[{"OA_place":"repository","scopus_import":"1","corr_author":"1","publication_identifier":{"issn":["1292-8941"],"eissn":["1292-895X"]},"publisher":"Springer Nature","acknowledgement":"MR-V and RS are supported by Fondecyt Grant No. 1220536 and Millennium Science Initiative Program NCN19_170D of ANID, Chile. P.d.C. was supported by Scholarships Nos. 2021/10139-2 and 2022/13872-5 and ICTP-SAIFR Grant No. 2021/14335-0, all granted by São Paulo Research Foundation (FAPESP), Brazil.","volume":46,"article_type":"original","pmid":1,"date_created":"2023-10-22T22:01:13Z","type":"journal_article","month":"10","arxiv":1,"language":[{"iso":"eng"}],"department":[{"_id":"AnSa"}],"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2111.05952","open_access":"1"}],"oa":1,"day":"01","date_updated":"2025-09-09T13:08:14Z","title":"Mixtures of self-propelled particles interacting with asymmetric obstacles","doi":"10.1140/epje/s10189-023-00354-y","quality_controlled":"1","fulldoi":"https://doi.org/10.1140/epje/s10189-023-00354-y","isi":1,"date_published":"2023-10-01T00:00:00Z","oa_version":"Preprint","abstract":[{"text":"In the presence of an obstacle, active particles condensate into a surface “wetting” layer due to persistent motion. If the obstacle is asymmetric, a rectification current arises in addition to wetting. Asymmetric geometries are therefore commonly used to concentrate microorganisms like bacteria and sperms. However, most studies neglect the fact that biological active matter is diverse, composed of individuals with distinct self-propulsions. Using simulations, we study a mixture of “fast” and “slow” active Brownian disks in two dimensions interacting with large half-disk obstacles. With this prototypical obstacle geometry, we analyze how the stationary collective behavior depends on the degree of self-propulsion “diversity,” defined as proportional to the difference between the self-propulsion speeds, while keeping the average self-propulsion speed fixed. A wetting layer rich in fast particles arises. The rectification current is amplified by speed diversity due to a superlinear dependence of rectification on self-propulsion speed, which arises from cooperative effects. Thus, the total rectification current cannot be obtained from an effective one-component active fluid with the same average self-propulsion speed, highlighting the importance of considering diversity in active matter.","lang":"eng"}],"intvolume":"        46","issue":"10","publication_status":"published","author":[{"first_name":"Mauricio Nicolas","id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d","full_name":"Rojas Vega, Mauricio Nicolas","last_name":"Rojas Vega"},{"first_name":"Pablo","full_name":"De Castro, Pablo","last_name":"De Castro"},{"first_name":"Rodrigo","last_name":"Soto","full_name":"Soto, Rodrigo"}],"external_id":{"pmid":["37819444"],"isi":["001187541900001"],"arxiv":["2111.05952"]},"article_processing_charge":"No","citation":{"ama":"Rojas Vega MN, De Castro P, Soto R. Mixtures of self-propelled particles interacting with asymmetric obstacles. <i>The European Physical Journal E</i>. 2023;46(10). doi:<a href=\"https://doi.org/10.1140/epje/s10189-023-00354-y\">10.1140/epje/s10189-023-00354-y</a>","ieee":"M. N. Rojas Vega, P. De Castro, and R. Soto, “Mixtures of self-propelled particles interacting with asymmetric obstacles,” <i>The European Physical Journal E</i>, vol. 46, no. 10. Springer Nature, 2023.","ista":"Rojas Vega MN, De Castro P, Soto R. 2023. Mixtures of self-propelled particles interacting with asymmetric obstacles. The European Physical Journal E. 46(10), 95.","apa":"Rojas Vega, M. N., De Castro, P., &#38; Soto, R. (2023). Mixtures of self-propelled particles interacting with asymmetric obstacles. <i>The European Physical Journal E</i>. Springer Nature. <a href=\"https://doi.org/10.1140/epje/s10189-023-00354-y\">https://doi.org/10.1140/epje/s10189-023-00354-y</a>","short":"M.N. Rojas Vega, P. De Castro, R. Soto, The European Physical Journal E 46 (2023).","chicago":"Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Mixtures of Self-Propelled Particles Interacting with Asymmetric Obstacles.” <i>The European Physical Journal E</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1140/epje/s10189-023-00354-y\">https://doi.org/10.1140/epje/s10189-023-00354-y</a>.","mla":"Rojas Vega, Mauricio Nicolas, et al. “Mixtures of Self-Propelled Particles Interacting with Asymmetric Obstacles.” <i>The European Physical Journal E</i>, vol. 46, no. 10, 95, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1140/epje/s10189-023-00354-y\">10.1140/epje/s10189-023-00354-y</a>."},"article_number":"95","publication":"The European Physical Journal E","year":"2023","OA_type":"green","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","_id":"14442"},{"date_created":"2023-10-30T16:38:32Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_published":"2023-10-31T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:14472","oa_version":"Published Version","type":"research_data","ddc":["570"],"month":"10","abstract":[{"lang":"eng","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."}],"file":[{"file_name":"SGporecondensation-main.zip","creator":"ipalaia","success":1,"date_updated":"2023-10-30T16:31:08Z","access_level":"open_access","date_created":"2023-10-30T16:31:08Z","file_id":"14473","file_size":62821432,"checksum":"a18706e952e8660c51ede52a167270b7","content_type":"application/zip","relation":"main_file"},{"file_id":"14474","file_size":1697,"checksum":"389eab31c6509dbc05795017fb618758","content_type":"text/plain","relation":"main_file","file_name":"README.txt","creator":"dernst","success":1,"date_updated":"2023-10-31T08:57:50Z","access_level":"open_access","date_created":"2023-10-31T08:57:50Z"}],"department":[{"_id":"AnSa"}],"author":[{"id":"3adeca52-9313-11ed-b1ac-c170b2505714","full_name":"Vanhille-Campos, Christian Eduardo","last_name":"Vanhille-Campos","first_name":"Christian Eduardo"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić"}],"has_accepted_license":"1","file_date_updated":"2023-10-31T08:57:50Z","corr_author":"1","doi":"10.15479/AT:ISTA:14472","publisher":"Institute of Science and Technology Austria","year":"2023","tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)"},"date_updated":"2025-09-09T13:30:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Stress granules plug and stabilize damaged endolysosomal membranes","status":"public","_id":"14472","article_processing_charge":"No","citation":{"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>.","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>.","short":"C.E. Vanhille-Campos, A. Šarić, (2023).","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>","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>.","ieee":"C. E. Vanhille-Campos and A. Šarić, “Stress granules plug and stabilize damaged endolysosomal membranes.” Institute of Science and Technology Austria, 2023.","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>"},"oa":1,"related_material":{"record":[{"id":"14610","relation":"used_in_publication","status":"public"}]},"day":"31"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","_id":"14610","year":"2023","publication":"Nature","external_id":{"pmid":["37968398"],"isi":["001105882300018"]},"article_processing_charge":"Yes (via OA deal)","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>","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. 623, 1062–1069.","ieee":"C. Bussi <i>et al.</i>, “Stress granules plug and stabilize damaged endolysosomal membranes,” <i>Nature</i>, vol. 623. Springer Nature, pp. 1062–1069, 2023.","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>.","mla":"Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” <i>Nature</i>, vol. 623, Springer Nature, 2023, pp. 1062–69, doi:<a href=\"https://doi.org/10.1038/s41586-023-06726-w\">10.1038/s41586-023-06726-w</a>.","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 623 (2023) 1062–1069.","ama":"Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and stabilize damaged endolysosomal membranes. <i>Nature</i>. 2023;623:1062-1069. doi:<a href=\"https://doi.org/10.1038/s41586-023-06726-w\">10.1038/s41586-023-06726-w</a>"},"abstract":[{"lang":"eng","text":"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."}],"intvolume":"       623","author":[{"first_name":"Claudio","full_name":"Bussi, Claudio","last_name":"Bussi"},{"first_name":"Agustín","full_name":"Mangiarotti, Agustín","last_name":"Mangiarotti"},{"first_name":"Christian Eduardo","last_name":"Vanhille-Campos","id":"3adeca52-9313-11ed-b1ac-c170b2505714","full_name":"Vanhille-Campos, Christian Eduardo"},{"full_name":"Aylan, Beren","last_name":"Aylan","first_name":"Beren"},{"first_name":"Enrica","full_name":"Pellegrino, Enrica","last_name":"Pellegrino"},{"first_name":"Natalia","full_name":"Athanasiadi, Natalia","last_name":"Athanasiadi"},{"first_name":"Antony","full_name":"Fearns, Antony","last_name":"Fearns"},{"last_name":"Rodgers","full_name":"Rodgers, Angela","first_name":"Angela"},{"last_name":"Franzmann","full_name":"Franzmann, Titus M.","first_name":"Titus M."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","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.","full_name":"Gutierrez, Maximiliano G.","last_name":"Gutierrez"}],"publication_status":"published","oa_version":"Published Version","fulldoi":"https://doi.org/10.1038/s41586-023-06726-w","date_published":"2023-11-30T00:00:00Z","isi":1,"doi":"10.1038/s41586-023-06726-w","quality_controlled":"1","title":"Stress granules plug and stabilize damaged endolysosomal membranes","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-09-09T13:30:34Z","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-023-06882-z"}],"record":[{"relation":"research_data","id":"14472","status":"public"}]},"day":"30","oa":1,"file":[{"success":1,"date_updated":"2024-07-16T07:41:39Z","date_created":"2024-07-16T07:41:39Z","access_level":"open_access","file_name":"2023_Nature_Bussi.pdf","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_id":"17248","file_size":17047711,"checksum":"b939a19e4c228fbf3beca298ac2ac014"}],"language":[{"iso":"eng"}],"department":[{"_id":"AnSa"}],"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.","article_type":"original","volume":623,"date_created":"2023-11-27T07:56:37Z","pmid":1,"page":"1062-1069","type":"journal_article","month":"11","ddc":["570"],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"publisher":"Springer Nature","has_accepted_license":"1","scopus_import":"1","file_date_updated":"2024-07-16T07:41:39Z"},{"day":"01","oa":1,"title":"Transverse fluctuations control the assembly of semiflexible filaments","date_updated":"2025-09-09T13:35:06Z","publisher":"American Physical Society","publication_identifier":{"issn":["0031-9007"],"eissn":["1079-7114"]},"corr_author":"1","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2303.03088","open_access":"1"}],"department":[{"_id":"AnSa"}],"arxiv":1,"language":[{"iso":"eng"}],"month":"12","type":"journal_article","pmid":1,"date_created":"2023-12-10T23:00:57Z","acknowledgement":"The authors thank C´ecile Leduc and Duc-Quang Tran for invaluable help with understanding the experimental behavior of intermediate filaments, and Raphael Voituriez, Nicolas Levernier, and Alexander Grosberg for fruitful discussion on the theoretical model. V. S. also thanks Davide Michieletto, Maria Panoukidou, and Lorenzo Rovigatti for very helpful suggestions on the simulation model. M. L. was supported by Marie Curie Integration Grant No. PCIG12-GA-2012-334053, “Investissements d’Avenir” LabEx PALM (ANR-10-LABX- 0039-PALM), ANR Grants No. ANR-15-CE13-0004-03, No. ANR-21-CE11-0004-02 and No. ANR-22-CE30-0024, as well as ERC Starting Grant No. 677532. M.L.’s group belongs to the CNRS consortium AQV. Part of this work was performed using HPC resources from GENCI–IDRIS (Grants No. 2020-A0090712066 and No. 2021-A0110712066).","article_type":"original","volume":131,"publication":"Physical Review Letters","article_number":"228401","citation":{"ama":"Sorichetti V, Lenz M. Transverse fluctuations control the assembly of semiflexible filaments. <i>Physical Review Letters</i>. 2023;131(22). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">10.1103/PhysRevLett.131.228401</a>","short":"V. Sorichetti, M. Lenz, Physical Review Letters 131 (2023).","chicago":"Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” <i>Physical Review Letters</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">https://doi.org/10.1103/PhysRevLett.131.228401</a>.","mla":"Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” <i>Physical Review Letters</i>, vol. 131, no. 22, 228401, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">10.1103/PhysRevLett.131.228401</a>.","apa":"Sorichetti, V., &#38; Lenz, M. (2023). Transverse fluctuations control the assembly of semiflexible filaments. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.131.228401\">https://doi.org/10.1103/PhysRevLett.131.228401</a>","ieee":"V. Sorichetti and M. Lenz, “Transverse fluctuations control the assembly of semiflexible filaments,” <i>Physical Review Letters</i>, vol. 131, no. 22. American Physical Society, 2023.","ista":"Sorichetti V, Lenz M. 2023. Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. 131(22), 228401."},"article_processing_charge":"No","external_id":{"arxiv":["2303.03088"],"pmid":["38101392"],"isi":["001163810200008"]},"_id":"14655","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","year":"2023","quality_controlled":"1","doi":"10.1103/PhysRevLett.131.228401","publication_status":"published","issue":"22","author":[{"first_name":"Valerio","orcid":"0000-0002-9645-6576","last_name":"Sorichetti","full_name":"Sorichetti, Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b"},{"first_name":"Martin","full_name":"Lenz, Martin","last_name":"Lenz"}],"intvolume":"       131","abstract":[{"lang":"eng","text":"The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime where filaments’ ends find each other through bending fluctuations without the need for the whole filament to diffuse. This results in a very substantial speedup of assembly in physiological regimes, and could help with understanding the dynamics of actin and intermediate filaments in biological processes such as wound healing and cell division."}],"oa_version":"Preprint","fulldoi":"https://doi.org/10.1103/PhysRevLett.131.228401","isi":1,"date_published":"2023-12-01T00:00:00Z"},{"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14782","year":"2023","keyword":["Biophysics"],"publication":"Biophysical Journal","external_id":{"pmid":["36806830"],"isi":["001016792600001"]},"article_processing_charge":"Yes (in subscription journal)","citation":{"ama":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. Branched actin cortices reconstituted in vesicles sense membrane curvature. <i>Biophysical Journal</i>. 2023;122(11):2311-2324. doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">10.1016/j.bpj.2023.02.018</a>","chicago":"Baldauf, Lucia, Felix F Frey, Marcos Arribas Perez, Timon Idema, and Gijsje H. Koenderink. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” <i>Biophysical Journal</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">https://doi.org/10.1016/j.bpj.2023.02.018</a>.","mla":"Baldauf, Lucia, et al. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” <i>Biophysical Journal</i>, vol. 122, no. 11, Elsevier, 2023, pp. 2311–24, doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">10.1016/j.bpj.2023.02.018</a>.","short":"L. Baldauf, F.F. Frey, M. Arribas Perez, T. Idema, G.H. Koenderink, Biophysical Journal 122 (2023) 2311–2324.","ieee":"L. Baldauf, F. F. Frey, M. Arribas Perez, T. Idema, and G. H. Koenderink, “Branched actin cortices reconstituted in vesicles sense membrane curvature,” <i>Biophysical Journal</i>, vol. 122, no. 11. Elsevier, pp. 2311–2324, 2023.","ista":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. 2023. Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. 122(11), 2311–2324.","apa":"Baldauf, L., Frey, F. F., Arribas Perez, M., Idema, T., &#38; Koenderink, G. H. (2023). Branched actin cortices reconstituted in vesicles sense membrane curvature. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">https://doi.org/10.1016/j.bpj.2023.02.018</a>"},"abstract":[{"text":"The actin cortex is a complex cytoskeletal machinery that drives and responds to changes in cell shape. It must generate or adapt to plasma membrane curvature to facilitate diverse functions such as cell division, migration, and phagocytosis. Due to the complex molecular makeup of the actin cortex, it remains unclear whether actin networks are inherently able to sense and generate membrane curvature, or whether they rely on their diverse binding partners to accomplish this. Here, we show that curvature sensing is an inherent capability of branched actin networks nucleated by Arp2/3 and VCA. We develop a robust method to encapsulate actin inside giant unilamellar vesicles (GUVs) and assemble an actin cortex at the inner surface of the GUV membrane. We show that actin forms a uniform and thin cortical layer when present at high concentration and distinct patches associated with negative membrane curvature at low concentration. Serendipitously, we find that the GUV production method also produces dumbbell-shaped GUVs, which we explain using mathematical modeling in terms of membrane hemifusion of nested GUVs. We find that branched actin networks preferentially assemble at the neck of the dumbbells, which possess a micrometer-range convex curvature comparable with the curvature of the actin patches found in spherical GUVs. Minimal branched actin networks can thus sense membrane curvature, which may help mammalian cells to robustly recruit actin to curved membranes to facilitate diverse cellular functions such as cytokinesis and migration.","lang":"eng"}],"intvolume":"       122","author":[{"full_name":"Baldauf, Lucia","last_name":"Baldauf","first_name":"Lucia"},{"last_name":"Frey","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F","first_name":"Felix F"},{"full_name":"Arribas Perez, Marcos","last_name":"Arribas Perez","first_name":"Marcos"},{"first_name":"Timon","last_name":"Idema","full_name":"Idema, Timon"},{"first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H.","last_name":"Koenderink"}],"issue":"11","publication_status":"published","isi":1,"fulldoi":"https://doi.org/10.1016/j.bpj.2023.02.018","oa_version":"Published Version","date_published":"2023-06-06T00:00:00Z","doi":"10.1016/j.bpj.2023.02.018","quality_controlled":"1","title":"Branched actin cortices reconstituted in vesicles sense membrane curvature","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_updated":"2024-01-16T09:20:03Z","related_material":{"link":[{"url":"https://github.com/BioSoftMatterGroup/actin-curvature-sensing","relation":"software"}]},"day":"06","oa":1,"file":[{"file_size":3285810,"file_id":"14807","checksum":"70566e54cd95ea6df340909ad44c5cd5","content_type":"application/pdf","relation":"main_file","file_name":"2023_BiophysicalJournal_Baldauf.pdf","creator":"dernst","date_updated":"2024-01-16T09:09:29Z","success":1,"access_level":"open_access","date_created":"2024-01-16T09:09:29Z"}],"language":[{"iso":"eng"}],"department":[{"_id":"AnSa"}],"acknowledgement":"We thank Jeffrey den Haan for protein purification, Kristina Ganzinger (AMOLF) for providing the 10xHis VCA construct, David Kovar (University of Chicago) for the CP constructs, and Michael Way (Crick Institute) for providing purified human Arp2/3 proteins. We are grateful to Iris Lambert for early actin encapsulation experiments that formed the basis for establishing the eDICE method, to Federico Fanalista for acquiring images of dumbbell-shaped GUVs in samples produced by cDICE, and to Tom Aarts for images of dumbbell-shaped GUVs produced by gel-assisted swelling. Lennard van Buren is thanked for his help with image analysis to quantify actin concentrations in GUVs. We thank Kristina Ganzinger (AMOLF) for hosting us to perform pyrene assays in her lab, and Balász Antalicz (AMOLF) for technical assistance with the spectrophotometer. The authors also thank Matthieu Piel and Daniel Fletcher for insightful and inspiring discussions. We acknowledge financial support from The Netherlands Organization of Scientific Research (NWO/OCW) Gravitation program Building a Synthetic Cell (BaSyC) (024.003.019). F.F. gratefully acknowledges funding from the Kavli Synergy program of the Kavli Institute of Nanoscience Delft.","article_type":"original","volume":122,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","page":"2311-2324","date_created":"2024-01-10T09:45:48Z","pmid":1,"ddc":["570"],"month":"06","type":"journal_article","publication_identifier":{"issn":["0006-3495"]},"publisher":"Elsevier","has_accepted_license":"1","file_date_updated":"2024-01-16T09:09:29Z"},{"title":"Clathrin coats partially preassemble and subsequently bend during endocytosis","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2024-01-16T10:17:05Z","day":"03","oa":1,"file":[{"creator":"dernst","file_name":"2023_JCB_Mund.pdf","access_level":"open_access","date_created":"2024-01-16T10:15:09Z","date_updated":"2024-01-16T10:15:09Z","success":1,"checksum":"505d5cac36c14b073b68c7fed1a92bd3","file_id":"14811","file_size":5678069,"relation":"main_file","content_type":"application/pdf"}],"department":[{"_id":"AnSa"}],"language":[{"iso":"eng"}],"pmid":1,"date_created":"2024-01-10T10:45:55Z","volume":222,"article_type":"original","acknowledgement":"We thank the entire Ries and Kaksonen labs for fruitful discussions and support. This work was supported by the European Research Council (ERC CoG-724489 to J. Ries), the National Institutes of Health Common Fund 4D Nucleome Program (Grant U01 to J. Ries), the Human Frontier Science Program (RGY0065/2017 to J. Ries), the EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Curie Actions COFUND (Grant 229597 to O. Avinoam), the European Molecular Biology Laboratory (M. Mund, A. Tschanz, Y.-L. Wu and J. Ries), and the Swiss National Science Foundation (grant 310030B_182825 and NCCR Chemical Biology to M. Kaksonen). O. Avinoam is an incumbent of the Miriam Berman Presidential Development Chair.","month":"02","ddc":["570"],"type":"journal_article","publication_identifier":{"eissn":["1540-8140"],"issn":["0021-9525"]},"publisher":"Rockefeller University Press","has_accepted_license":"1","file_date_updated":"2024-01-16T10:15:09Z","_id":"14788","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","keyword":["Cell Biology"],"year":"2023","article_number":"e202206038","publication":"Journal of Cell Biology","article_processing_charge":"No","external_id":{"isi":["000978065000001"],"pmid":["36734980"]},"citation":{"ama":"Mund M, Tschanz A, Wu Y-L, et al. Clathrin coats partially preassemble and subsequently bend during endocytosis. <i>Journal of Cell Biology</i>. 2023;222(3). doi:<a href=\"https://doi.org/10.1083/jcb.202206038\">10.1083/jcb.202206038</a>","apa":"Mund, M., Tschanz, A., Wu, Y.-L., Frey, F. F., Mehl, J. L., Kaksonen, M., … Ries, J. (2023). Clathrin coats partially preassemble and subsequently bend during endocytosis. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.202206038\">https://doi.org/10.1083/jcb.202206038</a>","ista":"Mund M, Tschanz A, Wu Y-L, Frey FF, Mehl JL, Kaksonen M, Avinoam O, Schwarz US, Ries J. 2023. Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. 222(3), e202206038.","ieee":"M. Mund <i>et al.</i>, “Clathrin coats partially preassemble and subsequently bend during endocytosis,” <i>Journal of Cell Biology</i>, vol. 222, no. 3. Rockefeller University Press, 2023.","short":"M. Mund, A. Tschanz, Y.-L. Wu, F.F. Frey, J.L. Mehl, M. Kaksonen, O. Avinoam, U.S. Schwarz, J. Ries, Journal of Cell Biology 222 (2023).","mla":"Mund, Markus, et al. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” <i>Journal of Cell Biology</i>, vol. 222, no. 3, e202206038, Rockefeller University Press, 2023, doi:<a href=\"https://doi.org/10.1083/jcb.202206038\">10.1083/jcb.202206038</a>.","chicago":"Mund, Markus, Aline Tschanz, Yu-Le Wu, Felix F Frey, Johanna L. Mehl, Marko Kaksonen, Ori Avinoam, Ulrich S. Schwarz, and Jonas Ries. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2023. <a href=\"https://doi.org/10.1083/jcb.202206038\">https://doi.org/10.1083/jcb.202206038</a>."},"abstract":[{"lang":"eng","text":"Eukaryotic cells use clathrin-mediated endocytosis to take up a large range of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma membrane, but it remains controversial when and how it is remodeled into a spherical vesicle.\r\nHere, we use 3D superresolution microscopy to determine the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determine the average trajectory of clathrin remodeling during endocytosis. We find that clathrin coats assemble first on flat membranes to 50% of the coat area before they become rapidly and continuously bent, and this mechanism is confirmed in three cell lines. We introduce the cooperative curvature model, which is based on positive feedback for curvature generation. It accurately describes the measured shapes and dynamics of the clathrin coat and could represent a general mechanism for clathrin coat remodeling on the plasma membrane."}],"intvolume":"       222","issue":"3","publication_status":"published","author":[{"first_name":"Markus","last_name":"Mund","full_name":"Mund, Markus"},{"last_name":"Tschanz","full_name":"Tschanz, Aline","first_name":"Aline"},{"last_name":"Wu","full_name":"Wu, Yu-Le","first_name":"Yu-Le"},{"orcid":"0000-0001-8501-6017","first_name":"Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F","last_name":"Frey"},{"last_name":"Mehl","full_name":"Mehl, Johanna L.","first_name":"Johanna L."},{"first_name":"Marko","full_name":"Kaksonen, Marko","last_name":"Kaksonen"},{"first_name":"Ori","last_name":"Avinoam","full_name":"Avinoam, Ori"},{"first_name":"Ulrich S.","full_name":"Schwarz, Ulrich S.","last_name":"Schwarz"},{"first_name":"Jonas","last_name":"Ries","full_name":"Ries, Jonas"}],"fulldoi":"https://doi.org/10.1083/jcb.202206038","date_published":"2023-02-03T00:00:00Z","isi":1,"oa_version":"Published Version","quality_controlled":"1","doi":"10.1083/jcb.202206038"},{"doi":"10.1021/acs.jpcb.3c04627","quality_controlled":"1","issue":"51","author":[{"full_name":"Sakref, Yann","last_name":"Sakref","first_name":"Yann"},{"orcid":"0000-0003-1483-1457","first_name":"Maitane","full_name":"Muñoz Basagoiti, Maitane","id":"1a8a7950-82cd-11ed-bd4f-9624c913a607","last_name":"Muñoz Basagoiti"},{"last_name":"Zeravcic","full_name":"Zeravcic, Zorana","first_name":"Zorana"},{"last_name":"Rivoire","full_name":"Rivoire, Olivier","first_name":"Olivier"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Catalysis, the acceleration of product formation by a substance that is left unchanged, typically results from multiple elementary processes, including diffusion of the reactants toward the catalyst, chemical steps, and release of the products. While efforts to design catalysts are often focused on accelerating the chemical reaction on the catalyst, catalysis is a global property of the catalytic cycle that involves all processes. These are controlled by both intrinsic parameters such as the composition and shape of the catalyst and extrinsic parameters such as the concentration of the chemical species at play. We examine here the conditions that catalysis imposes on the different steps of a reaction cycle and the respective role of intrinsic and extrinsic parameters of the system on the emergence of catalysis by using an approach based on first-passage times. We illustrate this approach for various decompositions of a catalytic cycle into elementary steps, including non-Markovian decompositions, which are useful when the presence and nature of intermediate states are a priori unknown. Our examples cover different types of reactions and clarify the constraints on elementary steps and the impact of species concentrations on catalysis."}],"intvolume":"       127","oa_version":"Preprint","fulldoi":"https://doi.org/10.1021/acs.jpcb.3c04627","isi":1,"date_published":"2023-12-13T00:00:00Z","publication":"The Journal of Physical Chemistry B","citation":{"ama":"Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. On kinetic constraints that catalysis imposes on elementary processes. <i>The Journal of Physical Chemistry B</i>. 2023;127(51):10950-10959. doi:<a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">10.1021/acs.jpcb.3c04627</a>","ista":"Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. 2023. On kinetic constraints that catalysis imposes on elementary processes. The Journal of Physical Chemistry B. 127(51), 10950–10959.","ieee":"Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, and O. Rivoire, “On kinetic constraints that catalysis imposes on elementary processes,” <i>The Journal of Physical Chemistry B</i>, vol. 127, no. 51. American Chemical Society, pp. 10950–10959, 2023.","apa":"Sakref, Y., Muñoz Basagoiti, M., Zeravcic, Z., &#38; Rivoire, O. (2023). On kinetic constraints that catalysis imposes on elementary processes. <i>The Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">https://doi.org/10.1021/acs.jpcb.3c04627</a>","short":"Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, O. Rivoire, The Journal of Physical Chemistry B 127 (2023) 10950–10959.","chicago":"Sakref, Yann, Maitane Muñoz Basagoiti, Zorana Zeravcic, and Olivier Rivoire. “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” <i>The Journal of Physical Chemistry B</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">https://doi.org/10.1021/acs.jpcb.3c04627</a>.","mla":"Sakref, Yann, et al. “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” <i>The Journal of Physical Chemistry B</i>, vol. 127, no. 51, American Chemical Society, 2023, pp. 10950–59, doi:<a href=\"https://doi.org/10.1021/acs.jpcb.3c04627\">10.1021/acs.jpcb.3c04627</a>."},"external_id":{"isi":["001134068000001"],"pmid":["38091487"],"arxiv":["2312.15940"]},"article_processing_charge":"No","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14831","year":"2023","keyword":["Materials Chemistry","Surfaces","Coatings and Films","Physical and Theoretical Chemistry"],"publisher":"American Chemical Society","publication_identifier":{"eissn":["1520-5207"],"issn":["1520-6106"]},"scopus_import":"1","arxiv":1,"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2312.15940","open_access":"1"}],"department":[{"_id":"AnSa"}],"month":"12","type":"journal_article","volume":127,"acknowledgement":"We acknowledge funding from ANR-22-CE06-0037-02. This work has received funding from the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754387.","article_type":"original","page":"10950-10959","pmid":1,"date_created":"2024-01-18T07:47:11Z","day":"13","oa":1,"title":"On kinetic constraints that catalysis imposes on elementary processes","date_updated":"2025-04-23T13:15:17Z"},{"has_accepted_license":"1","corr_author":"1","OA_place":"publisher","publisher":"Figshare","date_created":"2024-02-26T08:37:57Z","type":"research_data_reference","ddc":["570"],"month":"12","date_published":"2023-12-13T00:00:00Z","oa_version":"Published Version","abstract":[{"text":"This data repository underpins the paper, published in PNAS (doi pending) and bioarxiv (doi: https://doi.org/10.1101/2023.07.05.547777).","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://figshare.com/s/85798bba4ebc68d822ed"}],"department":[{"_id":"AnSa"}],"author":[{"orcid":"0000-0001-6160-9766","first_name":"Samo","full_name":"Curk, Samo","id":"031eff0d-d481-11ee-8508-cd12a7a86e5b","last_name":"Curk"}],"article_processing_charge":"No","oa":1,"citation":{"ama":"Curk S. aggregation_data. 2023.","short":"S. Curk, (2023).","chicago":"Curk, Samo. “Aggregation_data.” Figshare, 2023.","mla":"Curk, Samo. <i>Aggregation_data</i>. Figshare, 2023.","ista":"Curk S. 2023. aggregation_data, Figshare.","apa":"Curk, S. (2023). aggregation_data. Figshare.","ieee":"S. Curk, “aggregation_data.” Figshare, 2023."},"related_material":{"record":[{"relation":"used_in_publication","id":"15001","status":"public"}]},"day":"13","tmp":{"image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)"},"year":"2023","date_updated":"2026-09-24T10:27:35Z","OA_type":"gold","_id":"15027","title":"aggregation_data","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"doi":"10.1021/acs.jpcb.2c00028","quality_controlled":"1","author":[{"last_name":"Palaia","full_name":"Palaia, Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","first_name":"Ivan","orcid":" 0000-0002-8843-9485 "},{"full_name":"Goyal, Abhay","last_name":"Goyal","first_name":"Abhay"},{"last_name":"Del Gado","full_name":"Del Gado, Emanuela","first_name":"Emanuela"},{"first_name":"Ladislav","full_name":"Šamaj, Ladislav","last_name":"Šamaj"},{"last_name":"Trizac","full_name":"Trizac, Emmanuel","first_name":"Emmanuel"}],"issue":"16","publication_status":"published","intvolume":"       126","abstract":[{"text":"Like-charge attraction, driven by ionic correlations, challenges our understanding of electrostatics both in soft and hard matter. For two charged planar surfaces confining counterions and water, we prove that, even at relatively low correlation strength, the relevant physics is the ground-state one, oblivious of fluctuations. Based on this, we derive a simple and accurate interaction pressure that fulfills known exact requirements and can be used as an effective potential. We test this equation against implicit-solvent Monte Carlo simulations and against explicit-solvent simulations of cement and several types of clays. We argue that water destructuring under nanometric confinement drastically reduces dielectric screening, enhancing ionic correlations. Our equation of state at reduced permittivity therefore explains the exotic attractive regime reported for these materials, even in the absence of multivalent counterions.","lang":"eng"}],"isi":1,"fulldoi":"https://doi.org/10.1021/acs.jpcb.2c00028","oa_version":"Preprint","date_published":"2022-04-14T00:00:00Z","publication":"Journal of Physical Chemistry B","citation":{"apa":"Palaia, I., Goyal, A., Del Gado, E., Šamaj, L., &#38; Trizac, E. (2022). Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring. <i>Journal of Physical Chemistry B</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpcb.2c00028\">https://doi.org/10.1021/acs.jpcb.2c00028</a>","ieee":"I. Palaia, A. Goyal, E. Del Gado, L. Šamaj, and E. Trizac, “Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring,” <i>Journal of Physical Chemistry B</i>, vol. 126, no. 16. American Chemical Society, pp. 3143–3149, 2022.","ista":"Palaia I, Goyal A, Del Gado E, Šamaj L, Trizac E. 2022. Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring. Journal of Physical Chemistry B. 126(16), 3143–3149.","chicago":"Palaia, Ivan, Abhay Goyal, Emanuela Del Gado, Ladislav Šamaj, and Emmanuel Trizac. “Like-Charge Attraction at the Nanoscale: Ground-State Correlations and Water Destructuring.” <i>Journal of Physical Chemistry B</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acs.jpcb.2c00028\">https://doi.org/10.1021/acs.jpcb.2c00028</a>.","mla":"Palaia, Ivan, et al. “Like-Charge Attraction at the Nanoscale: Ground-State Correlations and Water Destructuring.” <i>Journal of Physical Chemistry B</i>, vol. 126, no. 16, American Chemical Society, 2022, pp. 3143–49, doi:<a href=\"https://doi.org/10.1021/acs.jpcb.2c00028\">10.1021/acs.jpcb.2c00028</a>.","short":"I. Palaia, A. Goyal, E. Del Gado, L. Šamaj, E. Trizac, Journal of Physical Chemistry B 126 (2022) 3143–3149.","ama":"Palaia I, Goyal A, Del Gado E, Šamaj L, Trizac E. Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring. <i>Journal of Physical Chemistry B</i>. 2022;126(16):3143-3149. doi:<a href=\"https://doi.org/10.1021/acs.jpcb.2c00028\">10.1021/acs.jpcb.2c00028</a>"},"external_id":{"pmid":["35420420"],"isi":["000796953700022"],"arxiv":["2203.10524"]},"article_processing_charge":"No","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11340","year":"2022","publisher":"American Chemical Society","publication_identifier":{"eissn":["1520-5207"],"issn":["1520-6106"]},"scopus_import":"1","language":[{"iso":"eng"}],"arxiv":1,"main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2203.10524","open_access":"1"}],"department":[{"_id":"AnSa"}],"month":"04","type":"journal_article","article_type":"original","volume":126,"acknowledgement":"We thank Martin Trulsson for useful discussions and for providing us with simulation data. This work has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement 674979-NANOTRANS. The support received from VEGA Grant No. 2/0092/21 is acknowledged.","pmid":1,"date_created":"2022-05-01T22:01:42Z","page":"3143-3149","day":"14","oa":1,"title":"Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring","date_updated":"2025-06-11T13:34:36Z"},{"keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"year":"2022","_id":"11400","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"isi":["000797236000004"],"pmid":["35597653"]},"citation":{"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.","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.","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>.","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>.","short":"I. Palaia, A. Šarić, The Journal of Chemical Physics 156 (2022)."},"article_number":"194902","publication":"The Journal of Chemical Physics","project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"},{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"fulldoi":"https://doi.org/10.1063/5.0087769","isi":1,"oa_version":"Published Version","date_published":"2022-05-16T00:00:00Z","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"}],"intvolume":"       156","publication_status":"published","issue":"19","author":[{"full_name":"Palaia, Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","last_name":"Palaia","orcid":" 0000-0002-8843-9485 ","first_name":"Ivan"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"}],"quality_controlled":"1","doi":"10.1063/5.0087769","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-06-11T14:00:32Z","title":"Controlling cluster size in 2D phase-separating binary mixtures with specific interactions","oa":1,"day":"16","pmid":1,"date_created":"2022-05-22T17:04:48Z","volume":156,"article_type":"original","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).","type":"journal_article","month":"05","ddc":["540"],"file":[{"date_updated":"2022-05-23T07:45:33Z","success":1,"date_created":"2022-05-23T07:45:33Z","access_level":"open_access","file_name":"2022_JourChemPhysics_Palaia.pdf","creator":"dernst","content_type":"application/pdf","relation":"main_file","file_size":6387208,"file_id":"11405","checksum":"7fada58059676a4bb0944b82247af740"}],"department":[{"_id":"AnSa"}],"language":[{"iso":"eng"}],"has_accepted_license":"1","corr_author":"1","file_date_updated":"2022-05-23T07:45:33Z","scopus_import":"1","ec_funded":1,"publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"publisher":"AIP Publishing"},{"article_number":"e2109718119","publication":"Proceedings of the National Academy of Sciences of the United States of America","article_processing_charge":"No","external_id":{"isi":["000903753500002"],"pmid":["35901206"]},"citation":{"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. National Academy of Sciences, 2022.","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>. National Academy of Sciences. <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, National Academy of Sciences, 2022, doi:<a href=\"https://doi.org/10.1073/pnas.2109718119\">10.1073/pnas.2109718119</a>.","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>. National Academy of Sciences, 2022. <a href=\"https://doi.org/10.1073/pnas.2109718119\">https://doi.org/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).","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>"},"_id":"11841","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","year":"2022","quality_controlled":"1","doi":"10.1073/pnas.2109718119","intvolume":"       119","abstract":[{"lang":"eng","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."}],"author":[{"first_name":"Zenon","full_name":"Toprakcioglu, Zenon","last_name":"Toprakcioglu"},{"first_name":"Ayaka","full_name":"Kamada, Ayaka","last_name":"Kamada"},{"full_name":"Michaels, Thomas C.T.","last_name":"Michaels","first_name":"Thomas C.T."},{"first_name":"Mengqi","full_name":"Xie, Mengqi","last_name":"Xie"},{"full_name":"Krausser, Johannes","last_name":"Krausser","first_name":"Johannes"},{"first_name":"Jiapeng","full_name":"Wei, Jiapeng","last_name":"Wei"},{"last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139"},{"first_name":"Michele","full_name":"Vendruscolo, Michele","last_name":"Vendruscolo"},{"first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J.","last_name":"Knowles"}],"publication_status":"published","issue":"31","fulldoi":"https://doi.org/10.1073/pnas.2109718119","project":[{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020"}],"date_published":"2022-07-28T00:00:00Z","oa_version":"Published Version","isi":1,"day":"28","oa":1,"title":"Adsorption free energy predicts amyloid protein nucleation rates","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"date_updated":"2025-06-12T06:21:34Z","ec_funded":1,"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"publisher":"National Academy of Sciences","has_accepted_license":"1","scopus_import":"1","file_date_updated":"2023-10-04T09:05:44Z","file":[{"file_name":"2022_PNAS_Toprakcioglu.pdf","creator":"dernst","success":1,"date_updated":"2023-10-04T09:05:44Z","access_level":"open_access","date_created":"2023-10-04T09:05:44Z","file_size":2476021,"file_id":"14386","checksum":"0fe3878896cbeb6c44e29222ec2f336a","content_type":"application/pdf","relation":"main_file"}],"department":[{"_id":"AnSa"}],"language":[{"iso":"eng"}],"pmid":1,"date_created":"2022-08-14T22:01:45Z","volume":119,"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).","article_type":"original","ddc":["570"],"type":"journal_article","month":"07"},{"year":"2022","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"12108","citation":{"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>","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>.","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>.","short":"B. Meadowcroft, I. Palaia, A.K. Pfitzner, A. Roux, B. Baum, A. Šarić, Physical Review Letters 129 (2022).","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>","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.","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."},"external_id":{"isi":["000906721500001"],"pmid":["36608212"]},"article_processing_charge":"No","publication":"Physical Review Letters","article_number":"268101","fulldoi":"https://doi.org/10.1103/PhysRevLett.129.268101","date_published":"2022-12-23T00:00:00Z","oa_version":"Preprint","project":[{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"},{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020"},{"_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","name":"The evolution of trafficking: from archaea to eukaryotes","grant_number":"96752"}],"isi":1,"issue":"26","publication_status":"published","author":[{"id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","full_name":"Meadowcroft, Billie","last_name":"Meadowcroft","orcid":"0000-0003-3441-1337","first_name":"Billie"},{"orcid":" 0000-0002-8843-9485 ","first_name":"Ivan","full_name":"Palaia, Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","last_name":"Palaia"},{"last_name":"Pfitzner","full_name":"Pfitzner, Anna Katharina","first_name":"Anna Katharina"},{"first_name":"Aurélien","full_name":"Roux, Aurélien","last_name":"Roux"},{"full_name":"Baum, Buzz","last_name":"Baum","first_name":"Buzz"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić"}],"abstract":[{"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.","lang":"eng"}],"intvolume":"       129","doi":"10.1103/PhysRevLett.129.268101","quality_controlled":"1","date_updated":"2025-04-14T07:54:53Z","title":"Mechanochemical rules for shape-shifting filaments that remodel membranes","oa":1,"day":"23","month":"12","type":"journal_article","article_type":"original","volume":129,"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). ","date_created":"2023-01-08T23:00:53Z","pmid":1,"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.05.10.490642 "}],"department":[{"_id":"AnSa"}],"scopus_import":"1","corr_author":"1","publisher":"American Physical Society","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"ec_funded":1},{"oa":1,"day":"17","related_material":{"link":[{"url":"https://github.com/sharonJXY/3-filament-model","relation":"software"}]},"date_updated":"2025-06-12T06:19:28Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Modelling membrane reshaping by staged polymerization of ESCRT-III filaments","file_date_updated":"2023-01-24T10:45:01Z","scopus_import":"1","corr_author":"1","has_accepted_license":"1","publisher":"Public Library of Science","publication_identifier":{"issn":["1553-7358"]},"ec_funded":1,"type":"journal_article","month":"10","ddc":["570"],"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.","article_type":"original","volume":18,"date_created":"2023-01-12T12:08:10Z","pmid":1,"language":[{"iso":"eng"}],"department":[{"_id":"AnSa"}],"file":[{"relation":"main_file","content_type":"application/pdf","checksum":"bada6a7865e470cf42bbdfa67dd471d2","file_size":2641067,"file_id":"12359","access_level":"open_access","date_created":"2023-01-24T10:45:01Z","success":1,"date_updated":"2023-01-24T10:45:01Z","creator":"dernst","file_name":"2022_PLoSCompBio_Jiang.pdf"}],"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>","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>","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>.","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>."},"external_id":{"isi":["000924885500005"],"pmid":["36251703"]},"article_processing_charge":"No","publication":"PLOS Computational Biology","article_number":"e1010586","year":"2022","keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","_id":"12152","doi":"10.1371/journal.pcbi.1010586","quality_controlled":"1","fulldoi":"https://doi.org/10.1371/journal.pcbi.1010586","isi":1,"project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"},{"_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","grant_number":"96752","name":"The evolution of trafficking: from archaea to eukaryotes"}],"oa_version":"Published Version","date_published":"2022-10-17T00:00:00Z","publication_status":"published","issue":"10","author":[{"full_name":"Jiang, Xiuyun","last_name":"Jiang","first_name":"Xiuyun"},{"last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, Lena","first_name":"Lena"},{"id":"3adeca52-9313-11ed-b1ac-c170b2505714","full_name":"Vanhille-Campos, Christian Eduardo","last_name":"Vanhille-Campos","first_name":"Christian Eduardo"},{"first_name":"Anna-Katharina","full_name":"Pfitzner, Anna-Katharina","last_name":"Pfitzner"},{"last_name":"Lominadze","full_name":"Lominadze, Elene","first_name":"Elene"},{"full_name":"Roux, Aurélien","last_name":"Roux","first_name":"Aurélien"},{"full_name":"Baum, Buzz","last_name":"Baum","first_name":"Buzz"},{"orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","last_name":"Šarić"}],"intvolume":"        18","abstract":[{"lang":"eng","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."}]},{"scopus_import":"1","file_date_updated":"2023-01-30T09:15:13Z","has_accepted_license":"1","publisher":"Frontiers Media","publication_identifier":{"issn":["1662-453X"]},"ddc":["570"],"type":"journal_article","month":"09","date_created":"2023-01-16T09:56:43Z","volume":16,"acknowledgement":"This work was supported by grants from the Swedish Research Council (grant no. 2015-00143) and the European Research Council (grant no. 340890).","article_type":"original","department":[{"_id":"AnSa"}],"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","date_created":"2023-01-30T09:15:13Z","success":1,"date_updated":"2023-01-30T09:15:13Z","creator":"dernst","file_name":"2022_FrontiersNeuroscience_Weiffert2.pdf","relation":"main_file","content_type":"application/pdf","checksum":"e67d16113ffb4fb4fa38a183d169f210","file_id":"12442","file_size":19798610}],"oa":1,"day":"20","date_updated":"2023-08-04T09:48:56Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"title":"Influence of denaturants on amyloid β42 aggregation kinetics","quality_controlled":"1","doi":"10.3389/fnins.2022.943355","isi":1,"fulldoi":"https://doi.org/10.3389/fnins.2022.943355","oa_version":"Published Version","date_published":"2022-09-20T00:00:00Z","author":[{"first_name":"Tanja","last_name":"Weiffert","full_name":"Weiffert, Tanja"},{"first_name":"Georg","last_name":"Meisl","full_name":"Meisl, Georg"},{"first_name":"Samo","full_name":"Curk, Samo","last_name":"Curk"},{"first_name":"Risto","last_name":"Cukalevski","full_name":"Cukalevski, Risto"},{"full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela"},{"last_name":"Knowles","full_name":"Knowles, Tuomas P. J.","first_name":"Tuomas P. J."},{"last_name":"Linse","full_name":"Linse, Sara","first_name":"Sara"}],"publication_status":"published","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."}],"intvolume":"        16","citation":{"short":"T. Weiffert, G. Meisl, S. Curk, R. Cukalevski, A. Šarić, T.P.J. Knowles, S. Linse, Frontiers in Neuroscience 16 (2022).","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>.","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>.","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>","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.","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.","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>"},"article_processing_charge":"No","external_id":{"isi":["000866287100001"]},"publication":"Frontiers in Neuroscience","article_number":"943355","keyword":["General Neuroscience"],"year":"2022","_id":"12251","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"}]