1
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Zhao AJ, Montes-Laing J, Perry WMG, Shiratori M, Merfeld E, Rogers SL, Applewhite DA. The Drosophila spectraplakin Short stop regulates focal adhesion dynamics by crosslinking microtubules and actin. Mol Biol Cell 2022; 33:ar19. [PMID: 35235367 PMCID: PMC9282009 DOI: 10.1091/mbc.e21-09-0434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
The spectraplakin family of proteins includes ACF7/MACF1 and BPAG1/dystonin in mammals, VAB-10 in Caenorhabditis elegans, Magellan in zebrafish, and Short stop (Shot), the sole Drosophila member. Spectraplakins are giant cytoskeletal proteins that cross-link actin, microtubules, and intermediate filaments, coordinating the activity of the entire cytoskeleton. We examined the role of Shot during cell migration using two systems: the in vitro migration of Drosophila tissue culture cells and in vivo through border cell migration. RNA interference (RNAi) depletion of Shot increases the rate of random cell migration in Drosophila tissue culture cells as well as the rate of wound closure during scratch-wound assays. This increase in cell migration prompted us to analyze focal adhesion dynamics. We found that the rates of focal adhesion assembly and disassembly were faster in Shot-depleted cells, leading to faster adhesion turnover that could underlie the increased migration speeds. This regulation of focal adhesion dynamics may be dependent on Shot being in an open confirmation. Using Drosophila border cells as an in vivo model for cell migration, we found that RNAi depletion led to precocious border cell migration. Collectively, these results suggest that spectraplakins not only function to cross-link the cytoskeleton but may regulate cell–matrix adhesion.
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Affiliation(s)
- Andrew J Zhao
- Department of Biology, Reed College, 3203 SE Woodstock Boulevard, Portland, OR 97202, USA
| | - Julia Montes-Laing
- Department of Biology, Reed College, 3203 SE Woodstock Boulevard, Portland, OR 97202, USA
| | - Wick M G Perry
- Department of Biology, Reed College, 3203 SE Woodstock Boulevard, Portland, OR 97202, USA
| | - Mari Shiratori
- Department of Biology, Reed College, 3203 SE Woodstock Boulevard, Portland, OR 97202, USA
| | - Emily Merfeld
- Department of Biology, Reed College, 3203 SE Woodstock Boulevard, Portland, OR 97202, USA
| | - Stephen L Rogers
- Department of Biology & Carolina Center for Genome Sciences, The University of North Carolina at Chapel Hill, Campus Box 3280, 422 Fordham Hall, Chapel Hill, NC 27599-3280, USA
| | - Derek A Applewhite
- Department of Biology, Reed College, 3203 SE Woodstock Boulevard, Portland, OR 97202, USA
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2
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Barbarino F, Wäschenbach L, Cavalho-Lemos V, Dillenberger M, Becker K, Gohlke H, Cortese-Krott MM. Targeting spectrin redox switches to regulate the mechanoproperties of red blood cells. Biol Chem 2020; 402:317-331. [PMID: 33544503 DOI: 10.1515/hsz-2020-0293] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/17/2020] [Indexed: 12/16/2022]
Abstract
The mechanical properties of red blood cells (RBCs) are fundamental for their physiological role as gas transporters. RBC flexibility and elasticity allow them to survive the hemodynamic changes in the different regions of the vascular tree, to dynamically contribute to the flow thereby decreasing vascular resistance, and to deform during the passage through narrower vessels. RBC mechanoproperties are conferred mainly by the structural characteristics of their cytoskeleton, which consists predominantly of a spectrin scaffold connected to the membrane via nodes of actin, ankyrin and adducin. Changes in redox state and treatment with thiol-targeting molecules decrease the deformability of RBCs and affect the structure and stability of the spectrin cytoskeleton, indicating that the spectrin cytoskeleton may contain redox switches. In this perspective review, we revise current knowledge about the structural and functional characterization of spectrin cysteine redox switches and discuss the current lines of research aiming to understand the role of redox regulation on RBC mechanical properties. These studies may provide novel functional targets to modulate RBC function, blood viscosity and flow, and tissue perfusion in disease conditions.
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Affiliation(s)
- Frederik Barbarino
- Myocardial Infarction Research Laboratory, Department of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty, Heinrich Heine University, Postfach 128, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Lucas Wäschenbach
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Virginia Cavalho-Lemos
- Myocardial Infarction Research Laboratory, Department of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty, Heinrich Heine University, Postfach 128, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Melissa Dillenberger
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, D-35392, Giessen, Germany
| | - Katja Becker
- Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, D-35392, Giessen, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), Forschungszentrum Jülich GmbH, D-52425, Jülich, Germany
| | - Miriam M Cortese-Krott
- Myocardial Infarction Research Laboratory, Department of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty, Heinrich Heine University, Postfach 128, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
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3
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Bose D, Chakrabarti A. Localizing the chaperone activity of erythroid spectrin. Cytoskeleton (Hoboken) 2019; 76:383-397. [DOI: 10.1002/cm.21556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/31/2019] [Accepted: 08/06/2019] [Indexed: 02/05/2023]
Affiliation(s)
- Dipayan Bose
- Crystallography and Molecular Biology DivisionSaha Institute of Nuclear Physics Kolkata India
- Homi Bhabha National Institute Mumbai India
| | - Abhijit Chakrabarti
- Crystallography and Molecular Biology DivisionSaha Institute of Nuclear Physics Kolkata India
- Homi Bhabha National Institute Mumbai India
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4
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Mias-Lucquin D, Chéron A, Le Rumeur E, Hubert JF, Delalande O. Fine mapping of hydrophobic contacts reassesses the organization of the first three dystrophin coiled-coil repeats. Protein Sci 2018; 28:561-570. [PMID: 30468271 DOI: 10.1002/pro.3557] [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: 07/09/2018] [Revised: 10/29/2018] [Accepted: 11/18/2018] [Indexed: 11/12/2022]
Abstract
Coiled-coil domain is a structural motif found in proteins crucial for achievement of central biological processes, such as cellular cohesion or neuro-transmission. The coiled-coil fold consists of alpha-helices bundle that can be repeated to form larger filament. Hydrophobic residues, distributed following a regular seven-residues' pattern, named heptad pattern, are commonly admitted to be essential for the formation and the stability of canonical coiled-coil repeats. Here we investigated the first three coiled-coil repeats (R1-R3) of the central domain of dystrophin, a scaffolding protein in muscle cells whose deficiency leads to Duchenne and Becker Muscular Dystrophies. By an atomic description of the hydrophobic interactions, we highlighted (i) that coiled-coil filament conformational changes are associated to specific patterns of inter-helices hydrophobic contacts, (ii) that inter-repeat hydrophobic interactions determine the behavior of linker regions including filament kinks, and (iii) that a non-strict conservation of the heptad patterns is leading to a relative plasticity of the dystrophin coiled-coil repeats. These structural features and modulations of the coiled-coil fold could better explain the mechanical properties of the central domain of dystrophin. This contribution to the understanding of the structure-function relationship of dystrophin, and especially of the R1-R3 fragment frequently used in the design of protein for gene therapies, should help in the improvement of the strategies for the cure of muscular dystrophies.
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5
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Delalande O, Molza AE, Dos Santos Morais R, Chéron A, Pollet É, Raguenes-Nicol C, Tascon C, Giudice E, Guilbaud M, Nicolas A, Bondon A, Leturcq F, Férey N, Baaden M, Perez J, Roblin P, Piétri-Rouxel F, Hubert JF, Czjzek M, Le Rumeur E. Dystrophin's central domain forms a complex filament that becomes disorganized by in-frame deletions. J Biol Chem 2018. [PMID: 29535188 DOI: 10.1074/jbc.m117.809798] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Dystrophin, encoded by the DMD gene, is critical for maintaining plasma membrane integrity during muscle contraction events. Mutations in the DMD gene disrupting the reading frame prevent dystrophin production and result in severe Duchenne muscular dystrophy (DMD); in-frame internal deletions allow production of partly functional internally deleted dystrophin and result in less severe Becker muscular dystrophy (BMD). Many known BMD deletions occur in dystrophin's central domain, generally considered to be a monotonous rod-shaped domain based on the knowledge of spectrin family proteins. However, the effects caused by these deletions, ranging from asymptomatic to severe BMD, argue against the central domain serving only as a featureless scaffold. We undertook structural studies combining small-angle X-ray scattering and molecular modeling in an effort to uncover the structure of the central domain, as dystrophin has been refractory to characterization. We show that this domain appears to be a tortuous and complex filament that is profoundly disorganized by the most severe BMD deletion (loss of exons 45-47). Despite the preservation of large parts of the binding site for neuronal nitric oxide synthase (nNOS) in this deletion, computational approaches failed to recreate the association of dystrophin with nNOS. This observation is in agreement with a strong decrease of nNOS immunolocalization in muscle biopsies, a parameter related to the severity of BMD phenotypes. The structural description of the whole dystrophin central domain we present here is a first necessary step to improve the design of microdystrophin constructs toward the goal of a successful gene therapy for DMD.
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Affiliation(s)
- Olivier Delalande
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France,
| | - Anne-Elisabeth Molza
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
| | - Raphael Dos Santos Morais
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France.,the Synchrotron SOLEIL, 91190 Saint Aubin, France.,the Laboratoire Léon-Brillouin, UMR 12 CEA-CNRS, Université Paris-Saclay, CEA-Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Angélique Chéron
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
| | - Émeline Pollet
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
| | - Céline Raguenes-Nicol
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
| | - Christophe Tascon
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
| | - Emmanuel Giudice
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
| | - Marine Guilbaud
- the Sorbonne Universités UPMC-INSERM-UMRS 97-CNRS FRE 3617, Institut de Myologie, 75013 Paris, France
| | - Aurélie Nicolas
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
| | - Arnaud Bondon
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France.,the Université Rennes, CNRS, Institut des Sciences Chimiques de Rennes-UMR 6226, PRISM, 35000 Rennes, France
| | - France Leturcq
- the Sorbonne Universités UPMC-INSERM-UMRS 97-CNRS FRE 3617, Institut de Myologie, 75013 Paris, France.,the AP-HP, Groupe Hospitalier Cochin-Broca-Hôtel Dieu, Laboratoire de Biochimie et Génétique Moléculaire, 75014 Paris, France
| | - Nicolas Férey
- the CNRS UPR3251, Université Paris XI, 91403 Orsay Cedex, France
| | - Marc Baaden
- the CNRS UPR9080, Université Paris Diderot, Sorbonne Paris Cité, 75005 Paris, France
| | - Javier Perez
- the Synchrotron SOLEIL, 91190 Saint Aubin, France
| | - Pierre Roblin
- the Synchrotron SOLEIL, 91190 Saint Aubin, France.,the INRA-Biopolymères, Interaction et Assemblages, 44000 Nantes, France
| | - France Piétri-Rouxel
- the Sorbonne Universités UPMC-INSERM-UMRS 97-CNRS FRE 3617, Institut de Myologie, 75013 Paris, France
| | - Jean-François Hubert
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
| | - Mirjam Czjzek
- the Sorbonne Universités, UPMC Université Paris 06, 75006 Paris, France, and.,the CNRS UMR 8227, Integrative Biology of Marine Models, 29688 Roscoff Cedex, France
| | - Elisabeth Le Rumeur
- From the Université de Rennes, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, 35000 Rennes, France
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6
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Delalande O, Czogalla A, Hubert JF, Sikorski A, Le Rumeur E. Dystrophin and Spectrin, Two Highly Dissimilar Sisters of the Same Family. Subcell Biochem 2017; 82:373-403. [PMID: 28101868 DOI: 10.1007/978-3-319-49674-0_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Dystrophin and Spectrin are two proteins essential for the organization of the cytoskeleton and for the stabilization of membrane cells. The comparison of these two sister proteins, and with the dystrophin homologue utrophin, enables us to emphasise that, despite a similar topology with common subdomains and a common structural basis of a three-helix coiled-coil, they show a large range of dissimilarities in terms of genetics, cell expression and higher level structural organisation. Interactions with cellular partners, including proteins and membrane phospholipids, also show both strikingly similar and very different behaviours. The differences between dystrophin and spectrin are also illustrated by the large variety of pathological anomalies emerging from the dysfunction or the absence of these proteins, showing that they are keystones in their function of providing a scaffold that sustains cell structure.
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Affiliation(s)
- Olivier Delalande
- Institut de Génétique et Développement de Rennes, UMR CNRS 6290, Université de Rennes 1, Rennes, France.
| | - Aleksander Czogalla
- Biotechnology Faculty, Department of Cytobiochemistry, University of Wrocław, ul. joliot-Curie 14a, 50-383, Wroclaw, Poland
| | - Jean-François Hubert
- Institut de Génétique et Développement de Rennes, UMR CNRS 6290, Université de Rennes 1, Rennes, France
| | - Aleksander Sikorski
- Biotechnology Faculty, Department of Cytobiochemistry, University of Wrocław, ul. joliot-Curie 14a, 50-383, Wroclaw, Poland
| | - Elisabeth Le Rumeur
- Institut de Génétique et Développement de Rennes, UMR CNRS 6290, Université de Rennes 1, Rennes, France
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7
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Structure and function of a spectrin-like regulator of bacterial cytokinesis. Nat Commun 2014; 5:5421. [PMID: 25403286 PMCID: PMC4243239 DOI: 10.1038/ncomms6421] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 09/30/2014] [Indexed: 11/09/2022] Open
Abstract
Bacterial cell division is facilitated by a molecular machine--the divisome--that assembles at mid-cell in dividing cells. The formation of the cytokinetic Z-ring by the tubulin homologue FtsZ is regulated by several factors, including the divisome component EzrA. Here we describe the structure of the 60-kDa cytoplasmic domain of EzrA, which comprises five linear repeats of an unusual triple helical bundle. The EzrA structure is bent into a semicircle, providing the protein with the potential to interact at both N- and C-termini with adjacent membrane-bound divisome components. We also identify at least two binding sites for FtsZ on EzrA and map regions of EzrA that are responsible for regulating FtsZ assembly. The individual repeats, and their linear organization, are homologous to the spectrin proteins that connect actin filaments to the membrane in eukaryotes, and we thus propose that EzrA is the founding member of the bacterial spectrin family.
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8
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Machnicka B, Czogalla A, Hryniewicz-Jankowska A, Bogusławska DM, Grochowalska R, Heger E, Sikorski AF. Spectrins: a structural platform for stabilization and activation of membrane channels, receptors and transporters. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:620-34. [PMID: 23673272 DOI: 10.1016/j.bbamem.2013.05.002] [Citation(s) in RCA: 113] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 04/25/2013] [Accepted: 05/06/2013] [Indexed: 12/22/2022]
Abstract
This review focuses on structure and functions of spectrin as a major component of the membrane skeleton. Recent advances on spectrin function as an interface for signal transduction mediation and a number of data concerning interaction of spectrin with membrane channels, adhesion molecules, receptors and transporters draw a picture of multifaceted protein. Here, we attempted to show the current depiction of multitask role of spectrin in cell physiology. This article is part of a Special Issue entitled: Reciprocal influences between cell cytoskeleton and membrane channels, receptors and transporters. Guest Editor: Jean Claude Hervé.
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Affiliation(s)
- Beata Machnicka
- University of Zielona Góra, Faculty of Biological Sciences, Poland
| | | | | | | | | | - Elżbieta Heger
- University of Zielona Góra, Faculty of Biological Sciences, Poland
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9
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Autore F, Pfuhl M, Quan X, Williams A, Roberts RG, Shanahan CM, Fraternali F. Large-scale modelling of the divergent spectrin repeats in nesprins: giant modular proteins. PLoS One 2013; 8:e63633. [PMID: 23671687 PMCID: PMC3646009 DOI: 10.1371/journal.pone.0063633] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 04/09/2013] [Indexed: 11/29/2022] Open
Abstract
Nesprin-1 and nesprin-2 are nuclear envelope (NE) proteins characterized by a common structure of an SR (spectrin repeat) rod domain and a C-terminal transmembrane KASH [Klarsicht-ANC-Syne-homology] domain and display N-terminal actin-binding CH (calponin homology) domains. Mutations in these proteins have been described in Emery-Dreifuss muscular dystrophy and attributed to disruptions of interactions at the NE with nesprins binding partners, lamin A/C and emerin. Evolutionary analysis of the rod domains of the nesprins has shown that they are almost entirely composed of unbroken SR-like structures. We present a bioinformatical approach to accurate definition of the boundaries of each SR by comparison with canonical SR structures, allowing for a large-scale homology modelling of the 74 nesprin-1 and 56 nesprin-2 SRs. The exposed and evolutionary conserved residues identify important pbs for protein-protein interactions that can guide tailored binding experiments. Most importantly, the bioinformatics analyses and the 3D models have been central to the design of selected constructs for protein expression. 1D NMR and CD spectra have been performed of the expressed SRs, showing a folded, stable, high content α-helical structure, typical of SRs. Molecular Dynamics simulations have been performed to study the structural and elastic properties of consecutive SRs, revealing insights in the mechanical properties adopted by these modules in the cell.
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Affiliation(s)
- Flavia Autore
- Randall Division of Cell and Molecular Biophysics, School of Physical Sciences and Engineering, King's College London, London, United Kingdom
- Division of Cardiovascular Medicine, BHF Centre of Research Excellence, King's College London, London, United Kingdom
| | - Mark Pfuhl
- Randall Division of Cell and Molecular Biophysics, School of Physical Sciences and Engineering, King's College London, London, United Kingdom
| | - Xueping Quan
- Randall Division of Cell and Molecular Biophysics, School of Physical Sciences and Engineering, King's College London, London, United Kingdom
| | - Aisling Williams
- Randall Division of Cell and Molecular Biophysics, School of Physical Sciences and Engineering, King's College London, London, United Kingdom
- Division of Cardiovascular Medicine, BHF Centre of Research Excellence, King's College London, London, United Kingdom
| | - Roland G. Roberts
- Division of Medical and Molecular Genetics, Kings College London, Guy's Hospital, London, United Kingdom
| | - Catherine M. Shanahan
- Division of Cardiovascular Medicine, BHF Centre of Research Excellence, King's College London, London, United Kingdom
| | - Franca Fraternali
- Randall Division of Cell and Molecular Biophysics, School of Physical Sciences and Engineering, King's College London, London, United Kingdom
- The Thomas Young Centre for Theory and Simulation of Materials, London, United Kingdom
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10
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Legrand B, Giudice E, Nicolas A, Delalande O, Le Rumeur E. Computational study of the human dystrophin repeats: interaction properties and molecular dynamics. PLoS One 2011; 6:e23819. [PMID: 21901138 PMCID: PMC3162007 DOI: 10.1371/journal.pone.0023819] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 07/26/2011] [Indexed: 01/16/2023] Open
Abstract
Dystrophin is a large protein involved in the rare genetic disease Duchenne muscular dystrophy (DMD). It functions as a mechanical linker between the cytoskeleton and the sarcolemma, and is able to resist shear stresses during muscle activity. In all, 75% of the dystrophin molecule consists of a large central rod domain made up of 24 repeat units that share high structural homology with spectrin-like repeats. However, in the absence of any high-resolution structure of these repeats, the molecular basis of dystrophin central domain's functions has not yet been deciphered. In this context, we have performed a computational study of the whole dystrophin central rod domain based on the rational homology modeling of successive and overlapping tandem repeats and the analysis of their surface properties. Each tandem repeat has very specific surface properties that make it unique. However, the repeats share enough electrostatic-surface similarities to be grouped into four separate clusters. Molecular dynamics simulations of four representative tandem repeats reveal specific flexibility or bending properties depending on the repeat sequence. We thus suggest that the dystrophin central rod domain is constituted of seven biologically relevant sub-domains. Our results provide evidence for the role of the dystrophin central rod domain as a scaffold platform with a wide range of surface features and biophysical properties allowing it to interact with its various known partners such as proteins and membrane lipids. This new integrative view is strongly supported by the previous experimental works that investigated the isolated domains and the observed heterogeneity of the severity of dystrophin related pathologies, especially Becker muscular dystrophy.
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Affiliation(s)
- Baptiste Legrand
- Université de Rennes 1, Rennes, France
- Equipe RMN-ILP, Faculté de médecine, UMR CNRS 6026, Rennes, France
- Université Européenne de Bretagne, Rennes, France
| | - Emmanuel Giudice
- Université de Rennes 1, Rennes, France
- Equipe SDM, UMR CNRS 6026, Rennes, France
- Université Européenne de Bretagne, Rennes, France
| | - Aurélie Nicolas
- Université de Rennes 1, Rennes, France
- Equipe RMN-ILP, Faculté de médecine, UMR CNRS 6026, Rennes, France
- Université Européenne de Bretagne, Rennes, France
| | - Olivier Delalande
- Université de Rennes 1, Rennes, France
- Equipe RMN-ILP, Faculté de médecine, UMR CNRS 6026, Rennes, France
- Université Européenne de Bretagne, Rennes, France
| | - Elisabeth Le Rumeur
- Université de Rennes 1, Rennes, France
- Equipe RMN-ILP, Faculté de médecine, UMR CNRS 6026, Rennes, France
- Université Européenne de Bretagne, Rennes, France
- * E-mail:
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11
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Wells DB, Aksimentiev A. Mechanical properties of a complete microtubule revealed through molecular dynamics simulation. Biophys J 2010; 99:629-37. [PMID: 20643083 DOI: 10.1016/j.bpj.2010.04.038] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Revised: 04/15/2010] [Accepted: 04/20/2010] [Indexed: 11/18/2022] Open
Abstract
Microtubules (MTs) are the largest type of cellular filament, essential in processes ranging from mitosis and meiosis to flagellar motility. Many of the processes depend critically on the mechanical properties of the MT, but the elastic moduli, notably the Young's modulus, are not directly revealed in experiment, which instead measures either flexural rigidity or response to radial deformation. Molecular dynamics (MD) is a method that allows the mechanical properties of single biomolecules to be investigated through computation. Typically, MD requires an atomic resolution structure of the molecule, which is unavailable for many systems, including MTs. By combining structural information from cryo-electron microscopy and electron crystallography, we have constructed an all-atom model of a complete MT and used MD to determine its mechanical properties. The simulations revealed nonlinear axial stress-strain behavior featuring a pronounced softening under extension, a possible plastic deformation transition under radial compression, and a distinct asymmetry in response to the two senses of twist. This work demonstrates the possibility of combining different levels of structural information to produce all-atom models suitable for quantitative MD simulations, which extends the range of systems amenable to the MD method and should enable exciting advances in our microscopic knowledge of biology.
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Affiliation(s)
- David B Wells
- Department of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana, Illinois, USA
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12
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Czogalla A, Grzymajło K, Jezierski A, Sikorski AF. Phospholipid-induced structural changes to an erythroid β spectrin ankyrin-dependent lipid-binding site. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:2612-20. [DOI: 10.1016/j.bbamem.2008.07.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2008] [Revised: 07/01/2008] [Accepted: 07/18/2008] [Indexed: 12/01/2022]
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13
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Abstract
BAR domains are proteins that sense and sculpt curved membranes in cells, furnishing a relatively well-studied example of mechanisms employed in cellular morphogenesis. We report a computational study of membrane bending by BAR domains at four levels of resolution, described by 1), all-atom molecular dynamics; 2), residue-based coarse-graining (resolving single amino acids and lipid molecules); 3), shape-based coarse-graining (resolving overall protein and membrane shapes); and 4), a continuum elastic membrane model. Membrane sculpting performed by BAR domains collectively is observed in agreement with experiments. Different arrangements of BAR domains on the membrane surface are found to lead to distinct membrane curvatures and bending dynamics.
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14
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Abstract
Modular proteins such as titin, fibronectin, and cadherin are ubiquitous components of living cells. Often involved in signaling and mechanical processes, their architecture is characterized by domains containing a variable number of heterogeneous "repeats" arranged in series, with either flexible or rigid linker regions that determine their elasticity. Cadherin repeats arranged in series are unique in that linker regions also feature calcium-binding motifs. While it is well known that the extracellular repeats of cadherin proteins mediate cell-cell adhesion in a calcium-dependent manner, the molecular mechanisms behind the influence of calcium in adhesion dynamics and cadherin's mechanical response are not well understood. Here we show, using molecular dynamics simulations, how calcium ions control the structural integrity of cadherin's linker regions, thereby affecting cadherin's equilibrium dynamics, the availability of key residues involved in cell-cell adhesion, and cadherin's mechanical response. The all-atom, multi-nanosecond molecular dynamics simulations involved the entire C-cadherin extracellular domain solvated in water (a 345,000 atom system). Equilibrium simulations show that the extracellular domain maintains its crystal conformation (elongated and slightly curved) when calcium ions are present. In the absence of calcium ions, however, it assumes a disordered conformation. The conserved residue Trp(2), which is thought to insert itself into a hydrophobic pocket of another cadherin molecule (thereby providing the basis for cell-cell adhesion), switches conformation from exposed to intermittently buried upon removal of calcium ions. Furthermore, the overall mechanical response of C-cadherin's extracellular domain is characterized at low force by changes in shape (tertiary structure elasticity), and at high force by unraveling of secondary structure elements (secondary structure elasticity). This mechanical response is modulated by calcium ions at both low and high force, switching from a stiff, rod-like to a soft, spring-like behavior upon removal of ions. The simulations provide an unprecedented molecular view of calcium-mediated allostery in cadherins, also illustrating the general principles of linker-mediated elasticity of modular proteins relevant not only for cell-cell adhesion and sound transduction, but also muscle elasticity.
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Unique elastic properties of the spectrin tetramer as revealed by multiscale coarse-grained modeling. Proc Natl Acad Sci U S A 2008; 105:1204-8. [PMID: 18202182 DOI: 10.1073/pnas.0707500105] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The force-extension profile of tetrameric spectrin is determined by using multiscale computer simulation. Fluctuation results of atomistic simulations of double spectrin repeat units (DSRU) are used to systematically build a coarse-grained (CG) model for the tetrameric form of spectrin. It is found that the spectrin tetramer can be modeled as a soft polymer with a unique flat force-extension profile over the range of biologically important lengths. It is also concluded that in the cytoskeletal network of the red blood cell the tetramer is in an "overcompressed" state. These findings are in contrast to the commonly used models of spectrin tetramer elasticity, namely the "entropic spring" polymer models. From these results, it is concluded that stable intact helical linker regions are needed to maintain the soft elasticity of the spectrin tetramer.
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