[{"oa":1,"language":[{"iso":"eng"}],"issue":"7","citation":{"chicago":"Curk, Samo, Johannes Krausser, Georg Meisl, Daan Frenkel, Sara Linse, Thomas C.T. Michaels, Tuomas P.J. Knowles, and Anđela Šarić. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2024. <a href=\"https://doi.org/10.1073/pnas.2220075121\">https://doi.org/10.1073/pnas.2220075121</a>.","ista":"Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ, Šarić A. 2024. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. Proceedings of the National Academy of Sciences of the United States of America. 121(7), e2220075121.","apa":"Curk, S., Krausser, J., Meisl, G., Frenkel, D., Linse, S., Michaels, T. C. T., … Šarić, A. (2024). Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2220075121\">https://doi.org/10.1073/pnas.2220075121</a>","mla":"Curk, Samo, et al. “Self-Replication of Aβ42 Aggregates Occurs on Small and Isolated Fibril Sites.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 7, e2220075121, Proceedings of the National Academy of Sciences, 2024, doi:<a href=\"https://doi.org/10.1073/pnas.2220075121\">10.1073/pnas.2220075121</a>.","ama":"Curk S, Krausser J, Meisl G, et al. Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2024;121(7). doi:<a href=\"https://doi.org/10.1073/pnas.2220075121\">10.1073/pnas.2220075121</a>","ieee":"S. Curk <i>et al.</i>, “Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 121, no. 7. Proceedings of the National Academy of Sciences, 2024.","short":"S. Curk, J. Krausser, G. Meisl, D. Frenkel, S. Linse, T.C.T. Michaels, T.P.J. Knowles, A. Šarić, Proceedings of the National Academy of Sciences of the United States of America 121 (2024)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"02","department":[{"_id":"AnSa"}],"file":[{"date_created":"2024-02-26T08:20:00Z","file_size":7699487,"date_updated":"2024-02-26T08:20:00Z","creator":"dernst","file_id":"15026","success":1,"file_name":"2024_PNAS_Curk.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","checksum":"5aeb65bcc0dd829b1f9ab307c5031d4b"}],"article_number":"e2220075121","has_accepted_license":"1","abstract":[{"text":"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\r\n amyloid fibrils formed in the presence of proSP-C Brichos inhibitors. We find that self-replication of A\r\n 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.","lang":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"intvolume":"       121","publication_identifier":{"eissn":["1091-6490"]},"publication_status":"published","file_date_updated":"2024-02-26T08:20:00Z","author":[{"first_name":"Samo","orcid":"0000-0001-6160-9766","last_name":"Curk","full_name":"Curk, Samo","id":"031eff0d-d481-11ee-8508-cd12a7a86e5b"},{"last_name":"Krausser","full_name":"Krausser, Johannes","first_name":"Johannes"},{"full_name":"Meisl, Georg","last_name":"Meisl","first_name":"Georg"},{"full_name":"Frenkel, Daan","last_name":"Frenkel","first_name":"Daan"},{"last_name":"Linse","full_name":"Linse, Sara","first_name":"Sara"},{"full_name":"Michaels, Thomas C.T.","last_name":"Michaels","first_name":"Thomas C.T."},{"full_name":"Knowles, Tuomas P.J.","last_name":"Knowles","first_name":"Tuomas P.J."},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139"}],"day":"13","scopus_import":"1","oa_version":"Published Version","title":"Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites","volume":121,"article_type":"original","date_created":"2024-02-18T23:01:00Z","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","status":"public","pmid":1,"ec_funded":1,"date_published":"2024-02-13T00:00:00Z","acknowledgement":"We acknowledge support from the Erasmus programme and the University College London Institute for the Physics of Living Systems (S.C., T.C.T.M., A.Š.), the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Engineering and Physical Sciences Research Council (D.F.), the European Research Council (T.P.J.K., S.L., D.F., and A.Š.), the Frances and Augustus Newman Foundation (T.P.J.K.), the Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (S.C. and A.Š.).","year":"2024","external_id":{"pmid":["38335256"]},"related_material":{"record":[{"status":"public","relation":"research_data","id":"15027"}]},"ddc":["570"],"quality_controlled":"1","doi":"10.1073/pnas.2220075121","article_processing_charge":"Yes","publisher":"Proceedings of the National Academy of Sciences","date_updated":"2024-02-26T08:45:56Z","_id":"15001","type":"journal_article"},{"status":"public","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2023-10-31T00:00:00Z","citation":{"ama":"Vanhille-Campos CE, Šarić A. Stress granules plug and stabilize damaged endolysosomal membranes. 2023. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14472\">10.15479/AT:ISTA:14472</a>","short":"C.E. Vanhille-Campos, A. Šarić, (2023).","ieee":"C. E. Vanhille-Campos and A. Šarić, “Stress granules plug and stabilize damaged endolysosomal membranes.” Institute of Science and Technology Austria, 2023.","ista":"Vanhille-Campos CE, Šarić A. 2023. Stress granules plug and stabilize damaged endolysosomal membranes, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:14472\">10.15479/AT:ISTA:14472</a>.","chicago":"Vanhille-Campos, Christian Eduardo, and Anđela Šarić. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Institute of Science and Technology Austria, 2023. <a href=\"https://doi.org/10.15479/AT:ISTA:14472\">https://doi.org/10.15479/AT:ISTA:14472</a>.","mla":"Vanhille-Campos, Christian Eduardo, and Anđela Šarić. <i>Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes</i>. Institute of Science and Technology Austria, 2023, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:14472\">10.15479/AT:ISTA:14472</a>.","apa":"Vanhille-Campos, C. E., &#38; Šarić, A. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:14472\">https://doi.org/10.15479/AT:ISTA:14472</a>"},"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14610"}]},"month":"10","year":"2023","file":[{"checksum":"a18706e952e8660c51ede52a167270b7","relation":"main_file","content_type":"application/zip","access_level":"open_access","file_name":"SGporecondensation-main.zip","success":1,"file_id":"14473","creator":"ipalaia","date_updated":"2023-10-30T16:31:08Z","date_created":"2023-10-30T16:31:08Z","file_size":62821432},{"access_level":"open_access","content_type":"text/plain","success":1,"file_name":"README.txt","checksum":"389eab31c6509dbc05795017fb618758","relation":"main_file","date_updated":"2023-10-31T08:57:50Z","creator":"dernst","file_size":1697,"date_created":"2023-10-31T08:57:50Z","file_id":"14474"}],"department":[{"_id":"AnSa"}],"ddc":["570"],"license":"https://creativecommons.org/publicdomain/zero/1.0/","abstract":[{"text":"Data related to the following paper:\r\n\"Stress granules plug and stabilize damaged endolysosomal membranes\" (https://doi.org/10.1038/s41586-023-06726-w)\r\n\r\nAbstract: \r\nEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. In this work we use a minimal coarse-grained molecular dynamics system to explore how lipid vesicles undergoing poration in a protein-rich medium can be plugged and stabilised by condensate formation. The solution of proteins in and out of the vesicle is described by beads dispersed in implicit solvent. The membrane is described as a one-bead-thick fluid elastic layer of mechanical properties that mimic biological membranes. We tune the interactions between solution beads in the different compartments to capture the differences between the cytoplasmic and endosomal protein solutions and explore how the system responds to different degrees of membrane poration. We find that, in the right interaction regime, condensates form rapidly at the damage site upon solution mixing and act as a plug that prevents futher mixing and destabilisation of the vesicle. Further, when the condensate can interact with the membrane (wetting interactions) we find that it mediates pore sealing and membrane repair. This research is part of the work published in \"Stress granules plug and stabilize damaged endolysosomal membranes\", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w.","lang":"eng"}],"tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","short":"CC0 (1.0)"},"has_accepted_license":"1","file_date_updated":"2023-10-31T08:57:50Z","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","title":"Stress granules plug and stabilize damaged endolysosomal membranes","article_processing_charge":"No","day":"31","doi":"10.15479/AT:ISTA:14472","author":[{"full_name":"Vanhille-Campos, Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714","last_name":"Vanhille-Campos","first_name":"Christian Eduardo"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"}],"date_created":"2023-10-30T16:38:32Z","type":"research_data","_id":"14472","date_updated":"2023-11-27T09:05:07Z"},{"external_id":{"pmid":["37968398"]},"related_material":{"link":[{"url":"https://doi.org/10.1038/s41586-023-06882-z","relation":"erratum"}],"record":[{"id":"14472","relation":"research_data","status":"public"}]},"year":"2023","keyword":["Multidisciplinary"],"publication":"Nature","status":"public","acknowledgement":"We thank the Human Embryonic Stem Cell Unit, Advanced Light Microscopy and High-throughput Screening facilities at the Crick for their support in various aspects of the work. We thank the laboratory of P. Anderson for providing the G3BP-DKO U2OS cells. The authors thank N. Chen for providing the purified glycinin protein; Z. Zhao for providing the microfluidic chip wafers; and M. Amaral and F. Frey for helpful discussions and valuable input regarding analysis methods. This work was supported by the Francis Crick Institute (to M.G.G.), which receives its core funding from Cancer Research UK (FC001092), the UK Medical Research Council (FC001092) and the Wellcome Trust (FC001092). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 772022 to M.G.G.). C.B. has received funding from the European Respiratory Society and the European Union’s H2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement no. 713406. A.M. acknowledges support from Alexander von Humboldt Foundation and C.V.-C. acknowledges funding by the Royal Society and the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (grant no. 802960 to A.S.). All simulations were carried out on the high-performance computing cluster at the Institute of Science and Technology Austria. For the purpose of Open Access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.\r\nOpen Access funding provided by The Francis Crick Institute.","date_published":"2023-11-15T00:00:00Z","pmid":1,"publisher":"Springer Nature","doi":"10.1038/s41586-023-06726-w","article_processing_charge":"Yes (via OA deal)","type":"journal_article","date_updated":"2023-11-27T09:05:08Z","_id":"14610","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41586-023-06726-w"}],"month":"11","department":[{"_id":"AnSa"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Bussi, C., Mangiarotti, A., Vanhille-Campos, C. E., Aylan, B., Pellegrino, E., Athanasiadi, N., … Gutierrez, M. G. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-023-06726-w\">https://doi.org/10.1038/s41586-023-06726-w</a>","mla":"Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” <i>Nature</i>, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41586-023-06726-w\">10.1038/s41586-023-06726-w</a>.","chicago":"Bussi, Claudio, Agustín Mangiarotti, Christian Eduardo Vanhille-Campos, Beren Aylan, Enrica Pellegrino, Natalia Athanasiadi, Antony Fearns, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” <i>Nature</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41586-023-06726-w\">https://doi.org/10.1038/s41586-023-06726-w</a>.","ista":"Bussi C, Mangiarotti A, Vanhille-Campos CE, Aylan B, Pellegrino E, Athanasiadi N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. 2023. Stress granules plug and stabilize damaged endolysosomal membranes. Nature.","ieee":"C. Bussi <i>et al.</i>, “Stress granules plug and stabilize damaged endolysosomal membranes,” <i>Nature</i>. Springer Nature, 2023.","short":"C. Bussi, A. Mangiarotti, C.E. Vanhille-Campos, B. Aylan, E. Pellegrino, N. Athanasiadi, A. Fearns, A. Rodgers, T.M. Franzmann, A. Šarić, R. Dimova, M.G. Gutierrez, Nature (2023).","ama":"Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and stabilize damaged endolysosomal membranes. <i>Nature</i>. 2023. doi:<a href=\"https://doi.org/10.1038/s41586-023-06726-w\">10.1038/s41586-023-06726-w</a>"},"oa_version":"Published Version","title":"Stress granules plug and stabilize damaged endolysosomal membranes","author":[{"first_name":"Claudio","last_name":"Bussi","full_name":"Bussi, Claudio"},{"full_name":"Mangiarotti, Agustín","last_name":"Mangiarotti","first_name":"Agustín"},{"first_name":"Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714","full_name":"Vanhille-Campos, Christian Eduardo","last_name":"Vanhille-Campos"},{"first_name":"Beren","full_name":"Aylan, Beren","last_name":"Aylan"},{"full_name":"Pellegrino, Enrica","last_name":"Pellegrino","first_name":"Enrica"},{"first_name":"Natalia","last_name":"Athanasiadi","full_name":"Athanasiadi, Natalia"},{"first_name":"Antony","last_name":"Fearns","full_name":"Fearns, Antony"},{"first_name":"Angela","full_name":"Rodgers, Angela","last_name":"Rodgers"},{"first_name":"Titus M.","full_name":"Franzmann, Titus M.","last_name":"Franzmann"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"first_name":"Rumiana","last_name":"Dimova","full_name":"Dimova, Rumiana"},{"first_name":"Maximiliano G.","last_name":"Gutierrez","full_name":"Gutierrez, Maximiliano G."}],"day":"15","article_type":"original","date_created":"2023-11-27T07:56:37Z","abstract":[{"text":"<jats:title>Abstract</jats:title><jats:p>Endomembrane damage represents a form of stress that is detrimental for eukaryotic cells<jats:sup>1,2</jats:sup>. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis<jats:sup>3–7</jats:sup>. 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 <jats:italic>Mycobacterium tuberculosis</jats:italic>, a human pathogen that exploits endomembrane damage to survive within the host.</jats:p>","lang":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]}},{"main_file_link":[{"url":"https://doi.org/10.1016/j.bpj.2023.12.020","open_access":"1"}],"quality_controlled":"1","ddc":["570"],"date_updated":"2024-01-23T09:26:35Z","_id":"14844","type":"journal_article","doi":"10.1016/j.bpj.2023.12.020","article_processing_charge":"No","publisher":"Elsevier","ec_funded":1,"date_published":"2023-12-29T00:00:00Z","acknowledgement":"We gratefully acknowledge useful discussions with Casper van der Wel, help by Yogesh Shelke with PAA coverslip preparation, and support by Rachel Doherty with particle functionalization. A.A. and D.J.K. would like to thank Timon Idema and George Dadunashvili for initial attempts to simulate the experimental system. D.J.K. would like to thank the physics department at Leiden University for funding the PhD position of A.A. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC starting grant no. 802960).","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}],"status":"public","publication":"Biophysical Journal","year":"2023","publication_status":"inpress","publication_identifier":{"issn":["0006-3495"],"eissn":["1542-0086"]},"abstract":[{"lang":"eng","text":"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."}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"article_type":"original","date_created":"2024-01-21T23:00:56Z","author":[{"last_name":"Azadbakht","full_name":"Azadbakht, Ali","first_name":"Ali"},{"first_name":"Billie","orcid":"0000-0003-3441-1337","full_name":"Meadowcroft, Billie","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","last_name":"Meadowcroft"},{"first_name":"Juraj","last_name":"Majek","full_name":"Majek, Juraj","id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1"},{"last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139"},{"first_name":"Daniela J.","last_name":"Kraft","full_name":"Kraft, Daniela J."}],"scopus_import":"1","day":"29","title":"Nonadditivity in interactions between three membrane-wrapped colloidal spheres","oa_version":"Published Version","citation":{"ama":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. <i>Biophysical Journal</i>. doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">10.1016/j.bpj.2023.12.020</a>","ieee":"A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, and D. J. Kraft, “Nonadditivity in interactions between three membrane-wrapped colloidal spheres,” <i>Biophysical Journal</i>. Elsevier.","short":"A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, D.J. Kraft, Biophysical Journal (n.d.).","ista":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal.","chicago":"Azadbakht, Ali, Billie Meadowcroft, Juraj Majek, Anđela Šarić, and Daniela J. Kraft. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” <i>Biophysical Journal</i>. Elsevier, n.d. <a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">https://doi.org/10.1016/j.bpj.2023.12.020</a>.","apa":"Azadbakht, A., Meadowcroft, B., Majek, J., Šarić, A., &#38; Kraft, D. J. (n.d.). Nonadditivity in interactions between three membrane-wrapped colloidal spheres. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">https://doi.org/10.1016/j.bpj.2023.12.020</a>","mla":"Azadbakht, Ali, et al. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” <i>Biophysical Journal</i>, Elsevier, doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">10.1016/j.bpj.2023.12.020</a>."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"AnSa"}],"month":"12"},{"external_id":{"pmid":["37141427"],"isi":["000985481400001"]},"isi":1,"year":"2023","acknowledgement":"We sincerely thank Casper van der Wel for providing open-source packages for tracking, as well as Yogesh Shelke for his assistance with PAA coverslip preparation and Rachel Doherty for her assistance with particle functionalization. We are grateful to Felix Frey for useful discussions on the theory of membrane wrapping. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC Starting Grant No. 802960).","date_published":"2023-05-04T00:00:00Z","pmid":1,"ec_funded":1,"project":[{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"status":"public","publication":"Nano Letters","type":"journal_article","date_updated":"2023-08-01T14:51:25Z","_id":"13094","publisher":"American Chemical Society","doi":"10.1021/acs.nanolett.3c00375","article_processing_charge":"No","quality_controlled":"1","ddc":["540"],"page":"4267–4273","file":[{"file_id":"13100","creator":"dernst","date_updated":"2023-05-30T07:55:31Z","file_size":3654910,"date_created":"2023-05-30T07:55:31Z","checksum":"9734d4c617bab3578ef62916b764547a","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2023_NanoLetters_Azadbakht.pdf"}],"department":[{"_id":"AnSa"}],"month":"05","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"10","citation":{"apa":"Azadbakht, A., Meadowcroft, B., Varkevisser, T., Šarić, A., &#38; Kraft, D. J. (2023). Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">https://doi.org/10.1021/acs.nanolett.3c00375</a>","mla":"Azadbakht, Ali, et al. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” <i>Nano Letters</i>, vol. 23, no. 10, American Chemical Society, 2023, pp. 4267–4273, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">10.1021/acs.nanolett.3c00375</a>.","ista":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. 2023. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. 23(10), 4267–4273.","chicago":"Azadbakht, Ali, Billie Meadowcroft, Thijs Varkevisser, Anđela Šarić, and Daniela J. Kraft. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” <i>Nano Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">https://doi.org/10.1021/acs.nanolett.3c00375</a>.","ieee":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, and D. J. Kraft, “Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles,” <i>Nano Letters</i>, vol. 23, no. 10. American Chemical Society, pp. 4267–4273, 2023.","short":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, D.J. Kraft, Nano Letters 23 (2023) 4267–4273.","ama":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. <i>Nano Letters</i>. 2023;23(10):4267–4273. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.3c00375\">10.1021/acs.nanolett.3c00375</a>"},"language":[{"iso":"eng"}],"oa":1,"article_type":"letter_note","date_created":"2023-05-28T22:01:03Z","volume":23,"title":"Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles","oa_version":"Published Version","author":[{"last_name":"Azadbakht","full_name":"Azadbakht, Ali","first_name":"Ali"},{"first_name":"Billie","full_name":"Meadowcroft, Billie","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","last_name":"Meadowcroft"},{"first_name":"Thijs","full_name":"Varkevisser, Thijs","last_name":"Varkevisser"},{"last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"first_name":"Daniela J.","last_name":"Kraft","full_name":"Kraft, Daniela J."}],"day":"04","scopus_import":"1","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"publication_status":"published","file_date_updated":"2023-05-30T07:55:31Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        23","abstract":[{"text":"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.","lang":"eng"}],"has_accepted_license":"1"},{"acknowledgement":"The authors acknowledge support from the Institute for the Physics of Living Systems, University College London (T.C.T.M.), the Swedish Research Council (2015-00143) (S.L.), the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969) (T.P.J.K.), the BBSRC (T.P.J.K.), the Newman Foundation (T.P.J.K.) and the Wellcome Trust Collaborative Award 203249/Z/16/Z (T.P.J.K.). The authors thank C. Flandoli for help with illustrations.","date_published":"2023-07-01T00:00:00Z","status":"public","publication":"Nature Reviews Physics","external_id":{"isi":["001017539800001"]},"year":"2023","isi":1,"quality_controlled":"1","page":"379–397","type":"journal_article","date_updated":"2023-08-02T06:28:38Z","_id":"13237","publisher":"Springer Nature","doi":"10.1038/s42254-023-00598-9","article_processing_charge":"No","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"short":"T.C.T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Reviews Physics 5 (2023) 379–397.","ieee":"T. C. T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, and T. P. J. Knowles, “Amyloid formation as a protein phase transition,” <i>Nature Reviews Physics</i>, vol. 5. Springer Nature, pp. 379–397, 2023.","ama":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. Amyloid formation as a protein phase transition. <i>Nature Reviews Physics</i>. 2023;5:379–397. doi:<a href=\"https://doi.org/10.1038/s42254-023-00598-9\">10.1038/s42254-023-00598-9</a>","mla":"Michaels, Thomas C. T., et al. “Amyloid Formation as a Protein Phase Transition.” <i>Nature Reviews Physics</i>, vol. 5, Springer Nature, 2023, pp. 379–397, doi:<a href=\"https://doi.org/10.1038/s42254-023-00598-9\">10.1038/s42254-023-00598-9</a>.","apa":"Michaels, T. C. T., Qian, D., Šarić, A., Vendruscolo, M., Linse, S., &#38; Knowles, T. P. J. (2023). Amyloid formation as a protein phase transition. <i>Nature Reviews Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42254-023-00598-9\">https://doi.org/10.1038/s42254-023-00598-9</a>","chicago":"Michaels, Thomas C.T., Daoyuan Qian, Anđela Šarić, Michele Vendruscolo, Sara Linse, and Tuomas P.J. Knowles. “Amyloid Formation as a Protein Phase Transition.” <i>Nature Reviews Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42254-023-00598-9\">https://doi.org/10.1038/s42254-023-00598-9</a>.","ista":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. 2023. Amyloid formation as a protein phase transition. Nature Reviews Physics. 5, 379–397."},"language":[{"iso":"eng"}],"department":[{"_id":"AnSa"}],"month":"07","publication_identifier":{"eissn":["2522-5820"]},"publication_status":"published","intvolume":"         5","abstract":[{"text":"The formation of amyloid fibrils is a general class of protein self-assembly behaviour, which is associated with both functional biology and the development of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review, we discuss how general physical concepts from the study of phase transitions can be used to illuminate the fundamental mechanisms of amyloid self-assembly. We summarize progress in the efforts to describe the essential biophysical features of amyloid self-assembly as a nucleation-and-growth process and discuss how master equation approaches can reveal the key molecular pathways underlying this process, including the role of secondary nucleation. Additionally, we outline how non-classical aspects of aggregate formation involving oligomers or biomolecular condensates have emerged, inspiring developments in understanding, modelling and modulating complex protein assembly pathways. Finally, we consider how these concepts can be applied to kinetics-based drug discovery and therapeutic design to develop treatments for protein aggregation diseases.","lang":"eng"}],"article_type":"original","date_created":"2023-07-16T22:01:12Z","volume":5,"title":"Amyloid formation as a protein phase transition","oa_version":"None","author":[{"last_name":"Michaels","full_name":"Michaels, Thomas C.T.","first_name":"Thomas C.T."},{"full_name":"Qian, Daoyuan","last_name":"Qian","first_name":"Daoyuan"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"full_name":"Vendruscolo, Michele","last_name":"Vendruscolo","first_name":"Michele"},{"full_name":"Linse, Sara","last_name":"Linse","first_name":"Sara"},{"full_name":"Knowles, Tuomas P.J.","last_name":"Knowles","first_name":"Tuomas P.J."}],"day":"01","scopus_import":"1"},{"month":"11","department":[{"_id":"EdHa"},{"_id":"AnSa"},{"_id":"JePa"}],"file":[{"relation":"main_file","checksum":"7e282c2ebc0ac82125a04f6b4742d4c1","success":1,"file_name":"2023_NaturePhysics_Grober.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"14906","file_size":6365607,"date_created":"2024-01-30T12:26:08Z","date_updated":"2024-01-30T12:26:08Z","creator":"dernst"}],"oa":1,"language":[{"iso":"eng"}],"citation":{"ista":"Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. 2023. Unconventional colloidal aggregation in chiral bacterial baths. Nature Physics. 19, 1680–1688.","chicago":"Grober, Daniel, Ivan Palaia, Mehmet C Ucar, Edouard B Hannezo, Anđela Šarić, and Jérémie A Palacci. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” <i>Nature Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41567-023-02136-x\">https://doi.org/10.1038/s41567-023-02136-x</a>.","mla":"Grober, Daniel, et al. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” <i>Nature Physics</i>, vol. 19, Springer Nature, 2023, pp. 1680–88, doi:<a href=\"https://doi.org/10.1038/s41567-023-02136-x\">10.1038/s41567-023-02136-x</a>.","apa":"Grober, D., Palaia, I., Ucar, M. C., Hannezo, E. B., Šarić, A., &#38; Palacci, J. A. (2023). Unconventional colloidal aggregation in chiral bacterial baths. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-023-02136-x\">https://doi.org/10.1038/s41567-023-02136-x</a>","ama":"Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. Unconventional colloidal aggregation in chiral bacterial baths. <i>Nature Physics</i>. 2023;19:1680-1688. doi:<a href=\"https://doi.org/10.1038/s41567-023-02136-x\">10.1038/s41567-023-02136-x</a>","short":"D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature Physics 19 (2023) 1680–1688.","ieee":"D. Grober, I. Palaia, M. C. Ucar, E. B. Hannezo, A. Šarić, and J. A. Palacci, “Unconventional colloidal aggregation in chiral bacterial baths,” <i>Nature Physics</i>, vol. 19. Springer Nature, pp. 1680–1688, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Grober","full_name":"Grober, Daniel","id":"abdfc56f-34fb-11ee-bd33-fd766fce5a99","first_name":"Daniel"},{"first_name":"Ivan","orcid":" 0000-0002-8843-9485 ","last_name":"Palaia","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","full_name":"Palaia, Ivan"},{"full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","last_name":"Ucar","orcid":"0000-0003-0506-4217","first_name":"Mehmet C"},{"first_name":"Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B"},{"first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić"},{"last_name":"Palacci","full_name":"Palacci, Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","orcid":"0000-0002-7253-9465"}],"day":"01","scopus_import":"1","oa_version":"Published Version","title":"Unconventional colloidal aggregation in chiral bacterial baths","volume":19,"article_type":"original","date_created":"2023-08-06T22:01:11Z","has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        19","abstract":[{"text":"When in equilibrium, thermal forces agitate molecules, which then diffuse, collide and bind to form materials. However, the space of accessible structures in which micron-scale particles can be organized by thermal forces is limited, owing to the slow dynamics and metastable states. Active agents in a passive fluid generate forces and flows, forming a bath with active fluctuations. Two unanswered questions are whether those active agents can drive the assembly of passive components into unconventional states and which material properties they will exhibit. Here we show that passive, sticky beads immersed in a bath of swimming Escherichia coli bacteria aggregate into unconventional clusters and gels that are controlled by the activity of the bath. We observe a slow but persistent rotation of the aggregates that originates in the chirality of the E. coli flagella and directs aggregation into structures that are not accessible thermally. We elucidate the aggregation mechanism with a numerical model of spinning, sticky beads and reproduce quantitatively the experimental results. We show that internal activity controls the phase diagram and the structure of the aggregates. Overall, our results highlight the promising role of active baths in designing the structural and mechanical properties of materials with unconventional phases.","lang":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1745-2473"],"eissn":["1745-2481"]},"file_date_updated":"2024-01-30T12:26:08Z","year":"2023","isi":1,"external_id":{"isi":["001037346400005"]},"project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","call_identifier":"H2020"},{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"publication":"Nature Physics","status":"public","ec_funded":1,"date_published":"2023-11-01T00:00:00Z","acknowledgement":"D.G. and J.P. thank E. Krasnopeeva, C. Guet, G. Guessous and T. Hwa for providing the E. coli strains. This material is based upon work supported by the US Department of Energy under award DE-SC0019769. I.P. acknowledges funding by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 101034413. A.Š. acknowledges funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant No. 802960). M.C.U. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 754411.","doi":"10.1038/s41567-023-02136-x","article_processing_charge":"Yes","publisher":"Springer Nature","date_updated":"2024-01-30T12:26:55Z","_id":"13971","type":"journal_article","page":"1680-1688","ddc":["530"],"quality_controlled":"1"},{"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through confinement. <i>Soft Matter</i>. 2023;19:1695-1704. doi:<a href=\"https://doi.org/10.1039/d2sm01562e\">10.1039/d2sm01562e</a>","short":"N.A.M. Araújo, L.M.C. Janssen, T. Barois, G. Boffetta, I. Cohen, A. Corbetta, O. Dauchot, M. Dijkstra, W.M. Durham, A. Dussutour, S. Garnier, H. Gelderblom, R. Golestanian, L. Isa, G.H. Koenderink, H. Löwen, R. Metzler, M. Polin, C.P. Royall, A. Šarić, A. Sengupta, C. Sykes, V. Trianni, I. Tuval, N. Vogel, J.M. Yeomans, I. Zuriguel, A. Marin, G. Volpe, Soft Matter 19 (2023) 1695–1704.","ieee":"N. A. M. Araújo <i>et al.</i>, “Steering self-organisation through confinement,” <i>Soft Matter</i>, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023.","ista":"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. 2023. Steering self-organisation through confinement. Soft Matter. 19, 1695–1704.","chicago":"Araújo, Nuno A.M., Liesbeth M.C. Janssen, Thomas Barois, Guido Boffetta, Itai Cohen, Alessandro Corbetta, Olivier Dauchot, et al. “Steering Self-Organisation through Confinement.” <i>Soft Matter</i>. Royal Society of Chemistry, 2023. <a href=\"https://doi.org/10.1039/d2sm01562e\">https://doi.org/10.1039/d2sm01562e</a>.","mla":"Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.” <i>Soft Matter</i>, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:<a href=\"https://doi.org/10.1039/d2sm01562e\">10.1039/d2sm01562e</a>.","apa":"Araújo, N. A. M., Janssen, L. M. C., Barois, T., Boffetta, G., Cohen, I., Corbetta, A., … Volpe, G. (2023). Steering self-organisation through confinement. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d2sm01562e\">https://doi.org/10.1039/d2sm01562e</a>"},"arxiv":1,"month":"02","file":[{"checksum":"af95aa18b9b01e32fb8f13477c0e2687","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2023_SoftMatter_Araujo.pdf","success":1,"file_id":"12711","date_updated":"2023-03-07T09:19:41Z","creator":"cchlebak","date_created":"2023-03-07T09:19:41Z","file_size":3581939}],"department":[{"_id":"AnSa"}],"intvolume":"        19","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"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."}],"has_accepted_license":"1","file_date_updated":"2023-03-07T09:19:41Z","publication_status":"published","publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"title":"Steering self-organisation through confinement","oa_version":"Published Version","day":"06","scopus_import":"1","author":[{"first_name":"Nuno A.M.","last_name":"Araújo","full_name":"Araújo, Nuno A.M."},{"first_name":"Liesbeth M.C.","last_name":"Janssen","full_name":"Janssen, Liesbeth M.C."},{"full_name":"Barois, Thomas","last_name":"Barois","first_name":"Thomas"},{"first_name":"Guido","last_name":"Boffetta","full_name":"Boffetta, Guido"},{"full_name":"Cohen, Itai","last_name":"Cohen","first_name":"Itai"},{"last_name":"Corbetta","full_name":"Corbetta, Alessandro","first_name":"Alessandro"},{"first_name":"Olivier","full_name":"Dauchot, Olivier","last_name":"Dauchot"},{"first_name":"Marjolein","full_name":"Dijkstra, Marjolein","last_name":"Dijkstra"},{"first_name":"William M.","last_name":"Durham","full_name":"Durham, William M."},{"full_name":"Dussutour, Audrey","last_name":"Dussutour","first_name":"Audrey"},{"last_name":"Garnier","full_name":"Garnier, Simon","first_name":"Simon"},{"first_name":"Hanneke","full_name":"Gelderblom, Hanneke","last_name":"Gelderblom"},{"first_name":"Ramin","full_name":"Golestanian, Ramin","last_name":"Golestanian"},{"first_name":"Lucio","last_name":"Isa","full_name":"Isa, Lucio"},{"last_name":"Koenderink","full_name":"Koenderink, Gijsje H.","first_name":"Gijsje H."},{"last_name":"Löwen","full_name":"Löwen, Hartmut","first_name":"Hartmut"},{"last_name":"Metzler","full_name":"Metzler, Ralf","first_name":"Ralf"},{"first_name":"Marco","last_name":"Polin","full_name":"Polin, Marco"},{"full_name":"Royall, C. Patrick","last_name":"Royall","first_name":"C. Patrick"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić","first_name":"Anđela","orcid":"0000-0002-7854-2139"},{"last_name":"Sengupta","full_name":"Sengupta, Anupam","first_name":"Anupam"},{"last_name":"Sykes","full_name":"Sykes, Cécile","first_name":"Cécile"},{"full_name":"Trianni, Vito","last_name":"Trianni","first_name":"Vito"},{"last_name":"Tuval","full_name":"Tuval, Idan","first_name":"Idan"},{"first_name":"Nicolas","full_name":"Vogel, Nicolas","last_name":"Vogel"},{"last_name":"Yeomans","full_name":"Yeomans, Julia M.","first_name":"Julia M."},{"last_name":"Zuriguel","full_name":"Zuriguel, Iker","first_name":"Iker"},{"first_name":"Alvaro","full_name":"Marin, Alvaro","last_name":"Marin"},{"first_name":"Giorgio","last_name":"Volpe","full_name":"Volpe, Giorgio"}],"date_created":"2023-03-05T23:01:06Z","article_type":"original","volume":19,"status":"public","publication":"Soft Matter","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"}],"acknowledgement":"All authors are grateful to the Lorentz Center for providing a venue for stimulating scientific discussions and to sponsor a workshop on the topic of “Self-organisation under confinement” along with the 4TU Federation, the J. M. Burgers Center for Fluid Dynamics and the MESA+ Institute for Nanotechnology at the University of Twente. The authors are also grateful to Paolo Malgaretti, Federico Toschi, Twan Wilting and Jaap den Toonder for valuable feedback. N. A. acknowledges financial support from the Portuguese Foundation for Science and Technology (FCT) under Contracts no. PTDC/FIS-MAC/28146/2017 (LISBOA-01-0145-FEDER-028146), UIDB/00618/2020, and UIDP/00618/2020. L. M. C. J. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a START-UP, Physics Projectruimte, and Vidi grant. I. C. was supported in part by a grant from by the Army Research Office (ARO W911NF-18-1-0032) and the Cornell Center for Materials Research (DMR-1719875). O. D. acknowledges funding by the Agence Nationale pour la Recherche under Grant No ANR-18-CE33-0006 MSR. M. D. acknowledges financial support from the European Research Council (Grant No. ERC-2019-ADV-H2020 884902 SoftML). W. M. D. acknowledges funding from a BBSRC New Investigator Grant (BB/R018383/1). S. G. was supported by DARPA Young Faculty Award # D19AP00046, and NSF IIS grant # 1955210. H. G. acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through Veni Grant No. 680-47-451. R. G. acknowledges support from the Max Planck School Matter to Life and the MaxSynBio Consortium, which are jointly funded by the Federal Ministry of Education and Research (BMBF) of Germany, and the Max Planck Society. L. I. acknowledges funding from the Horizon Europe ERC Consolidator Grant ACTIVE_ ADAPTIVE (Grant No. 101001514). G. H. K. gratefully acknowledges the NWO Talent Programme which is financed by the Dutch Research Council (project number VI.C.182.004). H. L. and N. V. acknowledge funding from the Deutsche Forschungsgemeinschaft (DFG) under grant numbers VO 1824/8-1 and LO 418/22-1. R. M. acknowledges funding from the Deutsche Forschungsgemeinschaft (DFG) under grant number ME 1535/13-1 and ME 1535/16-1. M. P. acknowledges funding from the Ramón y Cajal Program, grant no. RYC-2018-02534, and the Leverhulme Trust, grant no. RPG-2018-345. A. Š. acknowledges financial support from the European Research Council (Grant No. ERC-2018-STG-H2020 802960 NEPA). A. S. acknowledges funding from an ATTRACT Investigator Grant (No. A17/MS/11572821/MBRACE) from the Luxembourg National Research Fund. C. S. acknowledges funding from the French Agence Nationale pour la Recherche (ANR), grant ANR-14-CE090006 and ANR-12-BSV5001401, by the Fondation pour la Recherche Médicale (FRM), grant DEQ20120323737, and from the PIC3I of Institut Curie, France. I. T. acknowledges funding from grant IED2019-00058I/AEI/10.13039/501100011033. M. P. and I. T. also acknowledge funding from grant PID2019-104232B-I00/AEI/10.13039/501100011033 and from the H2020 MSCA ITN PHYMOT (Grant agreement No 95591). I. Z. acknowledges funding from Project PID2020-114839GB-I00 MINECO/AEI/FEDER, UE. A. M. acknowledges funding from the European Research Council, Starting Grant No. 678573 NanoPacks. G. V. acknowledges sponsorship for this work by the US Office of Naval Research Global (Award No. N62909-18-1-2170).","date_published":"2023-02-06T00:00:00Z","ec_funded":1,"external_id":{"arxiv":["2204.10059"],"isi":["000940388100001"]},"year":"2023","isi":1,"ddc":["540"],"page":"1695-1704","quality_controlled":"1","publisher":"Royal Society of Chemistry","article_processing_charge":"No","doi":"10.1039/d2sm01562e","type":"journal_article","_id":"12708","date_updated":"2023-08-01T13:28:39Z"},{"ddc":["570"],"quality_controlled":"1","publisher":"American Association for the Advancement of Science","article_processing_charge":"No","doi":"10.1126/sciadv.ade5224","type":"journal_article","_id":"12756","date_updated":"2023-08-01T13:45:54Z","status":"public","publication":"Science Advances","project":[{"call_identifier":"H2020","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"date_published":"2023-03-17T00:00:00Z","acknowledgement":"We thank Y. Liu and V. Hale for help with electron cryotomography; the Medical Research Council (MRC) LMB Electron Microscopy Facility for access, training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with computing infrastructure. We also thank the Flow Cytometry Facility and the MRC LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship: ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P. was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019). B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346). A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant no. 802960). L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and the Wellcome Trust (203276/Z/16/Z).","ec_funded":1,"external_id":{"isi":["000968083500010"]},"isi":1,"year":"2023","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"         9","abstract":[{"text":"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.","lang":"eng"}],"has_accepted_license":"1","file_date_updated":"2023-03-27T06:24:49Z","publication_identifier":{"eissn":["2375-2548"]},"publication_status":"published","title":"The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division","oa_version":"Published Version","day":"17","scopus_import":"1","author":[{"full_name":"Hurtig, Fredrik","last_name":"Hurtig","first_name":"Fredrik"},{"full_name":"Burgers, Thomas C.Q.","last_name":"Burgers","first_name":"Thomas C.Q."},{"full_name":"Cezanne, Alice","last_name":"Cezanne","first_name":"Alice"},{"full_name":"Jiang, Xiuyun","last_name":"Jiang","first_name":"Xiuyun"},{"first_name":"Frank N.","last_name":"Mol","full_name":"Mol, Frank N."},{"first_name":"Jovan","last_name":"Traparić","full_name":"Traparić, Jovan"},{"first_name":"Andre Arashiro","full_name":"Pulschen, Andre Arashiro","last_name":"Pulschen"},{"full_name":"Nierhaus, Tim","last_name":"Nierhaus","first_name":"Tim"},{"full_name":"Tarrason-Risa, Gabriel","last_name":"Tarrason-Risa","first_name":"Gabriel"},{"first_name":"Lena","last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, Lena"},{"full_name":"Löwe, Jan","last_name":"Löwe","first_name":"Jan"},{"first_name":"Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Vlijm, Rifka","last_name":"Vlijm","first_name":"Rifka"},{"first_name":"Buzz","full_name":"Baum, Buzz","last_name":"Baum"}],"date_created":"2023-03-26T22:01:06Z","article_type":"original","volume":9,"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ieee":"F. Hurtig <i>et al.</i>, “The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division,” <i>Science Advances</i>, vol. 9, no. 11. American Association for the Advancement of Science, 2023.","short":"F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A. Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić, R. Vlijm, B. Baum, Science Advances 9 (2023).","ama":"Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. <i>Science Advances</i>. 2023;9(11). doi:<a href=\"https://doi.org/10.1126/sciadv.ade5224\">10.1126/sciadv.ade5224</a>","apa":"Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić, J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.ade5224\">https://doi.org/10.1126/sciadv.ade5224</a>","mla":"Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” <i>Science Advances</i>, vol. 9, no. 11, eade5224, American Association for the Advancement of Science, 2023, doi:<a href=\"https://doi.org/10.1126/sciadv.ade5224\">10.1126/sciadv.ade5224</a>.","chicago":"Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” <i>Science Advances</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/sciadv.ade5224\">https://doi.org/10.1126/sciadv.ade5224</a>.","ista":"Hurtig F, Burgers TCQ, 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. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224."},"issue":"11","month":"03","article_number":"eade5224","file":[{"creator":"dernst","date_updated":"2023-03-27T06:24:49Z","date_created":"2023-03-27T06:24:49Z","file_size":1826471,"file_id":"12768","content_type":"application/pdf","access_level":"open_access","file_name":"2023_ScienceAdvances_Hurtig.pdf","success":1,"checksum":"6d7dbe9ed86a116c8a002d62971202c5","relation":"main_file"}],"department":[{"_id":"AnSa"}]},{"quality_controlled":"1","ddc":["540"],"type":"journal_article","_id":"11400","date_updated":"2023-09-05T11:59:00Z","publisher":"AIP Publishing","article_processing_charge":"No","doi":"10.1063/5.0087769","acknowledgement":"The authors thank Longhui Zeng and Xiaolei Su (Yale University) for bringing the topic to their attention and for useful comments. This work has received funding from the European Research Council under the European Union’s Horizon\r\n2020 research and innovation program (ERC Grant No. 802960 and Marie Skłodowska-Curie Grant No. 101034413). The authors are grateful to the UK Materials and Molecular Modeling Hub for computational resources, which is partially funded by EPSRC (Grant Nos. EP/P020194/1 and EP/T022213/1). The authors acknowledge support from ISTA and from the Royal Society (Grant No. UF160266).","date_published":"2022-05-16T00:00:00Z","ec_funded":1,"publication":"The Journal of Chemical Physics","status":"public","project":[{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"},{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}],"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"external_id":{"isi":["000797236000004"]},"isi":1,"year":"2022","file_date_updated":"2022-05-23T07:45:33Z","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"publication_status":"published","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"       156","abstract":[{"text":"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.","lang":"eng"}],"has_accepted_license":"1","date_created":"2022-05-22T17:04:48Z","article_type":"original","volume":156,"title":"Controlling cluster size in 2D phase-separating binary mixtures with specific interactions","oa_version":"Published Version","day":"16","author":[{"full_name":"Palaia, Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","last_name":"Palaia","orcid":" 0000-0002-8843-9485 ","first_name":"Ivan"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Palaia I, Šarić A. 2022. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. The Journal of Chemical Physics. 156(19), 194902.","chicago":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0087769\">https://doi.org/10.1063/5.0087769</a>.","apa":"Palaia, I., &#38; Šarić, A. (2022). Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0087769\">https://doi.org/10.1063/5.0087769</a>","mla":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” <i>The Journal of Chemical Physics</i>, vol. 156, no. 19, 194902, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0087769\">10.1063/5.0087769</a>.","ama":"Palaia I, Šarić A. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. <i>The Journal of Chemical Physics</i>. 2022;156(19). doi:<a href=\"https://doi.org/10.1063/5.0087769\">10.1063/5.0087769</a>","ieee":"I. Palaia and A. Šarić, “Controlling cluster size in 2D phase-separating binary mixtures with specific interactions,” <i>The Journal of Chemical Physics</i>, vol. 156, no. 19. AIP Publishing, 2022.","short":"I. Palaia, A. Šarić, The Journal of Chemical Physics 156 (2022)."},"issue":"19","language":[{"iso":"eng"}],"oa":1,"article_number":"194902","file":[{"checksum":"7fada58059676a4bb0944b82247af740","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2022_JourChemPhysics_Palaia.pdf","success":1,"file_id":"11405","date_updated":"2022-05-23T07:45:33Z","creator":"dernst","file_size":6387208,"date_created":"2022-05-23T07:45:33Z"}],"department":[{"_id":"AnSa"}],"month":"05"},{"oa_version":"Published Version","title":"Adsorption free energy predicts amyloid protein nucleation rates","author":[{"first_name":"Zenon","last_name":"Toprakcioglu","full_name":"Toprakcioglu, Zenon"},{"last_name":"Kamada","full_name":"Kamada, Ayaka","first_name":"Ayaka"},{"full_name":"Michaels, Thomas C.T.","last_name":"Michaels","first_name":"Thomas C.T."},{"first_name":"Mengqi","last_name":"Xie","full_name":"Xie, Mengqi"},{"first_name":"Johannes","full_name":"Krausser, Johannes","last_name":"Krausser"},{"first_name":"Jiapeng","last_name":"Wei","full_name":"Wei, Jiapeng"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Michele","last_name":"Vendruscolo","full_name":"Vendruscolo, Michele"},{"full_name":"Knowles, Tuomas P.J.","last_name":"Knowles","first_name":"Tuomas P.J."}],"day":"28","scopus_import":"1","article_type":"original","date_created":"2022-08-14T22:01:45Z","volume":119,"abstract":[{"text":"Primary nucleation is the fundamental event that initiates the conversion of proteins from their normal physiological forms into pathological amyloid aggregates associated with the onset and development of disorders including systemic amyloidosis, as well as the neurodegenerative conditions Alzheimer’s and Parkinson’s diseases. It has become apparent that the presence of surfaces can dramatically modulate nucleation. However, the underlying physicochemical parameters governing this process have been challenging to elucidate, with interfaces in some cases having been found to accelerate aggregation, while in others they can inhibit the kinetics of this process. Here we show through kinetic analysis that for three different fibril-forming proteins, interfaces affect the aggregation reaction mainly through modulating the primary nucleation step. Moreover, we show through direct measurements of the Gibbs free energy of adsorption, combined with theory and coarse-grained computer simulations, that overall nucleation rates are suppressed at high and at low surface interaction strengths but significantly enhanced at intermediate strengths, and we verify these regimes experimentally. Taken together, these results provide a quantitative description of the fundamental process which triggers amyloid formation and shed light on the key factors that control this process.","lang":"eng"}],"tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"intvolume":"       119","has_accepted_license":"1","publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"file_date_updated":"2023-10-04T09:05:44Z","month":"07","file":[{"file_id":"14386","date_updated":"2023-10-04T09:05:44Z","creator":"dernst","date_created":"2023-10-04T09:05:44Z","file_size":2476021,"checksum":"0fe3878896cbeb6c44e29222ec2f336a","relation":"main_file","content_type":"application/pdf","access_level":"open_access","file_name":"2022_PNAS_Toprakcioglu.pdf","success":1}],"article_number":"e2109718119","department":[{"_id":"AnSa"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"31","citation":{"chicago":"Toprakcioglu, Zenon, Ayaka Kamada, Thomas C.T. Michaels, Mengqi Xie, Johannes Krausser, Jiapeng Wei, Anđela Šarić, Michele Vendruscolo, and Tuomas P.J. Knowles. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2109718119\">https://doi.org/10.1073/pnas.2109718119</a>.","ista":"Toprakcioglu Z, Kamada A, Michaels TCT, Xie M, Krausser J, Wei J, Šarić A, Vendruscolo M, Knowles TPJ. 2022. Adsorption free energy predicts amyloid protein nucleation rates. Proceedings of the National Academy of Sciences of the United States of America. 119(31), e2109718119.","mla":"Toprakcioglu, Zenon, et al. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31, e2109718119, Proceedings of the National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2109718119\">10.1073/pnas.2109718119</a>.","apa":"Toprakcioglu, Z., Kamada, A., Michaels, T. C. T., Xie, M., Krausser, J., Wei, J., … Knowles, T. P. J. (2022). Adsorption free energy predicts amyloid protein nucleation rates. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. Proceedings of the National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2109718119\">https://doi.org/10.1073/pnas.2109718119</a>","ama":"Toprakcioglu Z, Kamada A, Michaels TCT, et al. Adsorption free energy predicts amyloid protein nucleation rates. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2022;119(31). doi:<a href=\"https://doi.org/10.1073/pnas.2109718119\">10.1073/pnas.2109718119</a>","short":"Z. Toprakcioglu, A. Kamada, T.C.T. Michaels, M. Xie, J. Krausser, J. Wei, A. Šarić, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy of Sciences of the United States of America 119 (2022).","ieee":"Z. Toprakcioglu <i>et al.</i>, “Adsorption free energy predicts amyloid protein nucleation rates,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022."},"publisher":"Proceedings of the National Academy of Sciences","doi":"10.1073/pnas.2109718119","article_processing_charge":"No","type":"journal_article","date_updated":"2023-10-04T09:06:52Z","_id":"11841","ddc":["570"],"quality_controlled":"1","external_id":{"isi":["000903753500002"]},"year":"2022","isi":1,"project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"status":"public","publication":"Proceedings of the National Academy of Sciences of the United States of America","acknowledgement":"The research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt\r\n(agreement 337969). We are grateful for financial support from the Biotechnology and Biological Sciences Research Council (BBSRC) (T.P.J.K.), the Newman\r\nFoundation (T.P.J.K.), the Wellcome Trust (T.P.J.K. and M.V.), Peterhouse College\r\nCambridge (T.C.T.M.), the ERC Starting Grant (StG) Non-Equilibrium Protein Assembly (NEPA) (A.S.), the Royal Society (A.S.), the Academy of Medical Sciences\r\n(A.S. and J.K.), and the Cambridge Centre for Misfolding Diseases (CMD).","date_published":"2022-07-28T00:00:00Z","ec_funded":1},{"doi":"10.1103/PhysRevLett.129.268101","article_processing_charge":"No","publisher":"American Physical Society","date_updated":"2023-08-03T14:10:59Z","_id":"12108","type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.05.10.490642 "}],"quality_controlled":"1","isi":1,"year":"2022","external_id":{"isi":["000906721500001"],"pmid":["36608212"]},"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"},{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"},{"name":"The evolution of trafficking: from archaea to eukaryotes","grant_number":"96752","_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222"}],"status":"public","publication":"Physical Review Letters","pmid":1,"ec_funded":1,"date_published":"2022-12-23T00:00:00Z","acknowledgement":"We thank T. C. T. Michaels and J. Palacci for useful discussions. We thank Claudia Flandoli for the illustrations in Fig. 1(b) and Fig. 2. We acknowledge funding by the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie Grant\r\nAgreement No. 101034413 (I. P.), the Royal Society Grant No. UF160266 (A. Š.), the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (Grant No. 802960; B. M., I. P., and A. Š.), and the Volkswagen Foundation\r\nLife Grant (B. B. and A. Š). ","author":[{"first_name":"Billie","last_name":"Meadowcroft","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","full_name":"Meadowcroft, Billie"},{"id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","full_name":"Palaia, Ivan","last_name":"Palaia","orcid":" 0000-0002-8843-9485 ","first_name":"Ivan"},{"first_name":"Anna Katharina","full_name":"Pfitzner, Anna Katharina","last_name":"Pfitzner"},{"first_name":"Aurélien","full_name":"Roux, Aurélien","last_name":"Roux"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"}],"day":"23","scopus_import":"1","oa_version":"Preprint","title":"Mechanochemical rules for shape-shifting filaments that remodel membranes","volume":129,"article_type":"original","date_created":"2023-01-08T23:00:53Z","abstract":[{"lang":"eng","text":"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."}],"intvolume":"       129","publication_status":"published","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"month":"12","department":[{"_id":"AnSa"}],"article_number":"268101","oa":1,"language":[{"iso":"eng"}],"issue":"26","citation":{"ieee":"B. Meadowcroft, I. Palaia, A. K. Pfitzner, A. Roux, B. Baum, and A. Šarić, “Mechanochemical rules for shape-shifting filaments that remodel membranes,” <i>Physical Review Letters</i>, vol. 129, no. 26. American Physical Society, 2022.","short":"B. Meadowcroft, I. Palaia, A.K. Pfitzner, A. Roux, B. Baum, A. Šarić, Physical Review Letters 129 (2022).","ama":"Meadowcroft B, Palaia I, Pfitzner AK, Roux A, Baum B, Šarić A. Mechanochemical rules for shape-shifting filaments that remodel membranes. <i>Physical Review Letters</i>. 2022;129(26). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.129.268101\">10.1103/PhysRevLett.129.268101</a>","apa":"Meadowcroft, B., Palaia, I., Pfitzner, A. K., Roux, A., Baum, B., &#38; Šarić, A. (2022). Mechanochemical rules for shape-shifting filaments that remodel membranes. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.129.268101\">https://doi.org/10.1103/PhysRevLett.129.268101</a>","mla":"Meadowcroft, Billie, et al. “Mechanochemical Rules for Shape-Shifting Filaments That Remodel Membranes.” <i>Physical Review Letters</i>, vol. 129, no. 26, 268101, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.129.268101\">10.1103/PhysRevLett.129.268101</a>.","ista":"Meadowcroft B, Palaia I, Pfitzner AK, Roux A, Baum B, Šarić A. 2022. Mechanochemical rules for shape-shifting filaments that remodel membranes. Physical Review Letters. 129(26), 268101.","chicago":"Meadowcroft, Billie, Ivan Palaia, Anna Katharina Pfitzner, Aurélien Roux, Buzz Baum, and Anđela Šarić. “Mechanochemical Rules for Shape-Shifting Filaments That Remodel Membranes.” <i>Physical Review Letters</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevLett.129.268101\">https://doi.org/10.1103/PhysRevLett.129.268101</a>."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"title":"Modelling membrane reshaping by staged polymerization of ESCRT-III filaments","oa_version":"Published Version","author":[{"first_name":"Xiuyun","last_name":"Jiang","full_name":"Jiang, Xiuyun"},{"last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, Lena","first_name":"Lena"},{"first_name":"Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714","full_name":"Vanhille-Campos, Christian Eduardo","last_name":"Vanhille-Campos"},{"first_name":"Anna-Katharina","last_name":"Pfitzner","full_name":"Pfitzner, Anna-Katharina"},{"first_name":"Elene","full_name":"Lominadze, Elene","last_name":"Lominadze"},{"first_name":"Aurélien","full_name":"Roux, Aurélien","last_name":"Roux"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"}],"scopus_import":"1","day":"17","article_type":"original","date_created":"2023-01-12T12:08:10Z","volume":18,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":"        18","abstract":[{"text":"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.","lang":"eng"}],"has_accepted_license":"1","publication_identifier":{"issn":["1553-7358"]},"publication_status":"published","file_date_updated":"2023-01-24T10:45:01Z","month":"10","file":[{"content_type":"application/pdf","access_level":"open_access","file_name":"2022_PLoSCompBio_Jiang.pdf","success":1,"checksum":"bada6a7865e470cf42bbdfa67dd471d2","relation":"main_file","date_updated":"2023-01-24T10:45:01Z","creator":"dernst","date_created":"2023-01-24T10:45:01Z","file_size":2641067,"file_id":"12359"}],"article_number":"e1010586","department":[{"_id":"AnSa"}],"language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"10","citation":{"ama":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, et al. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. <i>PLOS Computational Biology</i>. 2022;18(10). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">10.1371/journal.pcbi.1010586</a>","ieee":"X. Jiang <i>et al.</i>, “Modelling membrane reshaping by staged polymerization of ESCRT-III filaments,” <i>PLOS Computational Biology</i>, vol. 18, no. 10. Public Library of Science, 2022.","short":"X. Jiang, L. Harker-Kirschneck, C.E. Vanhille-Campos, A.-K. Pfitzner, E. Lominadze, A. Roux, B. Baum, A. Šarić, PLOS Computational Biology 18 (2022).","chicago":"Jiang, Xiuyun, Lena Harker-Kirschneck, Christian Eduardo Vanhille-Campos, Anna-Katharina Pfitzner, Elene Lominadze, Aurélien Roux, Buzz Baum, and Anđela Šarić. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” <i>PLOS Computational Biology</i>. Public Library of Science, 2022. <a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">https://doi.org/10.1371/journal.pcbi.1010586</a>.","ista":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, Pfitzner A-K, Lominadze E, Roux A, Baum B, Šarić A. 2022. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational Biology. 18(10), e1010586.","apa":"Jiang, X., Harker-Kirschneck, L., Vanhille-Campos, C. E., Pfitzner, A.-K., Lominadze, E., Roux, A., … Šarić, A. (2022). Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. <i>PLOS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">https://doi.org/10.1371/journal.pcbi.1010586</a>","mla":"Jiang, Xiuyun, et al. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” <i>PLOS Computational Biology</i>, vol. 18, no. 10, e1010586, Public Library of Science, 2022, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1010586\">10.1371/journal.pcbi.1010586</a>."},"publisher":"Public Library of Science","doi":"10.1371/journal.pcbi.1010586","article_processing_charge":"No","type":"journal_article","date_updated":"2023-08-04T09:03:21Z","_id":"12152","ddc":["570"],"quality_controlled":"1","external_id":{"isi":["000924885500005"]},"related_material":{"link":[{"relation":"software","url":"https://github.com/sharonJXY/3-filament-model"}]},"isi":1,"year":"2022","keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"},{"grant_number":"96752","name":"The evolution of trafficking: from archaea to eukaryotes","_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222"}],"status":"public","publication":"PLOS Computational Biology","acknowledgement":"A.S . received an award from European Research Council (https://erc.europa.eu, “NEPA\"\r\n802960), and an award from the Royal Society (https://royalsociety.org, UF160266). L. H.-K.\r\nreceived an award from the Biotechnology and Biological Sciences Research Council (https://\r\nwww.ukri.org/councils/bbsrc/). E. L. received an award from the University College London (https://www.ucl.ac.uk/biophysics/news/2022/feb/applications-biop-brian-duff-and-ipls-summerundergraduate-studentships-now-open, Brian Duff Undergraduate Summer Research Studentship). B.B. and A.S. received an award from Volkswagen Foundation https://www.volkswagenstiftung.de/en/foundation, Az 96727), and an award from Medical Research Council (https://www.ukri.org/councils/mrc, MC_CF1226). A. R. received an\r\naward from the Swiss National Fund for Research (https://www.snf.ch/en, 31003A_130520,\r\n31003A_149975, and 31003A_173087) and an award from the European Research Council\r\nConsolidator (https://erc.europa.eu, 311536). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","date_published":"2022-10-17T00:00:00Z","ec_funded":1},{"article_number":"943355","file":[{"checksum":"e67d16113ffb4fb4fa38a183d169f210","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2022_FrontiersNeuroscience_Weiffert2.pdf","file_id":"12442","date_updated":"2023-01-30T09:15:13Z","creator":"dernst","date_created":"2023-01-30T09:15:13Z","file_size":19798610}],"department":[{"_id":"AnSa"}],"month":"09","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Weiffert, Tanja, Georg Meisl, Samo Curk, Risto Cukalevski, Anđela Šarić, Tuomas P. J. Knowles, and Sara Linse. “Influence of Denaturants on Amyloid Β42 Aggregation Kinetics.” <i>Frontiers in Neuroscience</i>. Frontiers Media, 2022. <a href=\"https://doi.org/10.3389/fnins.2022.943355\">https://doi.org/10.3389/fnins.2022.943355</a>.","ista":"Weiffert T, Meisl G, Curk S, Cukalevski R, Šarić A, Knowles TPJ, Linse S. 2022. Influence of denaturants on amyloid β42 aggregation kinetics. Frontiers in Neuroscience. 16, 943355.","mla":"Weiffert, Tanja, et al. “Influence of Denaturants on Amyloid Β42 Aggregation Kinetics.” <i>Frontiers in Neuroscience</i>, vol. 16, 943355, Frontiers Media, 2022, doi:<a href=\"https://doi.org/10.3389/fnins.2022.943355\">10.3389/fnins.2022.943355</a>.","apa":"Weiffert, T., Meisl, G., Curk, S., Cukalevski, R., Šarić, A., Knowles, T. P. J., &#38; Linse, S. (2022). Influence of denaturants on amyloid β42 aggregation kinetics. <i>Frontiers in Neuroscience</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fnins.2022.943355\">https://doi.org/10.3389/fnins.2022.943355</a>","ama":"Weiffert T, Meisl G, Curk S, et al. Influence of denaturants on amyloid β42 aggregation kinetics. <i>Frontiers in Neuroscience</i>. 2022;16. doi:<a href=\"https://doi.org/10.3389/fnins.2022.943355\">10.3389/fnins.2022.943355</a>","short":"T. Weiffert, G. Meisl, S. Curk, R. Cukalevski, A. Šarić, T.P.J. Knowles, S. Linse, Frontiers in Neuroscience 16 (2022).","ieee":"T. Weiffert <i>et al.</i>, “Influence of denaturants on amyloid β42 aggregation kinetics,” <i>Frontiers in Neuroscience</i>, vol. 16. Frontiers Media, 2022."},"language":[{"iso":"eng"}],"oa":1,"article_type":"original","date_created":"2023-01-16T09:56:43Z","volume":16,"oa_version":"Published Version","title":"Influence of denaturants on amyloid β42 aggregation kinetics","author":[{"last_name":"Weiffert","full_name":"Weiffert, Tanja","first_name":"Tanja"},{"full_name":"Meisl, Georg","last_name":"Meisl","first_name":"Georg"},{"first_name":"Samo","last_name":"Curk","full_name":"Curk, Samo"},{"first_name":"Risto","last_name":"Cukalevski","full_name":"Cukalevski, Risto"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J.","last_name":"Knowles"},{"full_name":"Linse, Sara","last_name":"Linse","first_name":"Sara"}],"day":"20","scopus_import":"1","publication_identifier":{"issn":["1662-453X"]},"publication_status":"published","file_date_updated":"2023-01-30T09:15:13Z","intvolume":"        16","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"lang":"eng","text":"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 <jats:italic>in vitro</jats:italic> 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."}],"has_accepted_license":"1","keyword":["General Neuroscience"],"external_id":{"isi":["000866287100001"]},"year":"2022","isi":1,"date_published":"2022-09-20T00:00:00Z","acknowledgement":"This work was supported by grants from the Swedish Research Council (grant no. 2015-00143) and the European Research Council (grant no. 340890).","status":"public","publication":"Frontiers in Neuroscience","type":"journal_article","date_updated":"2023-08-04T09:48:56Z","_id":"12251","publisher":"Frontiers Media","doi":"10.3389/fnins.2022.943355","article_processing_charge":"No","quality_controlled":"1","ddc":["570"]},{"author":[{"last_name":"Palaia","full_name":"Palaia, Ivan","first_name":"Ivan"},{"first_name":"Alexandru","last_name":"Paraschiv","full_name":"Paraschiv, Alexandru"},{"full_name":"Debets, Vincent","last_name":"Debets","first_name":"Vincent"},{"first_name":"Cornelis","full_name":"Storm, Cornelis","last_name":"Storm"},{"last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","orcid":"0000-0002-7854-2139","first_name":"Anđela"}],"doi":"10.1021/acsnano.1c02777 ","article_processing_charge":"No","day":"22","publisher":"American Chemical Society","title":"Durotaxis of passive nanoparticles on elastic membranes","oa_version":"Preprint","date_updated":"2021-10-12T09:50:19Z","_id":"10124","type":"journal_article","article_type":"original","date_created":"2021-10-12T07:31:21Z","abstract":[{"text":"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 non-uniform mechanical environments. Specifically, we study the motion of a passive nanoparticle adhering to a mechanically non-uniform elastic membrane. We observe a non-monotonic 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.","lang":"eng"}],"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.04.01.438065","open_access":"1"}],"quality_controlled":"1","publication_status":"published","year":"2021","external_id":{"pmid":["34550677 "]},"month":"09","oa":1,"publication":"ACS Nano","language":[{"iso":"eng"}],"extern":"1","status":"public","pmid":1,"citation":{"mla":"Palaia, Ivan, et al. “Durotaxis of Passive Nanoparticles on Elastic Membranes.” <i>ACS Nano</i>, American Chemical Society, 2021, doi:<a href=\"https://doi.org/10.1021/acsnano.1c02777 \">10.1021/acsnano.1c02777 </a>.","apa":"Palaia, I., Paraschiv, A., Debets, V., Storm, C., &#38; Šarić, A. (2021). Durotaxis of passive nanoparticles on elastic membranes. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.1c02777 \">https://doi.org/10.1021/acsnano.1c02777 </a>","ista":"Palaia I, Paraschiv A, Debets V, Storm C, Šarić A. 2021. Durotaxis of passive nanoparticles on elastic membranes. ACS Nano.","chicago":"Palaia, Ivan, Alexandru Paraschiv, Vincent Debets, Cornelis Storm, and Anđela Šarić. “Durotaxis of Passive Nanoparticles on Elastic Membranes.” <i>ACS Nano</i>. American Chemical Society, 2021. <a href=\"https://doi.org/10.1021/acsnano.1c02777 \">https://doi.org/10.1021/acsnano.1c02777 </a>.","short":"I. Palaia, A. Paraschiv, V. Debets, C. Storm, A. Šarić, ACS Nano (2021).","ieee":"I. Palaia, A. Paraschiv, V. Debets, C. Storm, and A. Šarić, “Durotaxis of passive nanoparticles on elastic membranes,” <i>ACS Nano</i>. American Chemical Society, 2021.","ama":"Palaia I, Paraschiv A, Debets V, Storm C, Šarić A. Durotaxis of passive nanoparticles on elastic membranes. <i>ACS Nano</i>. 2021. doi:<a href=\"https://doi.org/10.1021/acsnano.1c02777 \">10.1021/acsnano.1c02777 </a>"},"acknowledgement":"We acknowledge support from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the Royal Society (A.Š.) and the European Research Council (I.P. and A.Š.).","date_published":"2021-09-22T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"extern":"1","status":"public","publication":"bioRxiv","language":[{"iso":"eng"}],"oa":1,"acknowledgement":"We acknowledge support from the Biotechnology and Biological Sciences Research Council (L.H.K.), EPSRC (A.E.H), UCL IPLS (T.Y and D. H.), Wellcome Trust (203276/Z/16/Z, A.P., S.C., R. H., B.B.), Volkswagen Foundation (Az 96727, A.P., B.B., A.Š.), MRC (MC CF1226, R.H., B.B., A.Š.), the ERC grant (”NEPA” 802960, A.Š.), the Royal Society (C.V.-H., A.Š.), the UK Materials and Molecular Modelling Hub for computational resources (EP/P020194/1).","date_published":"2021-03-23T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Harker-Kirschneck L, Hafner AE, Yao T, et al. Physical mechanisms of ESCRT-III-driven cell division in archaea. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2021.03.23.436559\">10.1101/2021.03.23.436559</a>","short":"L. Harker-Kirschneck, A.E. Hafner, T. Yao, A. Pulschen, F. Hurtig, C. Vanhille-Campos, D. Hryniuk, S. Culley, R. Henriques, B. Baum, A. Šarić, BioRxiv (n.d.).","ieee":"L. Harker-Kirschneck <i>et al.</i>, “Physical mechanisms of ESCRT-III-driven cell division in archaea,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory.","ista":"Harker-Kirschneck L, Hafner AE, Yao T, Pulschen A, Hurtig F, Vanhille-Campos C, Hryniuk D, Culley S, Henriques R, Baum B, Šarić A. Physical mechanisms of ESCRT-III-driven cell division in archaea. bioRxiv, <a href=\"https://doi.org/10.1101/2021.03.23.436559\">10.1101/2021.03.23.436559</a>.","chicago":"Harker-Kirschneck, L., A. E. Hafner, T. Yao, A. Pulschen, F. Hurtig, C. Vanhille-Campos, D. Hryniuk, et al. “Physical Mechanisms of ESCRT-III-Driven Cell Division in Archaea.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, n.d. <a href=\"https://doi.org/10.1101/2021.03.23.436559\">https://doi.org/10.1101/2021.03.23.436559</a>.","mla":"Harker-Kirschneck, L., et al. “Physical Mechanisms of ESCRT-III-Driven Cell Division in Archaea.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, doi:<a href=\"https://doi.org/10.1101/2021.03.23.436559\">10.1101/2021.03.23.436559</a>.","apa":"Harker-Kirschneck, L., Hafner, A. E., Yao, T., Pulschen, A., Hurtig, F., Vanhille-Campos, C., … Šarić, A. (n.d.). Physical mechanisms of ESCRT-III-driven cell division in archaea. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2021.03.23.436559\">https://doi.org/10.1101/2021.03.23.436559</a>"},"month":"03","year":"2021","abstract":[{"lang":"eng","text":"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 protein assemblies. Here we developed the first physical model for the division of archaeal cells, which despite their structural simplicity share machinery and evolutionary origins with eukaryotes. We show how active geometry changes of elastic ESCRT-III filaments, coupled to filament disassembly, are sufficient to efficiently split the cell. We explore how the non-equilibrium processes that govern the filament behaviour impact the resulting cell division. We show how a quantitative comparison between our simulations and dynamic data for ESCRTIII-mediated division in Sulfolobus acidocaldarius, the closest archaeal relative to eukaryotic cells that can currently be cultured in the lab, and reveal the most likely physical mechanism behind its division."}],"publication_status":"submitted","main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2021.03.23.436559","open_access":"1"}],"oa_version":"Preprint","title":"Physical mechanisms of ESCRT-III-driven cell division in archaea","publisher":"Cold Spring Harbor Laboratory","doi":"10.1101/2021.03.23.436559","author":[{"first_name":"L.","last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, L."},{"first_name":"A. E.","last_name":"Hafner","full_name":"Hafner, A. E."},{"first_name":"T.","last_name":"Yao","full_name":"Yao, T."},{"first_name":"A.","full_name":"Pulschen, A.","last_name":"Pulschen"},{"full_name":"Hurtig, F.","last_name":"Hurtig","first_name":"F."},{"full_name":"Vanhille-Campos, C.","last_name":"Vanhille-Campos","first_name":"C."},{"last_name":"Hryniuk","full_name":"Hryniuk, D.","first_name":"D."},{"last_name":"Culley","full_name":"Culley, S.","first_name":"S."},{"first_name":"R.","last_name":"Henriques","full_name":"Henriques, R."},{"first_name":"B.","last_name":"Baum","full_name":"Baum, B."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"}],"day":"23","article_processing_charge":"No","type":"preprint","date_created":"2021-10-12T07:45:07Z","date_updated":"2021-10-12T09:50:26Z","_id":"10125"},{"publisher":"Rockefeller University Press","doi":"10.1083/jcb.202009154","article_processing_charge":"No","type":"journal_article","date_updated":"2021-11-25T15:33:08Z","_id":"10337","quality_controlled":"1","external_id":{"pmid":["33929486"]},"year":"2021","keyword":["cell biology"],"status":"public","publication":"Journal of Cell Biology","extern":"1","date_published":"2021-04-30T00:00:00Z","acknowledgement":"Charles H. Hood Foundation (NO AWARD) ; Rally Foundation (NO AWARD)","pmid":1,"oa_version":"None","title":"PLCγ1 promotes phase separation of T cell signaling components","author":[{"last_name":"Zeng","full_name":"Zeng, Longhui","first_name":"Longhui"},{"full_name":"Palaia, Ivan","last_name":"Palaia","first_name":"Ivan"},{"last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"first_name":"Xiaolei","last_name":"Su","full_name":"Su, Xiaolei"}],"day":"30","scopus_import":"1","article_type":"original","date_created":"2021-11-25T15:21:30Z","volume":220,"abstract":[{"lang":"eng","text":"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."}],"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"intvolume":"       220","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"publication_status":"published","month":"04","article_number":"e202009154","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"6","citation":{"apa":"Zeng, L., Palaia, I., Šarić, A., &#38; Su, X. (2021). PLCγ1 promotes phase separation of T cell signaling components. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202009154\">https://doi.org/10.1083/jcb.202009154</a>","mla":"Zeng, Longhui, et al. “PLCγ1 Promotes Phase Separation of T Cell Signaling Components.” <i>Journal of Cell Biology</i>, vol. 220, no. 6, e202009154, Rockefeller University Press, 2021, doi:<a href=\"https://doi.org/10.1083/jcb.202009154\">10.1083/jcb.202009154</a>.","chicago":"Zeng, Longhui, Ivan Palaia, Anđela Šarić, and Xiaolei Su. “PLCγ1 Promotes Phase Separation of T Cell Signaling Components.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2021. <a href=\"https://doi.org/10.1083/jcb.202009154\">https://doi.org/10.1083/jcb.202009154</a>.","ista":"Zeng L, Palaia I, Šarić A, Su X. 2021. PLCγ1 promotes phase separation of T cell signaling components. Journal of Cell Biology. 220(6), e202009154.","ieee":"L. Zeng, I. Palaia, A. Šarić, and X. Su, “PLCγ1 promotes phase separation of T cell signaling components,” <i>Journal of Cell Biology</i>, vol. 220, no. 6. Rockefeller University Press, 2021.","short":"L. Zeng, I. Palaia, A. Šarić, X. Su, Journal of Cell Biology 220 (2021).","ama":"Zeng L, Palaia I, Šarić A, Su X. PLCγ1 promotes phase separation of T cell signaling components. <i>Journal of Cell Biology</i>. 2021;220(6). doi:<a href=\"https://doi.org/10.1083/jcb.202009154\">10.1083/jcb.202009154</a>"}},{"type":"journal_article","_id":"10338","date_updated":"2022-04-01T10:34:38Z","publisher":"Elsevier","article_processing_charge":"No","doi":"10.1016/j.bpj.2021.01.039","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.10.01.322156"}],"page":"1565-1577","keyword":["biophysics"],"external_id":{"pmid":["33617830"]},"year":"2021","date_published":"2021-02-19T00:00:00Z","pmid":1,"extern":"1","publication":"Biophysical Journal","status":"public","date_created":"2021-11-25T15:36:36Z","article_type":"original","volume":120,"oa_version":"Preprint","title":"Physical modeling of multivalent interactions in the nuclear pore complex","scopus_import":"1","day":"19","author":[{"full_name":"Davis, Luke K.","last_name":"Davis","first_name":"Luke K."},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić"},{"first_name":"Bart W.","full_name":"Hoogenboom, Bart W.","last_name":"Hoogenboom"},{"first_name":"Anton","last_name":"Zilman","full_name":"Zilman, Anton"}],"publication_status":"published","publication_identifier":{"issn":["0006-3495"]},"intvolume":"       120","abstract":[{"text":"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.","lang":"eng"}],"month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Davis, Luke K., et al. “Physical Modeling of Multivalent Interactions in the Nuclear Pore Complex.” <i>Biophysical Journal</i>, vol. 120, no. 9, Elsevier, 2021, pp. 1565–77, doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.01.039\">10.1016/j.bpj.2021.01.039</a>.","apa":"Davis, L. K., Šarić, A., Hoogenboom, B. W., &#38; Zilman, A. (2021). Physical modeling of multivalent interactions in the nuclear pore complex. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2021.01.039\">https://doi.org/10.1016/j.bpj.2021.01.039</a>","chicago":"Davis, Luke K., Anđela Šarić, Bart W. Hoogenboom, and Anton Zilman. “Physical Modeling of Multivalent Interactions in the Nuclear Pore Complex.” <i>Biophysical Journal</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.bpj.2021.01.039\">https://doi.org/10.1016/j.bpj.2021.01.039</a>.","ista":"Davis LK, Šarić A, Hoogenboom BW, Zilman A. 2021. Physical modeling of multivalent interactions in the nuclear pore complex. Biophysical Journal. 120(9), 1565–1577.","short":"L.K. Davis, A. Šarić, B.W. Hoogenboom, A. Zilman, Biophysical Journal 120 (2021) 1565–1577.","ieee":"L. K. Davis, A. Šarić, B. W. Hoogenboom, and A. Zilman, “Physical modeling of multivalent interactions in the nuclear pore complex,” <i>Biophysical Journal</i>, vol. 120, no. 9. Elsevier, pp. 1565–1577, 2021.","ama":"Davis LK, Šarić A, Hoogenboom BW, Zilman A. Physical modeling of multivalent interactions in the nuclear pore complex. <i>Biophysical Journal</i>. 2021;120(9):1565-1577. doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.01.039\">10.1016/j.bpj.2021.01.039</a>"},"issue":"9","language":[{"iso":"eng"}],"oa":1},{"language":[{"iso":"eng"}],"oa":1,"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","issue":"14","citation":{"mla":"Vanhille-Campos, Christian, and Anđela Šarić. “Modelling the Dynamics of Vesicle Reshaping and Scission under Osmotic Shocks.” <i>Soft Matter</i>, vol. 17, no. 14, Royal Society of Chemistry, 2021, pp. 3798–806, doi:<a href=\"https://doi.org/10.1039/d0sm02012e\">10.1039/d0sm02012e</a>.","apa":"Vanhille-Campos, C., &#38; Šarić, A. (2021). Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. <i>Soft Matter</i>. Royal Society of Chemistry. <a href=\"https://doi.org/10.1039/d0sm02012e\">https://doi.org/10.1039/d0sm02012e</a>","chicago":"Vanhille-Campos, Christian, and Anđela Šarić. “Modelling the Dynamics of Vesicle Reshaping and Scission under Osmotic Shocks.” <i>Soft Matter</i>. Royal Society of Chemistry, 2021. <a href=\"https://doi.org/10.1039/d0sm02012e\">https://doi.org/10.1039/d0sm02012e</a>.","ista":"Vanhille-Campos C, Šarić A. 2021. Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. Soft Matter. 17(14), 3798–3806.","short":"C. Vanhille-Campos, A. Šarić, Soft Matter 17 (2021) 3798–3806.","ieee":"C. Vanhille-Campos and A. Šarić, “Modelling the dynamics of vesicle reshaping and scission under osmotic shocks,” <i>Soft Matter</i>, vol. 17, no. 14. Royal Society of Chemistry, pp. 3798–3806, 2021.","ama":"Vanhille-Campos C, Šarić A. Modelling the dynamics of vesicle reshaping and scission under osmotic shocks. <i>Soft Matter</i>. 2021;17(14):3798-3806. doi:<a href=\"https://doi.org/10.1039/d0sm02012e\">10.1039/d0sm02012e</a>"},"month":"02","license":"https://creativecommons.org/licenses/by-nc/3.0/","tmp":{"image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/3.0/legalcode","short":"CC BY-NC (3.0)"},"abstract":[{"lang":"eng","text":"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."}],"intvolume":"        17","publication_identifier":{"issn":["1744-683X"],"eissn":["1744-6848"]},"publication_status":"published","title":"Modelling the dynamics of vesicle reshaping and scission under osmotic shocks","oa_version":"Published Version","author":[{"first_name":"Christian","last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian"},{"first_name":"Anđela","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić"}],"scopus_import":"1","day":"16","article_type":"original","date_created":"2021-11-25T16:06:42Z","volume":17,"extern":"1","publication":"Soft Matter","status":"public","acknowledgement":"We acknowledge support from the Royal Society (C. V. C. and A. Sˇ.), the Medical Research Council (C. V. C. and A. Sˇ.), and the European Research Council (Starting grant ‘‘NEPA’’ 802960 to A. Sˇ.). We thank Johannes Krausser and Ivan Palaia for fruitful discussions.","date_published":"2021-02-16T00:00:00Z","pmid":1,"external_id":{"pmid":["33629089"]},"related_material":{"link":[{"url":"https://www.biorxiv.org/content/10.1101/2020.11.16.384602v2","relation":"earlier_version"}]},"year":"2021","keyword":["condensed matter physics","general chemistry"],"page":"3798-3806","quality_controlled":"1","main_file_link":[{"url":"https://pubs.rsc.org/en/content/articlehtml/2021/sm/d0sm02012e","open_access":"1"}],"publisher":"Royal Society of Chemistry","doi":"10.1039/d0sm02012e","article_processing_charge":"No","type":"journal_article","date_updated":"2021-11-30T08:20:09Z","_id":"10339"},{"oa":1,"language":[{"iso":"eng"}],"issue":"4","citation":{"short":"A. Paraschiv, T.J. Lagny, C.V. Campos, E. Coudrier, P. Bassereau, A. Šarić, Biophysical Journal 120 (2021) 598–606.","ieee":"A. Paraschiv, T. J. Lagny, C. V. Campos, E. Coudrier, P. Bassereau, and A. Šarić, “Influence of membrane-cortex linkers on the extrusion of membrane tubes,” <i>Biophysical Journal</i>, vol. 120, no. 4. Cell Press, pp. 598–606, 2021.","ama":"Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. Influence of membrane-cortex linkers on the extrusion of membrane tubes. <i>Biophysical Journal</i>. 2021;120(4):598-606. doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">10.1016/j.bpj.2020.12.028</a>","mla":"Paraschiv, Alexandru, et al. “Influence of Membrane-Cortex Linkers on the Extrusion of Membrane Tubes.” <i>Biophysical Journal</i>, vol. 120, no. 4, Cell Press, 2021, pp. 598–606, doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">10.1016/j.bpj.2020.12.028</a>.","apa":"Paraschiv, A., Lagny, T. J., Campos, C. V., Coudrier, E., Bassereau, P., &#38; Šarić, A. (2021). Influence of membrane-cortex linkers on the extrusion of membrane tubes. <i>Biophysical Journal</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">https://doi.org/10.1016/j.bpj.2020.12.028</a>","chicago":"Paraschiv, Alexandru, Thibaut J. Lagny, Christian Vanhille Campos, Evelyne Coudrier, Patricia Bassereau, and Anđela Šarić. “Influence of Membrane-Cortex Linkers on the Extrusion of Membrane Tubes.” <i>Biophysical Journal</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">https://doi.org/10.1016/j.bpj.2020.12.028</a>.","ista":"Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. 2021. Influence of membrane-cortex linkers on the extrusion of membrane tubes. Biophysical Journal. 120(4), 598–606."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"01","abstract":[{"text":"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.","lang":"eng"}],"intvolume":"       120","publication_status":"published","publication_identifier":{"issn":["0006-3495"]},"author":[{"last_name":"Paraschiv","full_name":"Paraschiv, Alexandru","first_name":"Alexandru"},{"first_name":"Thibaut J.","full_name":"Lagny, Thibaut J.","last_name":"Lagny"},{"full_name":"Campos, Christian Vanhille","last_name":"Campos","first_name":"Christian Vanhille"},{"last_name":"Coudrier","full_name":"Coudrier, Evelyne","first_name":"Evelyne"},{"last_name":"Bassereau","full_name":"Bassereau, Patricia","first_name":"Patricia"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić"}],"day":"16","scopus_import":"1","title":"Influence of membrane-cortex linkers on the extrusion of membrane tubes","oa_version":"Preprint","volume":120,"article_type":"original","date_created":"2021-11-25T16:18:23Z","extern":"1","publication":"Biophysical Journal","status":"public","pmid":1,"date_published":"2021-01-16T00:00:00Z","acknowledgement":"We thank Ewa Paluch, Alba Diz-Muñoz, Guillaume Salbreux, Guillaume Charras, and Shiladitya Banerjee for helpful discussions. We acknowledge support from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the UCL Institute for the Physics of Living Systems (A.P., C.V.C., and A.Š.), the Royal Society (C.V.C. and A.Š.), and the European Research Council (Starting grant EP/R011818/1 to A.Š.; E.C. and P.B. are partners of the advanced grant, project 339847) and from Institut Curie (E.C. and P.B.) and Centre National de la Recherche Scientifique (CNRS) (E.C. and P.B.). The P.B. and E.C. groups belong to Labex CelTisPhyBio (ANR-11-LABX0038) and to Paris Sciences et Lettres (ANR-10-IDEX-0001-02). T.L. received a PhD grant from Paris Sciences et Lettres Research University and support from the Institut Curie.","year":"2021","external_id":{"pmid":["33460596"]},"keyword":["biophysics"],"page":"598-606","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.07.28.224741"}],"quality_controlled":"1","doi":"10.1016/j.bpj.2020.12.028","article_processing_charge":"No","publisher":"Cell Press","date_updated":"2022-04-01T10:38:01Z","_id":"10340","type":"journal_article"}]