecin71210Poland
| | - Marek Figlerowicz
- Institute of Bioorganic ChemistryPolish Academy of SciencesPoznan61704Poland
| | - Viatcheslav N. Ivanenko
- Department of Invertebrate ZoologyBiological FacultyLomonosov Moscow State UniversityMoscow119991Russian Federation
| | - Adam P. Summers
- Department of BiologyFriday Harbor LabsUniversity of WashingtonFriday HarborWA98195USA
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The Oxidative Balance Orchestrates the Main Keystones of the Functional Activity of Cardiomyocytes. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:7714542. [PMID: 35047109 PMCID: PMC8763515 DOI: 10.1155/2022/7714542] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 11/03/2021] [Accepted: 12/15/2021] [Indexed: 12/11/2022]
Abstract
This review is aimed at providing an overview of the key hallmarks of cardiomyocytes in physiological and pathological conditions. The main feature of cardiac tissue is the force generation through contraction. This process requires a conspicuous energy demand and therefore an active metabolism. The cardiac tissue is rich of mitochondria, the powerhouses in cells. These organelles, producing ATP, are also the main sources of ROS whose altered handling can cause their accumulation and therefore triggers detrimental effects on mitochondria themselves and other cell components thus leading to apoptosis and cardiac diseases. This review highlights the metabolic aspects of cardiomyocytes and wanders through the main systems of these cells: (a) the unique structural organization (such as different protein complexes represented by contractile, regulatory, and structural proteins); (b) the homeostasis of intracellular Ca2+ that represents a crucial ion for cardiac functions and E-C coupling; and (c) the balance of Zn2+, an ion with a crucial impact on the cardiovascular system. Although each system seems to be independent and finely controlled, the contractile proteins, intracellular Ca2+ homeostasis, and intracellular Zn2+ signals are strongly linked to each other by the intracellular ROS management in a fascinating way to form a "functional tetrad" which ensures the proper functioning of the myocardium. Nevertheless, if ROS balance is not properly handled, one or more of these components could be altered resulting in deleterious effects leading to an unbalance of this "tetrad" and promoting cardiovascular diseases. In conclusion, this "functional tetrad" is proposed as a complex network that communicates continuously in the cardiomyocytes and can drive the switch from physiological to pathological conditions in the heart.
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Discovery of Therapeutic Candidates for Diabetic Retinopathy Based on Molecular Switch Analysis: Application of a Systematic Process. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:3412032. [PMID: 35035658 PMCID: PMC8758313 DOI: 10.1155/2022/3412032] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/13/2021] [Accepted: 11/16/2021] [Indexed: 12/29/2022]
Abstract
The pathogenesis of diabetic retinopathy (DR) is complicated, and there is no effective drug. Oxidative stress-induced human retinal microvascular endothelial cells (HRMECs) injury is one of the pathogenic factors for DR. Molecular switches are considered high-risk targets in disease progression. Identification of molecular switch is crucial to interpret the pathogenesis of disease and screen effective ingredients. In this study, a systematic process was executed to discover therapeutic candidates for DR based on HRMECs injury. First of all, the molecular mechanism of HRMECs oxidative stress injury was revealed by transcriptomics and network pharmacology. We found that oxidative stress was one of the pivotal pathogenic factors, which interfered with vascular system development, inflammation, cell adhesion, and cytoskeleton damaged HRMECs through crosstalk. Then, network topology analysis was used to recognize molecular switches. The results indicated that the Keap1-Nrf2-ARE signaling pathway was the molecular switch in HRMECs oxidative stress injury. On this basis, the HEK293-ARE overexpression cell line was applied to obtain 18 active traditional Chinese medicine (TCM) ingredients. Furthermore, andrographolide, one of the 18 candidates, was applied in the HRMECs oxidative stress model to evaluate the accuracy of the systematic process. The efficacy evaluation results showed that andrographolide could regulate oxidative stress, vascular system development, inflammation, adhesion, and skeleton tissue to inhibit HRMECs injury cooperatively. And its mechanism was related to the Nrf2 signaling pathway. Overall, our data suggest that the Nrf2 signaling pathway is the molecular switch in the HRMECs oxidative stress injury. 18 potential Nrf2 agonists are likely to be promising DR candidates.
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49
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Boiero Sanders M, Toret CP, Guillotin A, Antkowiak A, Vannier T, Robinson RC, Michelot A. Specialization of actin isoforms derived from the loss of key interactions with regulatory factors. EMBO J 2022; 41:e107982. [PMID: 35178724 PMCID: PMC8886540 DOI: 10.15252/embj.2021107982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 11/09/2022] Open
Abstract
A paradox of eukaryotic cells is that while some species assemble a complex actin cytoskeleton from a single ortholog, other species utilize a greater diversity of actin isoforms. The physiological consequences of using different actin isoforms, and the molecular mechanisms by which highly conserved actin isoforms are segregated into distinct networks, are poorly known. Here, we sought to understand how a simple biological system, composed of a unique actin and a limited set of actin‐binding proteins, reacts to a switch to heterologous actin expression. Using yeast as a model system and biomimetic assays, we show that such perturbation causes drastic reorganization of the actin cytoskeleton. Our results indicate that defective interaction of a heterologous actin for important regulators of actin assembly limits certain actin assembly pathways while reinforcing others. Expression of two heterologous actin variants, each specialized in assembling a different network, rescues cytoskeletal organization and confers resistance to external perturbation. Hence, while species using a unique actin have homeostatic actin networks, actin assembly pathways in species using several actin isoforms may act more independently.
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Affiliation(s)
| | - Christopher P Toret
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
| | - Audrey Guillotin
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
| | - Adrien Antkowiak
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
| | - Thomas Vannier
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
| | - Robert C Robinson
- Research Institute for Interdisciplinary Science (RIIS), Okayama University, Okayama, Japan.,School of Biomolecular Science and Engineering (BSE), Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Alphée Michelot
- CNRS, IBDM, Turing Centre for Living Systems, Aix Marseille Univ, Marseille, France
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50
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Kim NH, Choi H, Shahzad ZM, Ki H, Lee J, Chae H, Kim YH. Supramolecular assembly of protein building blocks: from folding to function. NANO CONVERGENCE 2022; 9:4. [PMID: 35024976 PMCID: PMC8755899 DOI: 10.1186/s40580-021-00294-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Several phenomena occurring throughout the life of living things start and end with proteins. Various proteins form one complex structure to control detailed reactions. In contrast, one protein forms various structures and implements other biological phenomena depending on the situation. The basic principle that forms these hierarchical structures is protein self-assembly. A single building block is sufficient to create homogeneous structures with complex shapes, such as rings, filaments, or containers. These assemblies are widely used in biology as they enable multivalent binding, ultra-sensitive regulation, and compartmentalization. Moreover, with advances in the computational design of protein folding and protein-protein interfaces, considerable progress has recently been made in the de novo design of protein assemblies. Our review presents a description of the components of supramolecular protein assembly and their application in understanding biological phenomena to therapeutics.
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Affiliation(s)
- Nam Hyeong Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hojae Choi
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Zafar Muhammad Shahzad
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea
- School of Chemical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Heesoo Ki
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Jaekyoung Lee
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Heeyeop Chae
- School of Chemical Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Yong Ho Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Department of Nano Engineering, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
- Center for Neuroscience Imaging Research, Institute for Basic Science (IBS), Suwon, 16419, Republic of Korea.
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