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Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ, Šarić A. Self-replication of A β42 aggregates occurs on small and isolated fibril sites. Proc Natl Acad Sci U S A 2024; 121:e2220075121. [PMID: 38335256 PMCID: PMC10873593 DOI: 10.1073/pnas.2220075121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 11/17/2023] [Indexed: 02/12/2024] Open
Abstract
Self-replication of amyloid fibrils via secondary nucleation is an intriguing physicochemical phenomenon in which existing fibrils catalyze the formation of their own copies. The molecular events behind this fibril surface-mediated process remain largely inaccessible to current structural and imaging techniques. Using statistical mechanics, computer modeling, and chemical kinetics, we show that the catalytic structure of the fibril surface can be inferred from the aggregation behavior in the presence and absence of a fibril-binding inhibitor. We apply our approach to the case of Alzheimer's A[Formula: see text] amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A[Formula: see text] fibrils occurs on small catalytic sites on the fibril surface, which are far apart from each other, and each of which can be covered by a single Brichos inhibitor.
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Affiliation(s)
- Samo Curk
- Institute of Science and Technology Austria, Klosterneuburg3400, Austria
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - Johannes Krausser
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
| | - Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Daan Frenkel
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund22100, Sweden
| | - Thomas C. T. Michaels
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
- Department of Biology, Institute of Biochemistry, ETH Zürich, Zürich8093, Switzerland
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Anđela Šarić
- Institute of Science and Technology Austria, Klosterneuburg3400, Austria
- Department of Physics and Astronomy, Laboratory for Molecular Cell Biology, University College London, LondonWC1E 6BT, United Kingdom
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2
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Azadbakht A, Meadowcroft B, Májek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophys J 2024; 123:307-316. [PMID: 38158654 PMCID: PMC10870171 DOI: 10.1016/j.bpj.2023.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/27/2023] [Accepted: 12/22/2023] [Indexed: 01/03/2024] Open
Abstract
Many cell functions require a concerted effort from multiple membrane proteins, for example, for signaling, cell division, and endocytosis. One contribution to their successful self-organization stems from the membrane deformations that these proteins induce. While the pairwise interaction potential of two membrane-deforming spheres has recently been measured, membrane-deformation-induced interactions have been predicted to be nonadditive, and hence their collective behavior cannot be deduced from this measurement. We here employ a colloidal model system consisting of adhesive spheres and giant unilamellar vesicles to test these predictions by measuring the interaction potential of the simplest case of three membrane-deforming, spherical particles. We quantify their interactions and arrangements and, for the first time, experimentally confirm and quantify the nonadditive nature of membrane-deformation-induced interactions. We furthermore conclude that there exist two favorable configurations on the membrane: (1) a linear and (2) a triangular arrangement of the three spheres. Using Monte Carlo simulations, we corroborate the experimentally observed energy minima and identify a lowering of the membrane deformation as the cause for the observed configurations. The high symmetry of the preferred arrangements for three particles suggests that arrangements of many membrane-deforming objects might follow simple rules.
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Affiliation(s)
- Ali Azadbakht
- Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, the Netherlands
| | - Billie Meadowcroft
- Institute of Science and Technology Austria, Klosterneuburg, Austria; Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Juraj Májek
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Anđela Šarić
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Daniela J Kraft
- Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, the Netherlands.
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3
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Bussi C, Mangiarotti A, Vanhille-Campos C, Aylan B, Pellegrino E, Athanasiadi N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. Publisher Correction: Stress granules plug and stabilize damaged endolysosomal membranes. Nature 2023; 624:E3. [PMID: 37993723 DOI: 10.1038/s41586-023-06882-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Affiliation(s)
| | | | - Christian Vanhille-Campos
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, UK
| | | | | | | | | | | | - Titus M Franzmann
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Anđela Šarić
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
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4
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Bussi C, Mangiarotti A, Vanhille-Campos C, Aylan B, Pellegrino E, Athanasiadi N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. Stress granules plug and stabilize damaged endolysosomal membranes. Nature 2023; 623:1062-1069. [PMID: 37968398 PMCID: PMC10686833 DOI: 10.1038/s41586-023-06726-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 10/09/2023] [Indexed: 11/17/2023]
Abstract
Endomembrane damage represents a form of stress that is detrimental for eukaryotic cells1,2. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis3-7. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for Mycobacterium tuberculosis, a human pathogen that exploits endomembrane damage to survive within the host.
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Affiliation(s)
| | | | - Christian Vanhille-Campos
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, UK
| | | | | | | | | | | | - Titus M Franzmann
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Dresden, Germany
| | - Anđela Šarić
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Rumiana Dimova
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
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5
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Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles. Nano Lett 2023; 23:4267-4273. [PMID: 37141427 DOI: 10.1021/acs.nanolett.3c00375] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Endocytosis is a key cellular process involved in the uptake of nutrients, pathogens, or the therapy of diseases. Most studies have focused on spherical objects, whereas biologically relevant shapes can be highly anisotropic. In this letter, we use an experimental model system based on Giant Unilamellar Vesicles (GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first stage of the passive endocytic process: engulfment of an anisotropic object by the membrane. Our model has specific ligand-receptor interactions realized by mobile receptors on the vesicles and immobile ligands on the particles. Through a series of experiments, theory, and molecular dynamics simulations, we quantify the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages of the wrapping pathway. We find that the strong curvature variation in the neck of the dumbbell as well as membrane tension are crucial in determining both the speed of wrapping and the final states.
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Affiliation(s)
- Ali Azadbakht
- Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Billie Meadowcroft
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Thijs Varkevisser
- Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
- Van der Waals-Zeeman Institute, Institute of Physics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, Netherlands
| | - Anđela Šarić
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Daniela J Kraft
- Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
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6
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Hurtig F, Burgers TC, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA, Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum B. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Sci Adv 2023; 9:eade5224. [PMID: 36921039 PMCID: PMC10017037 DOI: 10.1126/sciadv.ade5224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/14/2023] [Indexed: 05/13/2023]
Abstract
ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA-adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III-dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III-dependent membrane remodeling.
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Affiliation(s)
- Fredrik Hurtig
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Thomas C. Q. Burgers
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
| | - Alice Cezanne
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Xiuyun Jiang
- Laboratory of Soft Matter Physics, The Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Frank N. Mol
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
| | - Jovan Traparić
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Tim Nierhaus
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Lena Harker-Kirschneck
- University College London, Institute for the Physics of Living Systems, WC1E 6BT London, UK
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Anđela Šarić
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Rifka Vlijm
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
| | - Buzz Baum
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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7
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Araújo NAM, Janssen LMC, Barois T, Boffetta G, Cohen I, Corbetta A, Dauchot O, Dijkstra M, Durham WM, Dussutour A, Garnier S, Gelderblom H, Golestanian R, Isa L, Koenderink GH, Löwen H, Metzler R, Polin M, Royall CP, Šarić A, Sengupta A, Sykes C, Trianni V, Tuval I, Vogel N, Yeomans JM, Zuriguel I, Marin A, Volpe G. Steering self-organisation through confinement. Soft Matter 2023; 19:1695-1704. [PMID: 36779972 PMCID: PMC9977364 DOI: 10.1039/d2sm01562e] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from physics, materials science and robotics to biology, geophysics and astronomy. Recent research has highlighted how self-organisation can be both mediated and controlled by confinement. Confinement is an action over a system that limits its units' translational and rotational degrees of freedom, thus also influencing the system's phase space probability density; it can function as either a catalyst or inhibitor of self-organisation. Confinement can then become a means to actively steer the emergence or suppression of collective phenomena in space and time. Here, to provide a common framework and perspective for future research, we examine the role of confinement in the self-organisation of soft-matter systems and identify overarching scientific challenges that need to be addressed to harness its full scientific and technological potential in soft matter and related fields. By drawing analogies with other disciplines, this framework will accelerate a common deeper understanding of self-organisation and trigger the development of innovative strategies to steer it using confinement, with impact on, e.g., the design of smarter materials, tissue engineering for biomedicine and in guiding active matter.
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Affiliation(s)
- Nuno A M Araújo
- Departamento de Física, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal.
- Centro de Física Teórica e Computacional, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Liesbeth M C Janssen
- Department of Applied Physics and Science Education, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Thomas Barois
- University of Bordeaux, CNRS, LOMA, UMR 5798, F-33400, Talence, France
| | - Guido Boffetta
- Department of Physics and INFN, University of Torino, via Pietro Giuria 1, 10125, Torino, Italy
| | - Itai Cohen
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, New York, USA
- Laboratory of Atomic and Solid-State Physics, Cornell University, Ithaca, New York, USA
| | - Alessandro Corbetta
- Department of Applied Physics and Science Education, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands.
| | - Olivier Dauchot
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005, Paris, France
| | - Marjolein Dijkstra
- Soft condensed matter, Department of Physics, Debye institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC, Utrecht, The Netherlands
| | - William M Durham
- Department of Physics and Astronomy, University of Sheffield, Hounsfield Road, Sheffield, S3 7RH, UK
| | - Audrey Dussutour
- Research Centre on Animal Cognition (CRCA), Centre for Integrative Biology (CBI), Toulouse University, CNRS, UPS, Toulouse, 31062, AD, France
| | - Simon Garnier
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Hanneke Gelderblom
- Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
- Department of Applied Physics and J. M. Burgers Center for Fluid Dynamics, Eindhoven University of Technology, P.O. Box 513, 5600 MB, Eindhoven, The Netherlands
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPI-DS), 37077, Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Lucio Isa
- Laboratory for Soft Materials and Interfaces, Department of Materials, ETH Zürich, 8093, Zürich, Switzerland
| | - Gijsje H Koenderink
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2629 HZ, Delft, The Netherlands
| | - Hartmut Löwen
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstrasse 1, 40225, Düsseldorf, Germany
| | - Ralf Metzler
- Institute of Physics & Astronomy, University of Potsdam, Karl-Liebknecht-Str 24/25, D-14476, Potsdam-Golm, Germany
| | - Marco Polin
- Mediterranean Institute for Advanced Studies, IMEDEA UIB-CSIC, C/Miquel Marqués 21, 07190, Esporles, Spain
- Department of Physics, University of Warwick, Gibbet Hill road, CV4 7AL, Coventry, UK
| | - C Patrick Royall
- Gulliver UMR CNRS 7083, ESPCI Paris, Université PSL, 75005, Paris, France
| | - Anđela Šarić
- Institute of Science and Technology Austria, 3400, Klosterneuburg, Austria
| | - Anupam Sengupta
- Physics of Living Matter, Department of Physics and Materials Science, University of Luxembourg, 162 A, Avenue de la Faïencerie, L-1511, Luxembourg
| | - Cécile Sykes
- Laboratoire de Physique de lÉcole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université Paris Cité, F-75005, Paris, France
| | - Vito Trianni
- Institute of Cognitive Sciences and Technologies, CNR, Via San Martino della Battaglia 44, 00185, Rome, Italy
| | - Idan Tuval
- Mediterranean Institute for Advanced Studies, IMEDEA UIB-CSIC, C/Miquel Marqués 21, 07190, Esporles, Spain
| | - Nicolas Vogel
- Institute of Particle Technology, Friedrich-Alexander Universität Erlangen-Nürnberg, Cauerstrasse 4, 91058, Erlangen, Germany
| | - Julia M Yeomans
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford, OX1 3PU, UK
| | - Iker Zuriguel
- Departamento de Física y Matemática Aplicada, Facultad de Ciencias, Universidad de Navarra, Pamplona, Spain
| | - Alvaro Marin
- Physics of Fluids Group, Mesa+ Institute, Max Planck Center for Complex Fluid Dynamics and J. M. Burgers Center for Fluid Dynamics, University of Twente, 7500AE, Enschede, The Netherlands.
| | - Giorgio Volpe
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, UK.
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8
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Meadowcroft B, Palaia I, Pfitzner AK, Roux A, Baum B, Šarić A. Mechanochemical Rules for Shape-Shifting Filaments that Remodel Membranes. Phys Rev Lett 2022; 129:268101. [PMID: 36608212 DOI: 10.1103/physrevlett.129.268101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
The sequential exchange of filament composition to increase filament curvature was proposed as a mechanism for how some biological polymers deform and cut membranes. The relationship between the filament composition and its mechanical effect is lacking. We develop a kinetic model for the assembly of composite filaments that includes protein-membrane adhesion, filament mechanics and membrane mechanics. We identify the physical conditions for such a membrane remodeling and show this mechanism of sequential polymer assembly lowers the energetic barrier for membrane deformation.
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Affiliation(s)
- Billie Meadowcroft
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Ivan Palaia
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | | | - Aurélien Roux
- Biochemistry Department, University of Geneva, CH-1211 Geneva, Switzerland
- Swiss National Centre for Competence in Research Programme Chemical Biology, CH-1211 Geneva, Switzerland
| | - Buzz Baum
- MRC Laboratory of Molecular Biology, University of Cambridge, Cambridge CB2 1TN, United Kingdom
| | - Anđela Šarić
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
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9
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Jiang X, Harker-Kirschneck L, Vanhille-Campos C, Pfitzner AK, Lominadze E, Roux A, Baum B, Šarić A. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. PLoS Comput Biol 2022; 18:e1010586. [PMID: 36251703 PMCID: PMC9612822 DOI: 10.1371/journal.pcbi.1010586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 10/27/2022] [Accepted: 09/19/2022] [Indexed: 12/24/2022] Open
Abstract
ESCRT-III filaments are composite cytoskeletal polymers that can constrict and cut cell membranes from the inside of the membrane neck. Membrane-bound ESCRT-III filaments undergo a series of dramatic composition and geometry changes in the presence of an ATP-consuming Vps4 enzyme, which causes stepwise changes in the membrane morphology. We set out to understand the physical mechanisms involved in translating the changes in ESCRT-III polymer composition into membrane deformation. We have built a coarse-grained model in which ESCRT-III polymers of different geometries and mechanical properties are allowed to copolymerise and bind to a deformable membrane. By modelling ATP-driven stepwise depolymerisation of specific polymers, we identify mechanical regimes in which changes in filament composition trigger the associated membrane transition from a flat to a buckled state, and then to a tubule state that eventually undergoes scission to release a small cargo-loaded vesicle. We then characterise how the location and kinetics of polymer loss affects the extent of membrane deformation and the efficiency of membrane neck scission. Our results identify the near-minimal mechanical conditions for the operation of shape-shifting composite polymers that sever membrane necks.
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Affiliation(s)
- Xiuyun Jiang
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Lena Harker-Kirschneck
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Christian Vanhille-Campos
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Elene Lominadze
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Buzz Baum
- Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
- Institute of Science and Technology Austria, Klosterneuburg, Austria
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10
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Weiffert T, Meisl G, Curk S, Cukalevski R, Šarić A, Knowles TPJ, Linse S. Influence of denaturants on amyloid β42 aggregation kinetics. Front Neurosci 2022; 16:943355. [PMID: 36203800 PMCID: PMC9531139 DOI: 10.3389/fnins.2022.943355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/08/2022] [Indexed: 11/24/2022] Open
Abstract
Amyloid formation is linked to devastating neurodegenerative diseases, motivating detailed studies of the mechanisms of amyloid formation. For Aβ, the peptide associated with Alzheimer’s disease, the mechanism and rate of aggregation have been established for a range of variants and conditions in vitro and in bodily fluids. A key outstanding question is how the relative stabilities of monomers, fibrils and intermediates affect each step in the fibril formation process. By monitoring the kinetics of aggregation of Aβ42, in the presence of urea or guanidinium hydrochloride (GuHCl), we here determine the rates of the underlying microscopic steps and establish the importance of changes in relative stability induced by the presence of denaturant for each individual step. Denaturants shift the equilibrium towards the unfolded state of each species. We find that a non-ionic denaturant, urea, reduces the overall aggregation rate, and that the effect on nucleation is stronger than the effect on elongation. Urea reduces the rate of secondary nucleation by decreasing the coverage of fibril surfaces and the rate of nucleus formation. It also reduces the rate of primary nucleation, increasing its reaction order. The ionic denaturant, GuHCl, accelerates the aggregation at low denaturant concentrations and decelerates the aggregation at high denaturant concentrations. Below approximately 0.25 M GuHCl, the screening of repulsive electrostatic interactions between peptides by the charged denaturant dominates, leading to an increased aggregation rate. At higher GuHCl concentrations, the electrostatic repulsion is completely screened, and the denaturing effect dominates. The results illustrate how the differential effects of denaturants on stability of monomer, oligomer and fibril translate to differential effects on microscopic steps, with the rate of nucleation being most strongly reduced.
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Affiliation(s)
- Tanja Weiffert
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Georg Meisl
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
| | - Samo Curk
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - Risto Cukalevski
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Anđela Šarić
- Department of Physics and Astronomy, University College London, London, United Kingdom
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge, United Kingdom
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, United Kingdom
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, United Kingdom
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
- *Correspondence: Sara Linse,
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11
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Palaia I, Šarić A. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. J Chem Phys 2022; 156:194902. [PMID: 35597653 DOI: 10.1063/5.0087769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
By varying the concentration of molecules in the cytoplasm or on the membrane, cells can induce the formation of condensates and liquid droplets, similar to phase separation. Their thermodynamics, much studied, depends on the mutual interactions between microscopic constituents. Here, we focus on the kinetics and size control of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids, we model a system of two species of proteins, giving origin to specific heterotypic bonds. We find that concentrations, together with valence and bond strength, control both the size and the growth time rate of the clusters. In particular, if one species is in large excess, it gradually saturates the binding sites of the other species; the system then becomes kinetically arrested and cluster coarsening slows down or stops, thus yielding effective size selection. This phenomenology is observed both in solid and fluid clusters, which feature additional generic homotypic interactions and are reminiscent of the ones observed on biological membranes.
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Affiliation(s)
- Ivan Palaia
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Anđela Šarić
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
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12
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Harker-Kirschneck L, Hafner AE, Yao T, Vanhille-Campos C, Jiang X, Pulschen A, Hurtig F, Hryniuk D, Culley S, Henriques R, Baum B, Šarić A. Physical mechanisms of ESCRT-III-driven cell division. Proc Natl Acad Sci U S A 2022; 119:e2107763119. [PMID: 34983838 PMCID: PMC8740586 DOI: 10.1073/pnas.2107763119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/15/2021] [Indexed: 11/25/2022] Open
Abstract
Living systems propagate by undergoing rounds of cell growth and division. Cell division is at heart a physical process that requires mechanical forces, usually exerted by assemblies of cytoskeletal polymers. Here we developed a physical model for the ESCRT-III-mediated division of archaeal cells, which despite their structural simplicity share machinery and evolutionary origins with eukaryotes. By comparing the dynamics of simulations with data collected from live cell imaging experiments, we propose that this branch of life uses a previously unidentified division mechanism. Active changes in the curvature of elastic cytoskeletal filaments can lead to filament perversions and supercoiling, to drive ring constriction and deform the overlying membrane. Abscission is then completed following filament disassembly. The model was also used to explore how different adenosine triphosphate (ATP)-driven processes that govern the way the structure of the filament is changed likely impact the robustness and symmetry of the resulting division. Comparisons between midcell constriction dynamics in simulations and experiments reveal a good agreement with the process when changes in curvature are implemented at random positions along the filament, supporting this as a possible mechanism of ESCRT-III-dependent division in this system. Beyond archaea, this study pinpoints a general mechanism of cytokinesis based on dynamic coupling between a coiling filament and the membrane.
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Affiliation(s)
- Lena Harker-Kirschneck
- Department of Physics & Astronomy, University College London, London WC1E 6BT, United Kingdom
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Anne E Hafner
- Department of Physics & Astronomy, University College London, London WC1E 6BT, United Kingdom
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Tina Yao
- Department of Physics & Astronomy, University College London, London WC1E 6BT, United Kingdom
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
| | - Christian Vanhille-Campos
- Department of Physics & Astronomy, University College London, London WC1E 6BT, United Kingdom
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Xiuyun Jiang
- Department of Physics & Astronomy, University College London, London WC1E 6BT, United Kingdom
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Andre Pulschen
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge CB2 0QH, United Kingdom
| | - Fredrik Hurtig
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge CB2 0QH, United Kingdom
| | - Dawid Hryniuk
- Department of Physics & Astronomy, University College London, London WC1E 6BT, United Kingdom
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
| | - Siân Culley
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Ricardo Henriques
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Buzz Baum
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
- Medical Research Council Laboratory of Molecular Biology, University of Cambridge, Cambridge CB2 0QH, United Kingdom
| | - Anđela Šarić
- Department of Physics & Astronomy, University College London, London WC1E 6BT, United Kingdom;
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
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13
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Abstract
The transport of macromolecules and nanoscopic particles to a target cellular site is a crucial aspect in many physiological processes. This directional motion is generally controlled via active mechanical and chemical processes. Here we show, by means of molecular dynamics simulations and an analytical theory, that completely passive nanoparticles can exhibit directional motion when embedded in nonuniform mechanical environments. Specifically, we study the motion of a passive nanoparticle adhering to a mechanically nonuniform elastic membrane. We observe a nonmonotonic affinity of the particle to the membrane as a function of the membrane's rigidity, which results in the particle transport. This transport can be both up or down the rigidity gradient, depending on the absolute values of the rigidities that the gradient spans across. We conclude that rigidity gradients can be used to direct average motion of passive macromolecules and nanoparticles on deformable membranes, resulting in the preferential accumulation of the macromolecules in regions of certain mechanical properties.
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Affiliation(s)
- Ivan Palaia
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Alexandru Paraschiv
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Vincent E Debets
- Department of Applied Physics, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Cornelis Storm
- Department of Applied Physics, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
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14
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Abstract
The transport of macromolecules and nanoscopic particles to a target cellular site is a crucial aspect in many physiological processes. This directional motion is generally controlled via active mechanical and chemical processes. Here we show, by means of molecular dynamics simulations and an analytical theory, that completely passive nanoparticles can exhibit directional motion when embedded in nonuniform mechanical environments. Specifically, we study the motion of a passive nanoparticle adhering to a mechanically nonuniform elastic membrane. We observe a nonmonotonic affinity of the particle to the membrane as a function of the membrane's rigidity, which results in the particle transport. This transport can be both up or down the rigidity gradient, depending on the absolute values of the rigidities that the gradient spans across. We conclude that rigidity gradients can be used to direct average motion of passive macromolecules and nanoparticles on deformable membranes, resulting in the preferential accumulation of the macromolecules in regions of certain mechanical properties.
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Affiliation(s)
- Ivan Palaia
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Alexandru Paraschiv
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Vincent E Debets
- Department of Applied Physics, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Cornelis Storm
- Department of Applied Physics, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
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15
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Davis LK, Šarić A, Hoogenboom BW, Zilman A. Physical modeling of multivalent interactions in the nuclear pore complex. Biophys J 2021; 120:1565-1577. [PMID: 33617830 PMCID: PMC8204217 DOI: 10.1016/j.bpj.2021.01.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/25/2021] [Accepted: 01/27/2021] [Indexed: 01/10/2023] Open
Abstract
In the nuclear pore complex, intrinsically disordered proteins (FG Nups), along with their interactions with more globular proteins called nuclear transport receptors (NTRs), are vital to the selectivity of transport into and out of the cell nucleus. Although such interactions can be modeled at different levels of coarse graining, in vitro experimental data have been quantitatively described by minimal models that describe FG Nups as cohesive homogeneous polymers and NTRs as uniformly cohesive spheres, in which the heterogeneous effects have been smeared out. By definition, these minimal models do not account for the explicit heterogeneities in FG Nup sequences, essentially a string of cohesive and noncohesive polymer units, and at the NTR surface. Here, we develop computational and analytical models that do take into account such heterogeneity in a minimal fashion and compare them with experimental data on single-molecule interactions between FG Nups and NTRs. Overall, we find that the heterogeneous nature of FG Nups and NTRs does play a role in determining equilibrium binding properties but is of much greater significance when it comes to unbinding and binding kinetics. Using our models, we predict how binding equilibria and kinetics depend on the distribution of cohesive blocks in the FG Nup sequences and of the binding pockets at the NTR surface, with multivalency playing a key role. Finally, we observe that single-molecule binding kinetics has a rather minor influence on the diffusion of NTRs in polymer melts consisting of FG-Nup-like sequences.
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Affiliation(s)
- Luke K Davis
- Department of Physics and Astronomy; Institute for the Physics of Living Systems; London Centre for Nanotechnology, University College London, London, United Kingdom
| | - Anđela Šarić
- Department of Physics and Astronomy; Institute for the Physics of Living Systems
| | - Bart W Hoogenboom
- Department of Physics and Astronomy; Institute for the Physics of Living Systems; London Centre for Nanotechnology, University College London, London, United Kingdom.
| | - Anton Zilman
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Institute for Biomedical Engineering, Toronto, Ontario, Canada.
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16
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Zeng L, Palaia I, Šarić A, Su X. PLCγ1 promotes phase separation of T cell signaling components. J Cell Biol 2021; 220:212040. [PMID: 33929486 PMCID: PMC8094118 DOI: 10.1083/jcb.202009154] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 01/21/2021] [Accepted: 03/05/2021] [Indexed: 02/07/2023] Open
Abstract
The T cell receptor (TCR) pathway receives, processes, and amplifies the signal from pathogenic antigens to the activation of T cells. Although major components in this pathway have been identified, the knowledge on how individual components cooperate to effectively transduce signals remains limited. Phase separation emerges as a biophysical principle in organizing signaling molecules into liquid-like condensates. Here, we report that phospholipase Cγ1 (PLCγ1) promotes phase separation of LAT, a key adaptor protein in the TCR pathway. PLCγ1 directly cross-links LAT through its two SH2 domains. PLCγ1 also protects LAT from dephosphorylation by the phosphatase CD45 and promotes LAT-dependent ERK activation and SLP76 phosphorylation. Intriguingly, a nonmonotonic effect of PLCγ1 on LAT clustering was discovered. Computer simulations, based on patchy particles, revealed how the cluster size is regulated by protein compositions. Together, these results define a critical function of PLCγ1 in promoting phase separation of the LAT complex and TCR signal transduction.
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Affiliation(s)
- Longhui Zeng
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - Ivan Palaia
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, UK.,Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, UK.,Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Xiaolei Su
- Department of Cell Biology, Yale School of Medicine, New Haven, CT.,Yale Cancer Center, Yale University, New Haven, CT
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17
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Abstract
We study the effects of osmotic shocks on lipid vesicles via coarse-grained molecular dynamics simulations by explicitly considering the solute in the system. We find that depending on their nature (hypo- or hypertonic) such shocks can lead to bursting events or engulfing of external material into inner compartments, among other morphology transformations. We characterize the dynamics of these processes and observe a separation of time scales between the osmotic shock absorption and the shape relaxation. Our work consequently provides an insight into the dynamics of compartmentalization in vesicular systems as a result of osmotic shocks, which can be of interest in the context of early proto-cell development and proto-cell compartmentalisation.
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Affiliation(s)
- Christian Vanhille-Campos
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, UK.
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18
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Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. Influence of membrane-cortex linkers on the extrusion of membrane tubes. Biophys J 2021; 120:598-606. [PMID: 33460596 PMCID: PMC7896025 DOI: 10.1016/j.bpj.2020.12.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 12/10/2020] [Accepted: 12/30/2020] [Indexed: 01/06/2023] Open
Abstract
The cell membrane is an inhomogeneous system composed of phospholipids, sterols, carbohydrates, and proteins that can be directly attached to underlying cytoskeleton. The protein linkers between the membrane and the cytoskeleton are believed to have a profound effect on the mechanical properties of the cell membrane and its ability to reshape. Here, we investigate the role of membrane-cortex linkers on the extrusion of membrane tubes using computer simulations and experiments. In simulations, we find that the force for tube extrusion has a nonlinear dependence on the density of membrane-cortex attachments: at a range of low and intermediate linker densities, the force is not significantly influenced by the presence of the membrane-cortex attachments and resembles that of the bare membrane. For large concentrations of linkers, however, the force substantially increases compared with the bare membrane. In both cases, the linkers provided membrane tubes with increased stability against coalescence. We then pulled tubes from HEK cells using optical tweezers for varying expression levels of the membrane-cortex attachment protein Ezrin. In line with simulations, we observed that overexpression of Ezrin led to an increased extrusion force, while Ezrin depletion had a negligible effect on the force. Our results shed light on the importance of local protein rearrangements for membrane reshaping at nanoscopic scales.
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Affiliation(s)
- Alexandru Paraschiv
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom; MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Thibaut J Lagny
- Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France; Sorbonne Université, Paris, France; Institut Curie, PSL Research University CNRS UMR 144, Paris, France
| | - Christian Vanhille Campos
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom; MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Evelyne Coudrier
- Institut Curie, PSL Research University CNRS UMR 144, Paris, France
| | - Patricia Bassereau
- Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Paris, France; Sorbonne Université, Paris, France
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom; MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom.
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19
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Debets VE, Janssen LMC, Šarić A. Characterising the diffusion of biological nanoparticles on fluid and cross-linked membranes. Soft Matter 2020; 16:10628-10639. [PMID: 33084724 DOI: 10.1039/d0sm00712a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Tracing the motion of macromolecules, viruses, and nanoparticles adsorbed onto cell membranes is currently the most direct way of probing the complex dynamic interactions behind vital biological processes, including cell signalling, trafficking, and viral infection. The resulting trajectories are usually consistent with some type of anomalous diffusion, but the molecular origins behind the observed anomalous behaviour are usually not obvious. Here we use coarse-grained molecular dynamics simulations to help identify the physical mechanisms that can give rise to experimentally observed trajectories of nanoscopic objects moving on biological membranes. We find that diffusion on membranes of high fluidities typically results in normal diffusion of the adsorbed nanoparticle, irrespective of the concentration of receptors, receptor clustering, or multivalent interactions between the particle and membrane receptors. Gel-like membranes on the other hand result in anomalous diffusion of the particle, which becomes more pronounced at higher receptor concentrations. This anomalous diffusion is characterised by local particle trapping in the regions of high receptor concentrations and fast hopping between such regions. The normal diffusion is recovered in the limit where the gel membrane is saturated with receptors. We conclude that hindered receptor diffusivity can be a common reason behind the observed anomalous diffusion of viruses, vesicles, and nanoparticles adsorbed on cell and model membranes. Our results enable direct comparison with experiments and offer a new route for interpreting motility experiments on cell membranes.
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Affiliation(s)
- V E Debets
- Department of Applied Physics, Eindhoven University of Technology, Eindhoven, The Netherlands.
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20
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Forster JC, Krausser J, Vuyyuru MR, Baum B, Šarić A. Exploring the Design Rules for Efficient Membrane-Reshaping Nanostructures. Phys Rev Lett 2020; 125:228101. [PMID: 33315453 DOI: 10.1103/physrevlett.125.228101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 10/06/2020] [Indexed: 06/12/2023]
Abstract
In this study, we investigate the role of the surface patterning of nanostructures for cell membrane reshaping. To accomplish this, we combine an evolutionary algorithm with coarse-grained molecular dynamics simulations and explore the solution space of ligand patterns on a nanoparticle that promote efficient and reliable cell uptake. Surprisingly, we find that in the regime of low ligand number the best-performing structures are characterized by ligands arranged into long one-dimensional chains that pattern the surface of the particle. We show that these chains of ligands provide particles with high rotational freedom and they lower the free energy barrier for membrane crossing. Our approach reveals a set of nonintuitive design rules that can be used to inform artificial nanoparticle construction and the search for inhibitors of viral entry.
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Affiliation(s)
- Joel C Forster
- Department of Physics and Astronomy, University College London, WC1E 6BS London, United Kingdom
- Institute for the Physics of Living Systems, University College London, WC1E 6BS London, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, WC1E 6BS London, United Kingdom
| | - Johannes Krausser
- Department of Physics and Astronomy, University College London, WC1E 6BS London, United Kingdom
- Institute for the Physics of Living Systems, University College London, WC1E 6BS London, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, WC1E 6BS London, United Kingdom
| | - Manish R Vuyyuru
- Department of Physics and Astronomy, University College London, WC1E 6BS London, United Kingdom
- Institute for the Physics of Living Systems, University College London, WC1E 6BS London, United Kingdom
| | - Buzz Baum
- Institute for the Physics of Living Systems, University College London, WC1E 6BS London, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, WC1E 6BS London, United Kingdom
| | - Anđela Šarić
- Department of Physics and Astronomy, University College London, WC1E 6BS London, United Kingdom
- Institute for the Physics of Living Systems, University College London, WC1E 6BS London, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, WC1E 6BS London, United Kingdom
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21
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Tian X, Leite DM, Scarpa E, Nyberg S, Fullstone G, Forth J, Matias D, Apriceno A, Poma A, Duro-Castano A, Vuyyuru M, Harker-Kirschneck L, Šarić A, Zhang Z, Xiang P, Fang B, Tian Y, Luo L, Rizzello L, Battaglia G. On the shuttling across the blood-brain barrier via tubule formation: Mechanism and cargo avidity bias. Sci Adv 2020; 6:6/48/eabc4397. [PMID: 33246953 PMCID: PMC7695481 DOI: 10.1126/sciadv.abc4397] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 10/02/2020] [Indexed: 05/20/2023]
Abstract
The blood-brain barrier is made of polarized brain endothelial cells (BECs) phenotypically conditioned by the central nervous system (CNS). Although transport across BECs is of paramount importance for nutrient uptake as well as ridding the brain of waste products, the intracellular sorting mechanisms that regulate successful receptor-mediated transcytosis in BECs remain to be elucidated. Here, we used a synthetic multivalent system with tunable avidity to the low-density lipoprotein receptor-related protein 1 (LRP1) to investigate the mechanisms of transport across BECs. We used a combination of conventional and super-resolution microscopy, both in vivo and in vitro, accompanied with biophysical modeling of transport kinetics and membrane-bound interactions to elucidate the role of membrane-sculpting protein syndapin-2 on fast transport via tubule formation. We show that high-avidity cargo biases the LRP1 toward internalization associated with fast degradation, while mid-avidity augments the formation of syndapin-2 tubular carriers promoting a fast shuttling across.
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Affiliation(s)
- Xiaohe Tian
- School of Life Science, Anhui University, Hefei, P. R. China
- Department of Chemistry, Anhui University, Hefei, P. R. China
- Institute of Physical Science and Information Technology, Anhui University, Hefei, P. R. China
| | - Diana M Leite
- Department of Chemistry, University College London, London, UK
- Institute for the Physics of Living Systems, University College London, London, UK
| | - Edoardo Scarpa
- Department of Chemistry, University College London, London, UK
- Institute for the Physics of Living Systems, University College London, London, UK
- SomaNautix Ltd., London, UK
| | - Sophie Nyberg
- Department of Chemistry, University College London, London, UK
- Institute for the Physics of Living Systems, University College London, London, UK
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Gavin Fullstone
- Department of Chemistry, University College London, London, UK
- Institute for the Physics of Living Systems, University College London, London, UK
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
| | - Joe Forth
- Department of Chemistry, University College London, London, UK
- Institute for the Physics of Living Systems, University College London, London, UK
| | - Diana Matias
- Department of Chemistry, University College London, London, UK
- Institute for the Physics of Living Systems, University College London, London, UK
| | - Azzurra Apriceno
- Department of Chemistry, University College London, London, UK
- Institute for the Physics of Living Systems, University College London, London, UK
| | - Alessandro Poma
- Department of Chemistry, University College London, London, UK
- Institute for the Physics of Living Systems, University College London, London, UK
| | - Aroa Duro-Castano
- Department of Chemistry, University College London, London, UK
- Institute for the Physics of Living Systems, University College London, London, UK
| | - Manish Vuyyuru
- Institute for the Physics of Living Systems, University College London, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Lena Harker-Kirschneck
- Institute for the Physics of Living Systems, University College London, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Anđela Šarić
- Institute for the Physics of Living Systems, University College London, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Zhongping Zhang
- Institute of Physical Science and Information Technology, Anhui University, Hefei, P. R. China
- CAS Center for Excellence in Nanoscience, Institute of Intelligent Machines, Chinese Academy of Science, Hefei, China
| | - Pan Xiang
- School of Life Science, Anhui University, Hefei, P. R. China
| | - Bin Fang
- Department of Chemistry, Anhui University, Hefei, P. R. China
| | - Yupeng Tian
- Department of Chemistry, Anhui University, Hefei, P. R. China
| | - Lei Luo
- College of Pharmaceutical Sciences, Southwest University, Chongqing, P. R. China
| | - Loris Rizzello
- Department of Chemistry, University College London, London, UK
- Institute for the Physics of Living Systems, University College London, London, UK
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
| | - Giuseppe Battaglia
- Department of Chemistry, Anhui University, Hefei, P. R. China.
- Department of Chemistry, University College London, London, UK
- Institute for the Physics of Living Systems, University College London, London, UK
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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22
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Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. Modeling Fibrillogenesis of Collagen-Mimetic Molecules. Biophys J 2020; 119:1791-1799. [PMID: 33049216 DOI: 10.1016/j.bpj.2020.09.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/18/2020] [Accepted: 09/08/2020] [Indexed: 12/29/2022] Open
Abstract
One of the most robust examples of self-assembly in living organisms is the formation of collagen architectures. Collagen type I molecules are a crucial component of the extracellular matrix, where they self-assemble into fibrils of well-defined axial striped patterns. This striped fibrillar pattern is preserved across the animal kingdom and is important for the determination of cell phenotype, cell adhesion, and tissue regulation and signaling. The understanding of the physical processes that determine such a robust morphology of self-assembled collagen fibrils is currently almost completely missing. Here, we develop a minimal coarse-grained computational model to identify the physical principles of the assembly of collagen-mimetic molecules. We find that screened electrostatic interactions can drive the formation of collagen-like filaments of well-defined striped morphologies. The fibril axial pattern is determined solely by the distribution of charges on the molecule and is robust to the changes in protein concentration, monomer rigidity, and environmental conditions. We show that the striped fibrillar pattern cannot be easily predicted from the interactions between two monomers but is an emergent result of multibody interactions. Our results can help address collagen remodeling in diseases and aging and guide the design of collagen scaffolds for biotechnological applications.
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Affiliation(s)
- Anne E Hafner
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom; MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom
| | - Noemi G Gyori
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Ciaran A Bench
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Luke K Davis
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom; London Centre for Nanotechnology, University College London, London, United Kingdom
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom; MRC Laboratory for Molecular Cell Biology, University College London, London, United Kingdom.
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23
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Pfitzner AK, Mercier V, Jiang X, Moser von Filseck J, Baum B, Šarić A, Roux A. An ESCRT-III Polymerization Sequence Drives Membrane Deformation and Fission. Cell 2020; 182:1140-1155.e18. [PMID: 32814015 PMCID: PMC7479521 DOI: 10.1016/j.cell.2020.07.021] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 05/04/2020] [Accepted: 07/15/2020] [Indexed: 01/02/2023]
Abstract
The endosomal sorting complex required for transport-III (ESCRT-III) catalyzes membrane fission from within membrane necks, a process that is essential for many cellular functions, from cell division to lysosome degradation and autophagy. How it breaks membranes, though, remains unknown. Here, we characterize a sequential polymerization of ESCRT-III subunits that, driven by a recruitment cascade and by continuous subunit-turnover powered by the ATPase Vps4, induces membrane deformation and fission. During this process, the exchange of Vps24 for Did2 induces a tilt in the polymer-membrane interface, which triggers transition from flat spiral polymers to helical filament to drive the formation of membrane protrusions, and ends with the formation of a highly constricted Did2-Ist1 co-polymer that we show is competent to promote fission when bound on the inside of membrane necks. Overall, our results suggest a mechanism of stepwise changes in ESCRT-III filament structure and mechanical properties via exchange of the filament subunits to catalyze ESCRT-III activity.
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Affiliation(s)
| | - Vincent Mercier
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland; National Center of Competence in Research in Chemical Biology, University of Geneva, 1211 Geneva, Switzerland
| | - Xiuyun Jiang
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK; Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK; MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Buzz Baum
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK; MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Anđela Šarić
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK; Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK; MRC Laboratory for Molecular Cell Biology, University College London, Gower Street, London WC1E 6BT, UK
| | - Aurélien Roux
- Department of Biochemistry, University of Geneva, 1211 Geneva, Switzerland; National Center of Competence in Research in Chemical Biology, University of Geneva, 1211 Geneva, Switzerland.
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24
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Tarrason Risa G, Hurtig F, Bray S, Hafner AE, Harker-Kirschneck L, Faull P, Davis C, Papatziamou D, Mutavchiev DR, Fan C, Meneguello L, Arashiro Pulschen A, Dey G, Culley S, Kilkenny M, Souza DP, Pellegrini L, de Bruin RAM, Henriques R, Snijders AP, Šarić A, Lindås AC, Robinson NP, Baum B. The proteasome controls ESCRT-III-mediated cell division in an archaeon. Science 2020; 369:eaaz2532. [PMID: 32764038 PMCID: PMC7116001 DOI: 10.1126/science.aaz2532] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 03/30/2020] [Accepted: 06/11/2020] [Indexed: 12/28/2022]
Abstract
Sulfolobus acidocaldarius is the closest experimentally tractable archaeal relative of eukaryotes and, despite lacking obvious cyclin-dependent kinase and cyclin homologs, has an ordered eukaryote-like cell cycle with distinct phases of DNA replication and division. Here, in exploring the mechanism of cell division in S. acidocaldarius, we identify a role for the archaeal proteasome in regulating the transition from the end of one cell cycle to the beginning of the next. Further, we identify the archaeal ESCRT-III homolog, CdvB, as a key target of the proteasome and show that its degradation triggers division by allowing constriction of the CdvB1:CdvB2 ESCRT-III division ring. These findings offer a minimal mechanism for ESCRT-III-mediated membrane remodeling and point to a conserved role for the proteasome in eukaryotic and archaeal cell cycle control.
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Affiliation(s)
- Gabriel Tarrason Risa
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Fredrik Hurtig
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Sian Bray
- Biochemistry Department, University of Cambridge, Cambridge, UK
| | - Anne E Hafner
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
- Institute for the Physics of Living Systems, UCL, London, UK
- Department of Physics and Astronomy, UCL, London, UK
| | - Lena Harker-Kirschneck
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
- Institute for the Physics of Living Systems, UCL, London, UK
- Department of Physics and Astronomy, UCL, London, UK
| | - Peter Faull
- Proteomics Platform, The Francis Crick Institute, London, UK
| | - Colin Davis
- Proteomics Platform, The Francis Crick Institute, London, UK
| | - Dimitra Papatziamou
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK
| | - Delyan R Mutavchiev
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Catherine Fan
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Leticia Meneguello
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | | | - Gautam Dey
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Siân Culley
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Mairi Kilkenny
- Biochemistry Department, University of Cambridge, Cambridge, UK
| | - Diorge P Souza
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Luca Pellegrini
- Biochemistry Department, University of Cambridge, Cambridge, UK
| | - Robertus A M de Bruin
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | - Ricardo Henriques
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
| | | | - Anđela Šarić
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK
- Institute for the Physics of Living Systems, UCL, London, UK
- Department of Physics and Astronomy, UCL, London, UK
| | - Ann-Christin Lindås
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Nicholas P Robinson
- Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK.
| | - Buzz Baum
- MRC-Laboratory for Molecular Cell Biology, University College London (UCL), London, UK.
- Institute for the Physics of Living Systems, UCL, London, UK
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25
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Dear AJ, Meisl G, Šarić A, Michaels TCT, Kjaergaard M, Linse S, Knowles TPJ. Identification of on- and off-pathway oligomers in amyloid fibril formation. Chem Sci 2020; 11:6236-6247. [PMID: 32953019 PMCID: PMC7480182 DOI: 10.1039/c9sc06501f] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 05/26/2020] [Indexed: 12/22/2022] Open
Abstract
A general non-binary definition for on- and off-pathway intermediates is developed, enabling comparison of amyloid oligomers' contributions to fibril formation.
The misfolding and aberrant aggregation of proteins into fibrillar structures is a key factor in some of the most prevalent human diseases, including diabetes and dementia. Low molecular weight oligomers are thought to be a central factor in the pathology of these diseases, as well as critical intermediates in the fibril formation process, and as such have received much recent attention. Moreover, on-pathway oligomeric intermediates are potential targets for therapeutic strategies aimed at interrupting the fibril formation process. However, a consistent framework for distinguishing on-pathway from off-pathway oligomers has hitherto been lacking and, in particular, no consensus definition of on- and off-pathway oligomers is available. In this paper, we argue that a non-binary definition of oligomers' contribution to fibril-forming pathways may be more informative and we suggest a quantitative framework, in which each oligomeric species is assigned a value between 0 and 1 describing its relative contribution to the formation of fibrils. First, we clarify the distinction between oligomers and fibrils, and then we use the formalism of reaction networks to develop a general definition for on-pathway oligomers, that yields meaningful classifications in the context of amyloid formation. By applying these concepts to Monte Carlo simulations of a minimal aggregating system, and by revisiting several previous studies of amyloid oligomers in light of our new framework, we demonstrate how to perform these classifications in practice. For each oligomeric species we obtain the degree to which it is on-pathway, highlighting the most effective pharmaceutical targets for the inhibition of amyloid fibril formation.
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Affiliation(s)
- Alexander J Dear
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK.,Department of Biochemistry and Structural Biology , Lund Univerisity , SE22100 Lund , Sweden .
| | - Georg Meisl
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
| | - Anđela Šarić
- Department of Physics and Astronomy , Institute for the Physics of Living Systems , University College London , Gower Street , London WC1E 6BT , UK.,MRC Laboratory for Molecular Cell Biology , University College London , Gower St, WC1E 6BT , London , UK
| | - Thomas C T Michaels
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK.,Paulson School of Engineering and Applied Sciences , Harvard University , Cambridge , MA 02138 , USA
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics , Aarhus University , Høegh-Guldbergs Gade 6B , DK-8000 Aarhus C , Denmark
| | - Sara Linse
- Department of Biochemistry and Structural Biology , Lund Univerisity , SE22100 Lund , Sweden .
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK.,Cavendish Laboratory , Department of Physics , University of Cambridge , J J Thomson Avenue , Cambridge CB3 0HE , UK .
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26
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Davis LK, Ford IJ, Šarić A, Hoogenboom BW. Intrinsically disordered nuclear pore proteins show ideal-polymer morphologies and dynamics. Phys Rev E 2020; 101:022420. [PMID: 32168597 DOI: 10.1103/physreve.101.022420] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 02/03/2020] [Indexed: 06/10/2023]
Abstract
In the nuclear pore complex, intrinsically disordered nuclear pore proteins (FG Nups) form a selective barrier for transport into and out of the cell nucleus, in a way that remains poorly understood. The collective FG Nup behavior has long been conceptualized either as a polymer brush, dominated by entropic and excluded-volume (repulsive) interactions, or as a hydrogel, dominated by cohesive (attractive) interactions between FG Nups. Here we compare mesoscale computational simulations with a wide range of experimental data to demonstrate that FG Nups are at the crossover point between these two regimes. Specifically, we find that repulsive and attractive interactions are balanced, resulting in morphologies and dynamics that are close to those of ideal polymer chains. We demonstrate that this property of FG Nups yields sufficient cohesion to seal the transport barrier, and yet maintains fast dynamics at the molecular scale, permitting the rapid polymer rearrangements needed for transport events.
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Affiliation(s)
- Luke K Davis
- London Centre for Nanotechnology, University College London, London WC1H OAH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
| | - Ian J Ford
- London Centre for Nanotechnology, University College London, London WC1H OAH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
| | - Anđela Šarić
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
| | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London WC1H OAH, United Kingdom
- Department of Physics and Astronomy, University College London, London WC1E 6BT, United Kingdom
- Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
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27
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Paraschiv A, Hegde S, Ganti R, Pilizota T, Šarić A. Dynamic Clustering Regulates Activity of Mechanosensitive Membrane Channels. Phys Rev Lett 2020; 124:048102. [PMID: 32058787 DOI: 10.1103/physrevlett.124.048102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Indexed: 06/10/2023]
Abstract
Experiments have suggested that bacterial mechanosensitive channels separate into 2D clusters, the role of which is unclear. By developing a coarse-grained computer model we find that clustering promotes the channel closure, which is highly dependent on the channel concentration and membrane stress. This behaviour yields a tightly regulated gating system, whereby at high tensions channels gate individually, and at lower tensions the channels spontaneously aggregate and inactivate. We implement this positive feedback into the model for cell volume regulation, and find that the channel clustering protects the cell against excessive loss of cytoplasmic content.
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Affiliation(s)
- Alexandru Paraschiv
- Department of Physics and Astronomy, Institute for the Physics of Living Systems University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
| | - Smitha Hegde
- Centre for Synthetic and Systems Biology University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Raman Ganti
- Institute for Medical Engineering and Science Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Teuta Pilizota
- Centre for Synthetic and Systems Biology University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems University College London, London WC1E 6BT, United Kingdom
- MRC Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, United Kingdom
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28
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Hafner AE, Krausser J, Šarić A. Minimal coarse-grained models for molecular self-organisation in biology. Curr Opin Struct Biol 2019; 58:43-52. [PMID: 31226513 DOI: 10.1016/j.sbi.2019.05.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/13/2019] [Accepted: 05/19/2019] [Indexed: 01/19/2023]
Abstract
The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, in which a whole macromolecule is represented by a small number of particles, can be of great value in identifying the main driving forces behind self-organisation in cell biology. Such models can incorporate data from both molecular and continuum scales, and their results can be directly compared to experiments. Here we review the state of the art of models for studying the formation and biological function of macromolecular assemblies in living organisms. We outline the key ingredients of each model and their main findings. We illustrate the contribution of this class of simulations to identifying the physical mechanisms behind life and diseases, and discuss their future developments.
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Affiliation(s)
- Anne E Hafner
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, UK
| | - Johannes Krausser
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, UK
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, UK.
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29
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Dear AJ, Šarić A, Michaels TCT, Dobson CM, Knowles TPJ. Statistical Mechanics of Globular Oligomer Formation by Protein Molecules. J Phys Chem B 2018; 122:11721-11730. [PMID: 30336667 DOI: 10.1021/acs.jpcb.8b07805] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The misfolding and aggregation of proteins into linear fibrils is widespread in human biology, for example, in connection with amyloid formation and the pathology of neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. The oligomeric species that are formed in the early stages of protein aggregation are of great interest, having been linked with the cellular toxicity associated with these conditions. However, these species are not characterized in any detail experimentally, and their properties are not well understood. Many of these species have been found to have approximately spherical morphology and to be held together by hydrophobic interactions. We present here an analytical statistical mechanical model of globular oligomer formation from simple idealized amphiphilic protein monomers and show that this correlates well with Monte Carlo simulations of oligomer formation. We identify the controlling parameters of the model, which are closely related to simple quantities that may be fitted directly from experiment. We predict that globular oligomers are unlikely to form at equilibrium in many polypeptide systems but instead form transiently in the early stages of amyloid formation. We contrast the globular model of oligomer formation to a well-established model of linear oligomer formation, highlighting how the differing ensemble properties of linear and globular oligomers offer a potential strategy for characterizing oligomers from experimental measurements.
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Affiliation(s)
- Alexander J Dear
- Centre for Misfolding Diseases, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems , University College London , Gower Street , London WC1E 6BT , U.K
| | - Thomas C T Michaels
- Centre for Misfolding Diseases, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.,Paulson School of Engineering and Applied Sciences , Harvard University , Cambridge , Massachusetts 02138 , United States
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , U.K.,Cavendish Laboratory, Department of Physics , University of Cambridge , JJ Thomson Avenue , Cambridge CB3 0HE , U.K
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30
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Abstract
Biological membranes typically contain a large number of different components dispersed in small concentrations in the main membrane phase, including proteins, sugars, and lipids of varying geometrical properties. Most of these components do not bind the cargo. Here, we show that such "inert" components can be crucial for the precise control of cross-membrane trafficking. Using a statistical mechanics model and molecular dynamics simulations, we demonstrate that the presence of inert membrane components of small isotropic curvatures dramatically influences cargo endocytosis, even if the total spontaneous curvature of such a membrane remains unchanged. Curved lipids, such as cholesterol, as well as asymmetrically included proteins and tethered sugars can, therefore, actively participate in the control of the membrane trafficking of nanoscopic cargo. We find that even a low-level expression of curved inert membrane components can determine the membrane selectivity toward the cargo size and can be used to selectively target membranes of certain compositions. Our results suggest a robust and general method of controlling cargo trafficking by adjusting the membrane composition without needing to alter the concentration of receptors or the average membrane curvature. This study indicates that cells can prepare for any trafficking event by incorporating curved inert components in either of the membrane leaflets.
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Affiliation(s)
- Tine Curk
- Institute of Physics , Chinese Academy of Sciences , Beijing , 100864 China
- Faculty of Chemistry and Chemical Engineering , University of Maribor , Maribor , 2000 Slovenia
| | - Peter Wirnsberger
- Department of Chemistry , University of Cambridge , Cambridge , CB2 1EW United Kingdom
| | - Jure Dobnikar
- Institute of Physics , Chinese Academy of Sciences , Beijing , 100864 China
- Department of Chemistry , University of Cambridge , Cambridge , CB2 1EW United Kingdom
| | - Daan Frenkel
- Department of Chemistry , University of Cambridge , Cambridge , CB2 1EW United Kingdom
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems , University College London , London , WC1E 6BT United Kingdom
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31
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Affiliation(s)
- Thomas C. T. Michaels
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Lucie X. Liu
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Samo Curk
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, UK
- Department of Physics, Faculty of Natural Sciences and Mathematics, University of Maribor, Maribor, Slovenia
| | - Peter G. Bolhuis
- van't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, UK
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK
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32
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Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM, Knowles TPJ. Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation. Annu Rev Phys Chem 2018; 69:273-298. [PMID: 29490200 DOI: 10.1146/annurev-physchem-050317-021322] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation.
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Affiliation(s)
- Thomas C T Michaels
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; .,Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Anđela Šarić
- Department of Physics and Astronomy, and Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
| | - Johnny Habchi
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Sean Chia
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Georg Meisl
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; .,Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 1HE, United Kingdom; ,
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33
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Cohen SIA, Cukalevski R, Michaels TCT, Šarić A, Törnquist M, Vendruscolo M, Dobson CM, Buell AK, Knowles TPJ, Linse S. Distinct thermodynamic signatures of oligomer generation in the aggregation of the amyloid-β peptide. Nat Chem 2018; 10:523-531. [PMID: 29581486 PMCID: PMC5911155 DOI: 10.1038/s41557-018-0023-x] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 02/06/2018] [Indexed: 12/23/2022]
Abstract
Mapping energy landscapes has proved to be a powerful tool for studying reaction mechanisms. Many complex biomolecular assembly processes, however, have remained challenging to access using this approach, including the aggregation of peptides and proteins into amyloid fibrils implicated in various disorders. Here we generalize the strategy used to probe energy landscapes in protein folding to determine the activation energies and entropies that characterise each of the molecular steps in the aggregation of the amyloid-β peptide (Aβ42), which is associated with Alzheimer’s disease. Our results reveal that interactions between monomeric Aβ and amyloid fibrils during fibril-dependent nucleation fundamentally reverse the thermodynamic signature of this process relative to primary nucleation, even though both processes generate aggregates from soluble peptides. By mapping the energetic and entropic contributions along the reactive trajectories, we show that the catalytic efficiency of Aβ42 fibril surfaces results from the enthalpic stabilisation of adsorbing peptides in conformations amenable to nucleation, driving a dramatic lowering of the activation energy barrier for nucleation.
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Affiliation(s)
- Samuel I A Cohen
- Department of Chemistry and Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Risto Cukalevski
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Lund, Sweden
| | - Thomas C T Michaels
- Department of Chemistry and Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK.,Paulson School of Engineering and Applied Science, Harvard University, Cambridge, MA, USA
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, UK
| | - Mattias Törnquist
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Lund, Sweden
| | - Michele Vendruscolo
- Department of Chemistry and Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Christopher M Dobson
- Department of Chemistry and Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK
| | - Alexander K Buell
- Institute of Physical Biology, University of Duesseldorf, Duesseldorf, Germany
| | - Tuomas P J Knowles
- Department of Chemistry and Centre for Misfolding Diseases, University of Cambridge, Cambridge, UK. .,Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge, UK.
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Lund, Sweden.
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Fisher PDE, Shen Q, Akpinar B, Davis LK, Chung KKH, Baddeley D, Šarić A, Melia TJ, Hoogenboom BW, Lin C, Lusk CP. A Programmable DNA Origami Platform for Organizing Intrinsically Disordered Nucleoporins within Nanopore Confinement. ACS Nano 2018; 12:1508-1518. [PMID: 29350911 PMCID: PMC5834394 DOI: 10.1021/acsnano.7b08044] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nuclear pore complexes (NPCs) form gateways that control molecular exchange between the nucleus and the cytoplasm. They impose a diffusion barrier to macromolecules and enable the selective transport of nuclear transport receptors with bound cargo. The underlying mechanisms that establish these permeability properties remain to be fully elucidated but require unstructured nuclear pore proteins rich in Phe-Gly (FG)-repeat domains of different types, such as FxFG and GLFG. While physical modeling and in vitro approaches have provided a framework for explaining how the FG network contributes to the barrier and transport properties of the NPC, it remains unknown whether the number and/or the spatial positioning of different FG-domains along a cylindrical, ∼40 nm diameter transport channel contributes to their collective properties and function. To begin to answer these questions, we have used DNA origami to build a cylinder that mimics the dimensions of the central transport channel and can house a specified number of FG-domains at specific positions with easily tunable design parameters, such as grafting density and topology. We find the overall morphology of the FG-domain assemblies to be dependent on their chemical composition, determined by the type and density of FG-repeat, and on their architectural confinement provided by the DNA cylinder, largely consistent with here presented molecular dynamics simulations based on a coarse-grained polymer model. In addition, high-speed atomic force microscopy reveals local and reversible FG-domain condensation that transiently occludes the lumen of the DNA central channel mimics, suggestive of how the NPC might establish its permeability properties.
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Affiliation(s)
- Patrick D. Ellis Fisher
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Qi Shen
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Bernice Akpinar
- Department of Chemistry, Imperial College London, London, SW7 2AZ, UK
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
| | - Luke K. Davis
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Kenny Kwok Hin Chung
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - David Baddeley
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
| | - Anđela Šarić
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Thomas J. Melia
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
| | - Bart W. Hoogenboom
- London Centre for Nanotechnology, University College London, 17–19 Gordon Street, London WC1H 0AH, UK
- Department of Physics and Astronomy, University College London, Gower Street, London WC1E 6BT, UK
- Institute for the Physics of Living Systems, University College London, Gower Street, London WC1E 6BT, UK
| | - Chenxiang Lin
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Nanobiology Institute, Yale University, West Haven, Connecticut 06516, USA
- Correspondence to: Chenxiang Lin: or C. Patrick Lusk:
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, Connecticut 06520, USA
- Correspondence to: Chenxiang Lin: or C. Patrick Lusk:
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35
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Simunovic M, Šarić A, Henderson JM, Lee KYC, Voth GA. Long-Range Organization of Membrane-Curving Proteins. ACS Cent Sci 2017; 3:1246-1253. [PMID: 29296664 PMCID: PMC5746856 DOI: 10.1021/acscentsci.7b00392] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Indexed: 05/02/2023]
Abstract
Biological membranes have a central role in mediating the organization of membrane-curving proteins, a dynamic process that has proven to be challenging to probe experimentally. Using atomic force microscopy, we capture the hierarchically organized assemblies of Bin/amphiphysin/Rvs (BAR) proteins on supported lipid membranes. Their structure reveals distinct long linear aggregates of proteins, regularly spaced by up to 300 nm. Employing accurate free-energy calculations from large-scale coarse-grained computer simulations, we found that the membrane mediates the interaction among protein filaments as a combination of short- and long-ranged interactions. The long-ranged component acts at strikingly long distances, giving rise to a variety of micron-sized ordered patterns. This mechanism may contribute to the long-ranged spatiotemporal control of membrane remodeling by proteins in the cell.
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Affiliation(s)
- Mijo Simunovic
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Anđela Šarić
- Department
of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, Gower Street, London, WC1E 6BT, U.K.
| | - J. Michael Henderson
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Ka Yee C. Lee
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Gregory A. Voth
- Department
of Chemistry, Institute for Biophysical Dynamics, and James Franck
Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
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36
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Helle SCJ, Feng Q, Aebersold MJ, Hirt L, Grüter RR, Vahid A, Sirianni A, Mostowy S, Snedeker JG, Šarić A, Idema T, Zambelli T, Kornmann B. Mechanical force induces mitochondrial fission. eLife 2017; 6. [PMID: 29119945 PMCID: PMC5679753 DOI: 10.7554/elife.30292] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 10/28/2017] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic cells are densely packed with macromolecular complexes and intertwining organelles, continually transported and reshaped. Intriguingly, organelles avoid clashing and entangling with each other in such limited space. Mitochondria form extensive networks constantly remodeled by fission and fusion. Here, we show that mitochondrial fission is triggered by mechanical forces. Mechano-stimulation of mitochondria – via encounter with motile intracellular pathogens, via external pressure applied by an atomic force microscope, or via cell migration across uneven microsurfaces – results in the recruitment of the mitochondrial fission machinery, and subsequent division. We propose that MFF, owing to affinity for narrow mitochondria, acts as a membrane-bound force sensor to recruit the fission machinery to mechanically strained sites. Thus, mitochondria adapt to the environment by sensing and responding to biomechanical cues. Our findings that mechanical triggers can be coupled to biochemical responses in membrane dynamics may explain how organelles orderly cohabit in the crowded cytoplasm.
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Affiliation(s)
| | - Qian Feng
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Mathias J Aebersold
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - Luca Hirt
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - Raphael R Grüter
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - Afshin Vahid
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Andrea Sirianni
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Serge Mostowy
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom
| | - Jess G Snedeker
- Balgrist University Hospital, University of Zurich, Zurich, Switzerland.,Institute for Biomechanics, ETH Zurich, Zurich, Switzerland
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Timon Idema
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, Netherlands
| | - Tomaso Zambelli
- Laboratory of Biosensors and Bioelectronics, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
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37
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Meisl G, Rajah L, Cohen SAI, Pfammatter M, Šarić A, Hellstrand E, Buell AK, Aguzzi A, Linse S, Vendruscolo M, Dobson CM, Knowles TPJ. Scaling behaviour and rate-determining steps in filamentous self-assembly. Chem Sci 2017; 8:7087-7097. [PMID: 29147538 PMCID: PMC5637470 DOI: 10.1039/c7sc01965c] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 07/31/2017] [Indexed: 12/30/2022] Open
Abstract
The formation of filaments from naturally occurring protein molecules is a process at the core of a range of functional and aberrant biological phenomena, such as the assembly of the cytoskeleton or the appearance of aggregates in Alzheimer's disease. The macroscopic behaviour associated with such processes is remarkably diverse, ranging from simple nucleated growth to highly cooperative processes with a well-defined lagtime. Thus, conventionally, different molecular mechanisms have been used to explain the self-assembly of different proteins. Here we show that this range of behaviour can be quantitatively captured by a single unifying Petri net that describes filamentous growth in terms of aggregate number and aggregate mass concentrations. By considering general features associated with a particular network connectivity, we are able to establish directly the rate-determining steps of the overall aggregation reaction from the system's scaling behaviour. We illustrate the power of this framework on a range of different experimental and simulated aggregating systems. The approach is general and will be applicable to any future extensions of the reaction network of filamentous self-assembly.
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Affiliation(s)
- Georg Meisl
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK . ;
| | - Luke Rajah
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK . ;
| | - Samuel A I Cohen
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK . ;
| | - Manuela Pfammatter
- Institute of Neuropathology , University Hospital of Zurich , Schmelzbergstrasse 12 , 8091 Zurich , Switzerland
| | - Anđela Šarić
- Department of Physics and Astronomy , Institute for the Physics of Living Systems , University College London , London WC1E 6BT , UK
| | - Erik Hellstrand
- Chemistry Department and Molecular Protein Science , Lund University , P. O. Box 124 , SE221 00 Lund , Sweden
| | - Alexander K Buell
- Institute of Physical Biology , University of Duesseldorf , Universitaetsstr. 1 , 40225 Duesseldorf , Germany
| | - Adriano Aguzzi
- Institute of Neuropathology , University Hospital of Zurich , Schmelzbergstrasse 12 , 8091 Zurich , Switzerland
| | - Sara Linse
- Chemistry Department and Molecular Protein Science , Lund University , P. O. Box 124 , SE221 00 Lund , Sweden
| | - Michele Vendruscolo
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK . ;
| | - Christopher M Dobson
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK . ;
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK . ;
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Abstract
Cellular membranes exhibit a large variety of shapes, strongly coupled to their function. Many biological processes involve dynamic reshaping of membranes, usually mediated by proteins. This interaction works both ways: while proteins influence the membrane shape, the membrane shape affects the interactions between the proteins. To study these membrane-mediated interactions on closed and anisotropically curved membranes, we use colloids adhered to ellipsoidal membrane vesicles as a model system. We find that two particles on a closed system always attract each other, and tend to align with the direction of largest curvature. Multiple particles form arcs, or, at large enough numbers, a complete ring surrounding the vesicle in its equatorial plane. The resulting vesicle shape resembles a snowman. Our results indicate that these physical interactions on membranes with anisotropic shapes can be exploited by cells to drive macromolecules to preferred regions of cellular or intracellular membranes, and utilized to initiate dynamic processes such as cell division. The same principle could be used to find the midplane of an artificial vesicle, as a first step towards dividing it into two equal parts.
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Affiliation(s)
- Afshin Vahid
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
| | - Anđela Šarić
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Timon Idema
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands.
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39
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Šarić A, Michaels TCT, Zaccone A, Knowles TPJ, Frenkel D. Kinetics of spontaneous filament nucleation via oligomers: Insights from theory and simulation. J Chem Phys 2016; 145:211926. [DOI: 10.1063/1.4965040] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Anđela Šarić
- Department of Physics and Astronomy, Institute for the
Physics of Living Systems, University College London,
Gower Street, London WC1E 6BT, United Kingdom
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Thomas C. T. Michaels
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Paulson School of Engineering and Applied Sciences,
Harvard University, Cambridge, Massachusetts 02138,
USA
| | - Alessio Zaccone
- Department of Chemical Engineering, University of Cambridge, Pembroke St., Cambridge CB2 3RA, United Kingdom
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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40
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Bachmann SJ, Kotar J, Parolini L, Šarić A, Cicuta P, Di Michele L, Mognetti BM. Melting transition in lipid vesicles functionalised by mobile DNA linkers. Soft Matter 2016; 12:7804-7817. [PMID: 27722701 DOI: 10.1039/c6sm01515h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We study phase behaviour of lipid-bilayer vesicles functionalised by ligand-receptor complexes made of synthetic DNA by introducing a modelling framework and a dedicated experimental platform. In particular, we perform Monte Carlo simulations that combine a coarse grained description of the lipid bilayer with state of art analytical models for multivalent ligand-receptor interactions. Using density of state calculations, we derive the partition function in pairs of vesicles and compute the number of ligand-receptor bonds as a function of temperature. Numerical results are compared to microscopy and fluorimetry experiments on large unilamellar vesicles decorated by DNA linkers carrying complementary overhangs. We find that vesicle aggregation is suppressed when the total number of linkers falls below a threshold value. Within the model proposed here, this is due to the higher configurational costs required to form inter-vesicle bridges as compared to intra-vesicle loops, which are in turn related to membrane deformability. Our findings and our numerical/experimental methodologies are applicable to the rational design of liposomes used as functional materials and drug delivery applications, as well as to study inter-membrane interactions in living systems, such as cell adhesion.
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Affiliation(s)
- Stephan Jan Bachmann
- Université Libre de Bruxelles (ULB), Department of Physics, Interdisciplinary Center for Nonlinear Phenomena and Complex Systems & Service de Physique des Systèmes Complexes et Mécanique Statistique, Campus Plaine, CP 231, Blvd du Triomphe, B-1050 Brussels, Belgium.
| | - Jurij Kotar
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| | - Lucia Parolini
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| | - Anđela Šarić
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK and Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, WC1E 6BT, UK
| | - Pietro Cicuta
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| | - Lorenzo Di Michele
- Biological and Soft Systems, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, UK.
| | - Bortolo Matteo Mognetti
- Université Libre de Bruxelles (ULB), Department of Physics, Interdisciplinary Center for Nonlinear Phenomena and Complex Systems & Service de Physique des Systèmes Complexes et Mécanique Statistique, Campus Plaine, CP 231, Blvd du Triomphe, B-1050 Brussels, Belgium.
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41
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Šarić A, Buell AK, Meisl G, Michaels TCT, Dobson CM, Linse S, Knowles TPJ, Frenkel D. Physical determinants of the self-replication of protein fibrils. Nat Phys 2016; 12:874-880. [PMID: 31031819 PMCID: PMC6485595 DOI: 10.1038/nphys3828] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The ability of biological molecules to replicate themselves, achieved with the aid of a complex cellular machinery, is the foundation of life. However, a range of aberrant processes involve the self-replication of pathological protein structures without any additional factors. A dramatic example is the autocatalytic replication of pathological protein aggregates, including amyloid fibrils and prions, involved in neurodegenerative disorders. Here, we use computer simulations to identify the necessary requirements for the self-replication of fibrillar assemblies of proteins. We establish that a key physical determinant for this process is the affinity of proteins for the surfaces of fibrils. We find that self-replication can only take place in a very narrow regime of inter-protein interactions, implying a high level of sensitivity to system parameters and experimental conditions. We then compare our theoretical predictions with kinetic and biosensor measurements of fibrils formed from the Aβ peptide associated with Alzheimer's disease. Our results show a quantitative connection between the kinetics of self-replication and the surface coverage of fibrils by monomeric proteins. These findings reveal the fundamental physical requirements for the formation of supra-molecular structures able to replicate themselves, and shed light on mechanisms in play in the proliferation of protein aggregates in nature.
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Affiliation(s)
- Anđela Šarić
- Department of Chemistry, University of Cambridge, Cambridge, UK
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London, UK
| | - Alexander K Buell
- Institute of Physical Biology, University of Duesseldorf, Duesseldorf Germany
| | - Georg Meisl
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | | | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | | | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Cambridge, UK
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Wirnsberger P, Fijan D, Šarić A, Neumann M, Dellago C, Frenkel D. Non-equilibrium simulations of thermally induced electric fields in water. J Chem Phys 2016; 144:224102. [DOI: 10.1063/1.4953036] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- P. Wirnsberger
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - D. Fijan
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, United Kingdom
| | - A. Šarić
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
- Department of Physics and Astronomy, Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
| | - M. Neumann
- Faculty of Physics, University of Vienna, 1090 Vienna, Austria
| | - C. Dellago
- Faculty of Physics, University of Vienna, 1090 Vienna, Austria
| | - D. Frenkel
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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Mačak Šafranko Ž, Sobočanec S, Šarić A, Jajčanin-Jozić N, Krsnik Ž, Aralica G, Balog T, Abramić M. The effect of 17β-estradiol on the expression of dipeptidyl peptidase III and heme oxygenase 1 in liver of CBA/H mice. J Endocrinol Invest 2015; 38:471-9. [PMID: 25432329 DOI: 10.1007/s40618-014-0217-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 11/19/2014] [Indexed: 12/26/2022]
Abstract
BACKGROUND 17β-estradiol (E₂) has well-established cardioprotective, antioxidant and neuroprotective role, and exerts a vast range of biological effects in both sexes. Dipeptidyl peptidase III (DPP III) is protease involved as activator in Keap1-Nrf2 signalling pathway, which is important in cellular defense to oxidative and electrophilic stress. It is generally accepted that oxidative stress is crucial in promoting liver diseases. OBJECTIVE To examine the effect of E₂ on the expression of DPP III and haeme oxygenase 1 (HO-1) in liver of adult CBA/H mice of both sexes. METHODS Gene and protein expressions of studied enzymes were determined by quantitative real-time PCR and Western blot analysis. Immunohistochemistry was performed to analyse the localization of both proteins in different liver cell types. RESULTS Ovariectomy diminished expression of DPP III and HO-1 proteins. E₂ administration abolished this effect, and even increased these proteins above the control. A significant enhancement in DPP III protein was found in E₂-treated males, as well. A decrease in the expression of HO-1, but not of the DPP III gene, was detected in the liver of ovariectomized females. HO-1 protein was found localized in the pericentral areas of hepatic lobules (Kupffer cells and hepatocytes), whilst DPP III showed a uniform distribution within hepatic tissue. CONCLUSIONS We demonstrate for the first time that E₂ influences the protein level of DPP III in vivo, and confirm earlier finding on HO-1 gene upregulation by 17β-estradiol. These results additionally confer new insights into complexity of protective action of E₂.
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Affiliation(s)
- Ž Mačak Šafranko
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - S Sobočanec
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia.
| | - A Šarić
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - N Jajčanin-Jozić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ž Krsnik
- Croatian Institute for Brain Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - G Aralica
- Department of Pathology, Medical School University of Zagreb and University Hospital, Dubrava, Zagreb, Croatia
| | - T Balog
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - M Abramić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
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44
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Mallory SA, Šarić A, Valeriani C, Cacciuto A. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Phys Rev E Stat Nonlin Soft Matter Phys 2014; 89:052303. [PMID: 25353796 DOI: 10.1103/physreve.89.052303] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Indexed: 06/04/2023]
Abstract
We use numerical simulations to compute the equation of state of a suspension of spherical self-propelled nanoparticles in two and three dimensions. We study in detail the effect of excluded volume interactions and confinement as a function of the system's temperature, concentration, and strength of the propulsion. We find a striking nonmonotonic dependence of the pressure on the temperature and provide simple scaling arguments to predict and explain the occurrence of such anomalous behavior. We explicitly show how our results have important implications for the effective forces on passive components suspended in a bath of active particles.
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Affiliation(s)
- S A Mallory
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
| | - A Šarić
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
| | - C Valeriani
- Departamento de Quimica Fisica, Facultad de Ciencias Quimicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - A Cacciuto
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, USA
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45
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Abstract
We report numerical simulations of membrane tubulation driven by large colloidal particles. Using Monte Carlo simulations we study how the process depends on particle size and binding strength, and present accurate free energy calculations to sort out how tube formation compares with the competing budding process. We find that tube formation is a result of the collective behavior of the particles adhering on the surface, and it occurs for binding strengths that are smaller than those required for budding. We also find that long linear aggregates of particles forming on the membrane surface act as nucleation seeds for tubulation by lowering the free energy barrier associated to the process.
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Affiliation(s)
- Anđela Šarić
- Department of Chemistry, Columbia University, 3000 Broadway, MC 3123, New York, NY 10027, USA
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46
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Affiliation(s)
- Anđela Šarić
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Behnaz Bozorgui
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
| | - Angelo Cacciuto
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027, United States
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47
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Šarić A, Hrenar T, Mališ M, Došlić N. Quantum mechanical study of secondary structure formation in protected dipeptides. Phys Chem Chem Phys 2010; 12:4678-85. [DOI: 10.1039/b923041f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Šarić A, Musić S, Nomura K, Popović S. FT-IR and 57Fe Mössbauer spectroscopic investigation of oxide phases precipitated from Fe(NO3)3 solutions. J Mol Struct 1999. [DOI: 10.1016/s0022-2860(98)00829-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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