[{"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","_id":"15001","file_date_updated":"2024-02-26T08:20:00Z","department":[{"_id":"AnSa"}],"ddc":["570"],"date_updated":"2024-02-26T08:45:56Z","intvolume":" 121","month":"02","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","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."}],"ec_funded":1,"related_material":{"record":[{"relation":"research_data","id":"15027","status":"public"}]},"volume":121,"issue":"7","language":[{"iso":"eng"}],"file":[{"file_id":"15026","checksum":"5aeb65bcc0dd829b1f9ab307c5031d4b","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2024-02-26T08:20:00Z","file_name":"2024_PNAS_Curk.pdf","date_updated":"2024-02-26T08:20:00Z","file_size":7699487,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["1091-6490"]},"project":[{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"article_number":"e2220075121","title":"Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites","article_processing_charge":"Yes","external_id":{"pmid":["38335256"]},"author":[{"last_name":"Curk","orcid":"0000-0001-6160-9766","full_name":"Curk, Samo","id":"031eff0d-d481-11ee-8508-cd12a7a86e5b","first_name":"Samo"},{"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"},{"full_name":"Linse, Sara","last_name":"Linse","first_name":"Sara"},{"last_name":"Michaels","full_name":"Michaels, Thomas C.T.","first_name":"Thomas C.T."},{"first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J.","last_name":"Knowles"},{"last_name":"Šarić","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2220075121.","ama":"Curk S, Krausser J, Meisl G, et al. 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. 2024;121(7). doi:10.1073/pnas.2220075121","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. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2220075121","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).","ieee":"S. Curk et al., “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, vol. 121, no. 7. Proceedings of the National Academy of Sciences, 2024.","mla":"Curk, Samo, et al. “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, vol. 121, no. 7, e2220075121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2220075121."},"oa":1,"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","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.).","date_created":"2024-02-18T23:01:00Z","date_published":"2024-02-13T00:00:00Z","doi":"10.1073/pnas.2220075121","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"13","year":"2024","has_accepted_license":"1"},{"publisher":"Proceedings of the National Academy of Sciences","quality_controlled":"1","oa":1,"acknowledgement":"We thank Dr. Steven Roeters (Aarhus University), Dr. Federica Burla, and Prof. Dr. Mischa Bonn (Institute for Polymer Research, Mainz, Germany) for the useful discussions. We thank Dr. Wim Roeterdink and Michiel Hilberts for technical support. G.H.K. acknowledges financial support by the “BaSyC Building a Synthetic Cell” Gravitation grant (024.003.019) of The Netherlands Ministry of Education, Culture and Science (OCW) and The Netherlands Organization for Scientific Research and from NWO grant OCENW.GROOT.2019.022. This work has received support from the National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT, under Grant No. 2022K1A3A1A04062969. This publication is part of the project (with Project Number VI.Veni.212.240) of the research programme NWO Talent Programme Veni 2021, which is financed by the Dutch Research Council (NWO). I.M.I. acknowledges support from the Sectorplan Bèta & Techniek of the Dutch Government and the Dementia Research - Synapsis Foundation Switzerland. A.Š. and K.K. acknowledge support from Royal Society and European Research Council Starting Grant. G. Giubertoni kindly thanks to the Care4Bones community and the Collagen Café community for reminding that we do not own the knowledge we create, but it is, rather, a collective resource intended for the advancement of human progress.","doi":"10.1073/pnas.2313162121","date_published":"2024-03-12T00:00:00Z","date_created":"2024-03-17T23:00:57Z","has_accepted_license":"1","year":"2024","day":"12","publication":"Proceedings of the National Academy of Sciences of the United States of America","article_number":"e2313162121","author":[{"first_name":"Giulia","last_name":"Giubertoni","full_name":"Giubertoni, Giulia"},{"first_name":"Liru","full_name":"Feng, Liru","last_name":"Feng"},{"last_name":"Klein","full_name":"Klein, Kevin","first_name":"Kevin"},{"last_name":"Giannetti","full_name":"Giannetti, Guido","first_name":"Guido"},{"last_name":"Rutten","full_name":"Rutten, Luco","first_name":"Luco"},{"last_name":"Choi","full_name":"Choi, Yeji","first_name":"Yeji"},{"full_name":"Van Der Net, Anouk","last_name":"Van Der Net","first_name":"Anouk"},{"first_name":"Gerard","last_name":"Castro-Linares","full_name":"Castro-Linares, Gerard"},{"first_name":"Federico","last_name":"Caporaletti","full_name":"Caporaletti, Federico"},{"last_name":"Micha","full_name":"Micha, Dimitra","first_name":"Dimitra"},{"full_name":"Hunger, Johannes","last_name":"Hunger","first_name":"Johannes"},{"first_name":"Antoine","full_name":"Deblais, Antoine","last_name":"Deblais"},{"last_name":"Bonn","full_name":"Bonn, Daniel","first_name":"Daniel"},{"full_name":"Sommerdijk, Nico","last_name":"Sommerdijk","first_name":"Nico"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"first_name":"Ioana M.","last_name":"Ilie","full_name":"Ilie, Ioana M."},{"first_name":"Gijsje H.","last_name":"Koenderink","full_name":"Koenderink, Gijsje H."},{"last_name":"Woutersen","full_name":"Woutersen, Sander","first_name":"Sander"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["38451946"]},"title":"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration","citation":{"mla":"Giubertoni, Giulia, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11, e2313162121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2313162121.","ieee":"G. Giubertoni et al., “Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11. Proceedings of the National Academy of Sciences, 2024.","short":"G. Giubertoni, L. Feng, K. Klein, G. Giannetti, L. Rutten, Y. Choi, A. Van Der Net, G. Castro-Linares, F. Caporaletti, D. Micha, J. Hunger, A. Deblais, D. Bonn, N. Sommerdijk, A. Šarić, I.M. Ilie, G.H. Koenderink, S. Woutersen, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ama":"Giubertoni G, Feng L, Klein K, et al. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(11). doi:10.1073/pnas.2313162121","apa":"Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., … Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2313162121","chicago":"Giubertoni, Giulia, Liru Feng, Kevin Klein, Guido Giannetti, Luco Rutten, Yeji Choi, Anouk Van Der Net, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2313162121.","ista":"Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, Van Der Net A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. 2024. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2313162121."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","month":"03","intvolume":" 121","abstract":[{"text":"Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water–collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H2O/D2O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H2O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D2O is less hydrated than in H2O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen–water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"issue":"11","related_material":{"record":[{"status":"public","id":"15126","relation":"research_data"}]},"volume":121,"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"publication_status":"published","file":[{"file_size":12952586,"date_updated":"2024-03-19T10:22:42Z","creator":"dernst","file_name":"2024_PNAS_Giubertoni.pdf","date_created":"2024-03-19T10:22:42Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"15125","checksum":"a3f7fdc29dd9f0a38952ab4e322b3a05"}],"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"15116","file_date_updated":"2024-03-19T10:22:42Z","department":[{"_id":"AnSa"}],"date_updated":"2024-03-19T11:41:32Z","ddc":["550"]},{"isi":1,"has_accepted_license":"1","year":"2023","day":"06","publication":"Soft Matter","page":"1695-1704","date_published":"2023-02-06T00:00:00Z","doi":"10.1039/d2sm01562e","date_created":"2023-03-05T23:01:06Z","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).","quality_controlled":"1","publisher":"Royal Society of Chemistry","oa":1,"citation":{"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 et al., “Steering self-organisation through confinement,” Soft Matter, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023.","ama":"Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through confinement. Soft Matter. 2023;19:1695-1704. doi:10.1039/d2sm01562e","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. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d2sm01562e","mla":"Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.” Soft Matter, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:10.1039/d2sm01562e.","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.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d2sm01562e."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Nuno A.M.","last_name":"Araújo","full_name":"Araújo, Nuno A.M."},{"full_name":"Janssen, Liesbeth M.C.","last_name":"Janssen","first_name":"Liesbeth M.C."},{"first_name":"Thomas","full_name":"Barois, Thomas","last_name":"Barois"},{"last_name":"Boffetta","full_name":"Boffetta, Guido","first_name":"Guido"},{"first_name":"Itai","full_name":"Cohen, Itai","last_name":"Cohen"},{"last_name":"Corbetta","full_name":"Corbetta, Alessandro","first_name":"Alessandro"},{"first_name":"Olivier","full_name":"Dauchot, Olivier","last_name":"Dauchot"},{"first_name":"Marjolein","last_name":"Dijkstra","full_name":"Dijkstra, Marjolein"},{"first_name":"William M.","full_name":"Durham, William M.","last_name":"Durham"},{"last_name":"Dussutour","full_name":"Dussutour, Audrey","first_name":"Audrey"},{"last_name":"Garnier","full_name":"Garnier, Simon","first_name":"Simon"},{"first_name":"Hanneke","full_name":"Gelderblom, Hanneke","last_name":"Gelderblom"},{"full_name":"Golestanian, Ramin","last_name":"Golestanian","first_name":"Ramin"},{"last_name":"Isa","full_name":"Isa, Lucio","first_name":"Lucio"},{"last_name":"Koenderink","full_name":"Koenderink, Gijsje H.","first_name":"Gijsje H."},{"last_name":"Löwen","full_name":"Löwen, Hartmut","first_name":"Hartmut"},{"full_name":"Metzler, Ralf","last_name":"Metzler","first_name":"Ralf"},{"last_name":"Polin","full_name":"Polin, Marco","first_name":"Marco"},{"first_name":"C. Patrick","last_name":"Royall","full_name":"Royall, C. Patrick"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"first_name":"Anupam","full_name":"Sengupta, Anupam","last_name":"Sengupta"},{"first_name":"Cécile","last_name":"Sykes","full_name":"Sykes, Cécile"},{"first_name":"Vito","full_name":"Trianni, Vito","last_name":"Trianni"},{"first_name":"Idan","last_name":"Tuval","full_name":"Tuval, Idan"},{"first_name":"Nicolas","full_name":"Vogel, Nicolas","last_name":"Vogel"},{"last_name":"Yeomans","full_name":"Yeomans, Julia M.","first_name":"Julia M."},{"first_name":"Iker","full_name":"Zuriguel, Iker","last_name":"Zuriguel"},{"last_name":"Marin","full_name":"Marin, Alvaro","first_name":"Alvaro"},{"full_name":"Volpe, Giorgio","last_name":"Volpe","first_name":"Giorgio"}],"article_processing_charge":"No","external_id":{"arxiv":["2204.10059"],"isi":["000940388100001"]},"title":"Steering self-organisation through confinement","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"}],"publication_identifier":{"eissn":["1744-6848"],"issn":["1744-683X"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"af95aa18b9b01e32fb8f13477c0e2687","file_id":"12711","file_size":3581939,"date_updated":"2023-03-07T09:19:41Z","creator":"cchlebak","file_name":"2023_SoftMatter_Araujo.pdf","date_created":"2023-03-07T09:19:41Z"}],"language":[{"iso":"eng"}],"volume":19,"ec_funded":1,"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."}],"oa_version":"Published Version","scopus_import":"1","month":"02","intvolume":" 19","date_updated":"2023-08-01T13:28:39Z","ddc":["540"],"file_date_updated":"2023-03-07T09:19:41Z","department":[{"_id":"AnSa"}],"_id":"12708","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public"},{"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","_id":"12756","department":[{"_id":"AnSa"}],"file_date_updated":"2023-03-27T06:24:49Z","date_updated":"2023-08-01T13:45:54Z","ddc":["570"],"scopus_import":"1","month":"03","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"}],"oa_version":"Published Version","issue":"11","volume":9,"ec_funded":1,"publication_identifier":{"eissn":["2375-2548"]},"publication_status":"published","file":[{"date_created":"2023-03-27T06:24:49Z","file_name":"2023_ScienceAdvances_Hurtig.pdf","creator":"dernst","date_updated":"2023-03-27T06:24:49Z","file_size":1826471,"checksum":"6d7dbe9ed86a116c8a002d62971202c5","file_id":"12768","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"project":[{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020"}],"article_number":"eade5224","author":[{"first_name":"Fredrik","last_name":"Hurtig","full_name":"Hurtig, Fredrik"},{"first_name":"Thomas C.Q.","last_name":"Burgers","full_name":"Burgers, Thomas C.Q."},{"first_name":"Alice","full_name":"Cezanne, Alice","last_name":"Cezanne"},{"full_name":"Jiang, Xiuyun","last_name":"Jiang","first_name":"Xiuyun"},{"full_name":"Mol, Frank N.","last_name":"Mol","first_name":"Frank N."},{"first_name":"Jovan","full_name":"Traparić, Jovan","last_name":"Traparić"},{"last_name":"Pulschen","full_name":"Pulschen, Andre Arashiro","first_name":"Andre Arashiro"},{"last_name":"Nierhaus","full_name":"Nierhaus, Tim","first_name":"Tim"},{"first_name":"Gabriel","full_name":"Tarrason-Risa, Gabriel","last_name":"Tarrason-Risa"},{"last_name":"Harker-Kirschneck","full_name":"Harker-Kirschneck, Lena","first_name":"Lena"},{"last_name":"Löwe","full_name":"Löwe, Jan","first_name":"Jan"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"},{"full_name":"Vlijm, Rifka","last_name":"Vlijm","first_name":"Rifka"},{"full_name":"Baum, Buzz","last_name":"Baum","first_name":"Buzz"}],"article_processing_charge":"No","external_id":{"isi":["000968083500010"]},"title":"The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division","citation":{"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.","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.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.ade5224.","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. Science Advances. 2023;9(11). doi:10.1126/sciadv.ade5224","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. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.ade5224","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).","ieee":"F. Hurtig et al., “The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division,” Science Advances, vol. 9, no. 11. American Association for the Advancement of Science, 2023.","mla":"Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science Advances, vol. 9, no. 11, eade5224, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.ade5224."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","quality_controlled":"1","publisher":"American Association for the Advancement of Science","oa":1,"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).","doi":"10.1126/sciadv.ade5224","date_published":"2023-03-17T00:00:00Z","date_created":"2023-03-26T22:01:06Z","isi":1,"has_accepted_license":"1","year":"2023","day":"17","publication":"Science Advances"},{"ec_funded":1,"volume":23,"issue":"10","publication_status":"published","publication_identifier":{"issn":["1530-6984"],"eissn":["1530-6992"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"13100","checksum":"9734d4c617bab3578ef62916b764547a","success":1,"date_updated":"2023-05-30T07:55:31Z","file_size":3654910,"creator":"dernst","date_created":"2023-05-30T07:55:31Z","file_name":"2023_NanoLetters_Azadbakht.pdf"}],"scopus_import":"1","intvolume":" 23","month":"05","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"}],"oa_version":"Published Version","pmid":1,"department":[{"_id":"AnSa"}],"file_date_updated":"2023-05-30T07:55:31Z","date_updated":"2023-08-01T14:51:25Z","ddc":["540"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"letter_note","type":"journal_article","status":"public","_id":"13094","page":"4267–4273","date_created":"2023-05-28T22:01:03Z","doi":"10.1021/acs.nanolett.3c00375","date_published":"2023-05-04T00:00:00Z","year":"2023","has_accepted_license":"1","isi":1,"publication":"Nano Letters","day":"04","oa":1,"publisher":"American Chemical Society","quality_controlled":"1","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).","article_processing_charge":"No","external_id":{"isi":["000985481400001"],"pmid":["37141427"]},"author":[{"last_name":"Azadbakht","full_name":"Azadbakht, Ali","first_name":"Ali"},{"last_name":"Meadowcroft","full_name":"Meadowcroft, Billie","first_name":"Billie","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1"},{"full_name":"Varkevisser, Thijs","last_name":"Varkevisser","first_name":"Thijs"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"full_name":"Kraft, Daniela J.","last_name":"Kraft","first_name":"Daniela J."}],"title":"Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles","citation":{"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.” Nano Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.nanolett.3c00375.","short":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, D.J. Kraft, Nano Letters 23 (2023) 4267–4273.","ieee":"A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, and D. J. Kraft, “Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles,” Nano Letters, vol. 23, no. 10. American Chemical Society, pp. 4267–4273, 2023.","ama":"Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. 2023;23(10):4267–4273. doi:10.1021/acs.nanolett.3c00375","apa":"Azadbakht, A., Meadowcroft, B., Varkevisser, T., Šarić, A., & Kraft, D. J. (2023). Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.3c00375","mla":"Azadbakht, Ali, et al. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant Unilamellar Vesicles.” Nano Letters, vol. 23, no. 10, American Chemical Society, 2023, pp. 4267–4273, doi:10.1021/acs.nanolett.3c00375."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"}]},{"department":[{"_id":"AnSa"}],"date_updated":"2023-08-02T06:28:38Z","status":"public","type":"journal_article","article_type":"original","_id":"13237","volume":5,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["2522-5820"]},"intvolume":" 5","month":"07","scopus_import":"1","oa_version":"None","abstract":[{"lang":"eng","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."}],"title":"Amyloid formation as a protein phase transition","external_id":{"isi":["001017539800001"]},"article_processing_charge":"No","author":[{"full_name":"Michaels, Thomas C.T.","last_name":"Michaels","first_name":"Thomas C.T."},{"first_name":"Daoyuan","full_name":"Qian, Daoyuan","last_name":"Qian"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"first_name":"Michele","last_name":"Vendruscolo","full_name":"Vendruscolo, Michele"},{"last_name":"Linse","full_name":"Linse, Sara","first_name":"Sara"},{"first_name":"Tuomas P.J.","full_name":"Knowles, Tuomas P.J.","last_name":"Knowles"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Michaels, Thomas C. T., et al. “Amyloid Formation as a Protein Phase Transition.” Nature Reviews Physics, vol. 5, Springer Nature, 2023, pp. 379–397, doi:10.1038/s42254-023-00598-9.","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,” Nature Reviews Physics, vol. 5. Springer Nature, pp. 379–397, 2023.","short":"T.C.T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Reviews Physics 5 (2023) 379–397.","apa":"Michaels, T. C. T., Qian, D., Šarić, A., Vendruscolo, M., Linse, S., & Knowles, T. P. J. (2023). Amyloid formation as a protein phase transition. Nature Reviews Physics. Springer Nature. https://doi.org/10.1038/s42254-023-00598-9","ama":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. Amyloid formation as a protein phase transition. Nature Reviews Physics. 2023;5:379–397. doi:10.1038/s42254-023-00598-9","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.” Nature Reviews Physics. Springer Nature, 2023. https://doi.org/10.1038/s42254-023-00598-9.","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."},"date_created":"2023-07-16T22:01:12Z","doi":"10.1038/s42254-023-00598-9","date_published":"2023-07-01T00:00:00Z","page":"379–397","publication":"Nature Reviews Physics","day":"01","year":"2023","isi":1,"publisher":"Springer Nature","quality_controlled":"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."},{"issue":"7","volume":158,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0021-9606"],"eissn":["1089-7690"]},"intvolume":" 158","month":"02","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04810"}],"scopus_import":"1","pmid":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The elasticity of disordered and polydisperse polymer networks is a fundamental problem of soft matter physics that is still open. Here, we self-assemble polymer networks via simulations of a mixture of bivalent and tri- or tetravalent patchy particles, which result in an exponential strand length distribution analogous to that of experimental randomly cross-linked systems. After assembly, the network connectivity and topology are frozen and the resulting system is characterized. We find that the fractal structure of the network depends on the number density at which the assembly has been carried out, but that systems with the same mean valence and same assembly density have the same structural properties. Moreover, we compute the long-time limit of the mean-squared displacement, also known as the (squared) localization length, of the cross-links and of the middle monomers of the strands, showing that the dynamics of long strands is well described by the tube model. Finally, we find a relation connecting these two localization lengths at high density and connect the cross-link localization length to the shear modulus of the system."}],"department":[{"_id":"AnSa"}],"date_updated":"2023-10-03T11:31:51Z","status":"public","article_type":"original","type":"journal_article","_id":"12705","date_created":"2023-03-05T23:01:05Z","doi":"10.1063/5.0134271","date_published":"2023-02-21T00:00:00Z","publication":"Journal of Chemical Physics","day":"21","year":"2023","isi":1,"oa":1,"publisher":"American Institute of Physics","quality_controlled":"1","acknowledgement":"We thank Michael Lang for helpful discussions. We acknowledge financial support from the European Research Council (ERC Consolidator Grant No. 681597, MIMIC) and from LabEx NUMEV (Grant No. ANR-10-LABX-20) funded by the “Investissements d’Avenir” French Government program, managed by the French National Research Agency (ANR). W.K. is a senior member of the Institut Universitaire de France.","title":"Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks","article_processing_charge":"No","external_id":{"arxiv":["2211.04810"],"isi":["000936943800002"],"pmid":["36813705"]},"author":[{"first_name":"Valerio","id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","last_name":"Sorichetti","orcid":"0000-0002-9645-6576","full_name":"Sorichetti, Valerio"},{"first_name":"Andrea","full_name":"Ninarello, Andrea","last_name":"Ninarello"},{"first_name":"José","full_name":"Ruiz-Franco, José","last_name":"Ruiz-Franco"},{"first_name":"Virginie","last_name":"Hugouvieux","full_name":"Hugouvieux, Virginie"},{"first_name":"Emanuela","last_name":"Zaccarelli","full_name":"Zaccarelli, Emanuela"},{"last_name":"Micheletti","full_name":"Micheletti, Cristian","first_name":"Cristian"},{"last_name":"Kob","full_name":"Kob, Walter","first_name":"Walter"},{"full_name":"Rovigatti, Lorenzo","last_name":"Rovigatti","first_name":"Lorenzo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Sorichetti V, Ninarello A, Ruiz-Franco J, et al. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. 2023;158(7). doi:10.1063/5.0134271","apa":"Sorichetti, V., Ninarello, A., Ruiz-Franco, J., Hugouvieux, V., Zaccarelli, E., Micheletti, C., … Rovigatti, L. (2023). Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/5.0134271","short":"V. Sorichetti, A. Ninarello, J. Ruiz-Franco, V. Hugouvieux, E. Zaccarelli, C. Micheletti, W. Kob, L. Rovigatti, Journal of Chemical Physics 158 (2023).","ieee":"V. Sorichetti et al., “Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks,” Journal of Chemical Physics, vol. 158, no. 7. American Institute of Physics, 2023.","mla":"Sorichetti, Valerio, et al. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” Journal of Chemical Physics, vol. 158, no. 7, 074905, American Institute of Physics, 2023, doi:10.1063/5.0134271.","ista":"Sorichetti V, Ninarello A, Ruiz-Franco J, Hugouvieux V, Zaccarelli E, Micheletti C, Kob W, Rovigatti L. 2023. Structure and elasticity of model disordered, polydisperse, and defect-free polymer networks. Journal of Chemical Physics. 158(7), 074905.","chicago":"Sorichetti, Valerio, Andrea Ninarello, José Ruiz-Franco, Virginie Hugouvieux, Emanuela Zaccarelli, Cristian Micheletti, Walter Kob, and Lorenzo Rovigatti. “Structure and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.” Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0134271."},"article_number":"074905"},{"scopus_import":"1","month":"10","intvolume":" 46","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"}],"pmid":1,"oa_version":"None","issue":"10","volume":46,"publication_identifier":{"issn":["1292-8941"],"eissn":["1292-895X"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","_id":"14442","department":[{"_id":"AnSa"}],"date_updated":"2023-10-31T11:16:41Z","publisher":"Springer Nature","quality_controlled":"1","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.","date_published":"2023-10-01T00:00:00Z","doi":"10.1140/epje/s10189-023-00354-y","date_created":"2023-10-22T22:01:13Z","year":"2023","day":"01","publication":"The European Physical Journal E","article_number":"95","author":[{"full_name":"Rojas Vega, Mauricio Nicolas","last_name":"Rojas Vega","first_name":"Mauricio Nicolas","id":"441e7207-f91f-11ec-b67c-9e6fe3d8fd6d"},{"full_name":"De Castro, Pablo","last_name":"De Castro","first_name":"Pablo"},{"last_name":"Soto","full_name":"Soto, Rodrigo","first_name":"Rodrigo"}],"external_id":{"pmid":["37819444"]},"article_processing_charge":"No","title":"Mixtures of self-propelled particles interacting with asymmetric obstacles","citation":{"chicago":"Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Mixtures of Self-Propelled Particles Interacting with Asymmetric Obstacles.” The European Physical Journal E. Springer Nature, 2023. https://doi.org/10.1140/epje/s10189-023-00354-y.","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.","mla":"Rojas Vega, Mauricio Nicolas, et al. “Mixtures of Self-Propelled Particles Interacting with Asymmetric Obstacles.” The European Physical Journal E, vol. 46, no. 10, 95, Springer Nature, 2023, doi:10.1140/epje/s10189-023-00354-y.","ama":"Rojas Vega MN, De Castro P, Soto R. Mixtures of self-propelled particles interacting with asymmetric obstacles. The European Physical Journal E. 2023;46(10). doi:10.1140/epje/s10189-023-00354-y","apa":"Rojas Vega, M. N., De Castro, P., & Soto, R. (2023). Mixtures of self-propelled particles interacting with asymmetric obstacles. The European Physical Journal E. Springer Nature. https://doi.org/10.1140/epje/s10189-023-00354-y","short":"M.N. Rojas Vega, P. De Castro, R. Soto, The European Physical Journal E 46 (2023).","ieee":"M. N. Rojas Vega, P. De Castro, and R. Soto, “Mixtures of self-propelled particles interacting with asymmetric obstacles,” The European Physical Journal E, vol. 46, no. 10. Springer Nature, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"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.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Nature","day":"15","year":"2023","date_created":"2023-11-27T07:56:37Z","date_published":"2023-11-15T00:00:00Z","doi":"10.1038/s41586-023-06726-w","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Nature, Springer Nature, 2023, doi:10.1038/s41586-023-06726-w.","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. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06726-w","ama":"Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and stabilize damaged endolysosomal membranes. Nature. 2023. doi:10.1038/s41586-023-06726-w","ieee":"C. Bussi et al., “Stress granules plug and stabilize damaged endolysosomal membranes,” Nature. 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).","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.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-06726-w.","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."},"title":"Stress granules plug and stabilize damaged endolysosomal membranes","article_processing_charge":"Yes (via OA deal)","external_id":{"pmid":["37968398"]},"author":[{"first_name":"Claudio","full_name":"Bussi, Claudio","last_name":"Bussi"},{"last_name":"Mangiarotti","full_name":"Mangiarotti, Agustín","first_name":"Agustín"},{"last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian Eduardo","first_name":"Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714"},{"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"},{"full_name":"Fearns, Antony","last_name":"Fearns","first_name":"Antony"},{"last_name":"Rodgers","full_name":"Rodgers, Angela","first_name":"Angela"},{"full_name":"Franzmann, Titus M.","last_name":"Franzmann","first_name":"Titus M."},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Dimova, Rumiana","last_name":"Dimova","first_name":"Rumiana"},{"full_name":"Gutierrez, Maximiliano G.","last_name":"Gutierrez","first_name":"Maximiliano G."}],"pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"AbstractEndomembrane damage represents a form of stress that is detrimental for eukaryotic cells1,2. To cope with this threat, cells possess mechanisms that repair the damage and restore cellular homeostasis3–7. Endomembrane damage also results in organelle instability and the mechanisms by which cells stabilize damaged endomembranes to enable membrane repair remains unknown. Here, by combining in vitro and in cellulo studies with computational modelling we uncover a biological function for stress granules whereby these biomolecular condensates form rapidly at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane. Functionally, we demonstrate that stress granule formation and membrane stabilization enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal sorting complex required for transport)-dependent and independent mechanisms. We also show that blocking stress granule formation in human macrophages creates a permissive environment for Mycobacterium tuberculosis, a human pathogen that exploits endomembrane damage to survive within the host."}],"month":"11","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41586-023-06726-w"}],"language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"related_material":{"record":[{"id":"14472","status":"public","relation":"research_data"}],"link":[{"url":"https://doi.org/10.1038/s41586-023-06882-z","relation":"erratum"}]},"_id":"14610","keyword":["Multidisciplinary"],"status":"public","article_type":"original","type":"journal_article","date_updated":"2023-11-27T09:05:08Z","department":[{"_id":"AnSa"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"chicago":"Vanhille-Campos, Christian Eduardo, and Anđela Šarić. “Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14472.","ista":"Vanhille-Campos CE, Šarić A. 2023. Stress granules plug and stabilize damaged endolysosomal membranes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14472.","mla":"Vanhille-Campos, Christian Eduardo, and Anđela Šarić. Stress Granules Plug and Stabilize Damaged Endolysosomal Membranes. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14472.","apa":"Vanhille-Campos, C. E., & Šarić, A. (2023). Stress granules plug and stabilize damaged endolysosomal membranes. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14472","ama":"Vanhille-Campos CE, Šarić A. Stress granules plug and stabilize damaged endolysosomal membranes. 2023. doi:10.15479/AT:ISTA:14472","ieee":"C. E. Vanhille-Campos and A. Šarić, “Stress granules plug and stabilize damaged endolysosomal membranes.” Institute of Science and Technology Austria, 2023.","short":"C.E. Vanhille-Campos, A. Šarić, (2023)."},"date_updated":"2023-11-27T09:05:07Z","department":[{"_id":"AnSa"}],"file_date_updated":"2023-10-31T08:57:50Z","title":"Stress granules plug and stabilize damaged endolysosomal membranes","author":[{"last_name":"Vanhille-Campos","full_name":"Vanhille-Campos, Christian Eduardo","id":"3adeca52-9313-11ed-b1ac-c170b2505714","first_name":"Christian Eduardo"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"}],"article_processing_charge":"No","_id":"14472","status":"public","type":"research_data","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"day":"31","file":[{"success":1,"file_id":"14473","checksum":"a18706e952e8660c51ede52a167270b7","relation":"main_file","access_level":"open_access","content_type":"application/zip","file_name":"SGporecondensation-main.zip","date_created":"2023-10-30T16:31:08Z","creator":"ipalaia","file_size":62821432,"date_updated":"2023-10-30T16:31:08Z"},{"date_created":"2023-10-31T08:57:50Z","file_name":"README.txt","date_updated":"2023-10-31T08:57:50Z","file_size":1697,"creator":"dernst","checksum":"389eab31c6509dbc05795017fb618758","file_id":"14474","success":1,"content_type":"text/plain","access_level":"open_access","relation":"main_file"}],"has_accepted_license":"1","year":"2023","related_material":{"record":[{"relation":"used_in_publication","id":"14610","status":"public"}]},"doi":"10.15479/AT:ISTA:14472","date_published":"2023-10-31T00:00:00Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2023-10-30T16:38:32Z","oa_version":"Published Version","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."}],"month":"10","publisher":"Institute of Science and Technology Austria","oa":1},{"quality_controlled":"1","publisher":"American Physical Society","oa":1,"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).","doi":"10.1103/PhysRevLett.131.228401","date_published":"2023-12-01T00:00:00Z","date_created":"2023-12-10T23:00:57Z","day":"01","publication":"Physical Review Letters","year":"2023","article_number":"228401","title":"Transverse fluctuations control the assembly of semiflexible filaments","author":[{"id":"ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b","first_name":"Valerio","full_name":"Sorichetti, Valerio","orcid":"0000-0002-9645-6576","last_name":"Sorichetti"},{"first_name":"Martin","full_name":"Lenz, Martin","last_name":"Lenz"}],"article_processing_charge":"No","external_id":{"arxiv":["2303.03088"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Sorichetti V, Lenz M. 2023. Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. 131(22), 228401.","chicago":"Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” Physical Review Letters. American Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.228401.","short":"V. Sorichetti, M. Lenz, Physical Review Letters 131 (2023).","ieee":"V. Sorichetti and M. Lenz, “Transverse fluctuations control the assembly of semiflexible filaments,” Physical Review Letters, vol. 131, no. 22. American Physical Society, 2023.","ama":"Sorichetti V, Lenz M. Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. 2023;131(22). doi:10.1103/PhysRevLett.131.228401","apa":"Sorichetti, V., & Lenz, M. (2023). Transverse fluctuations control the assembly of semiflexible filaments. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.131.228401","mla":"Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the Assembly of Semiflexible Filaments.” Physical Review Letters, vol. 131, no. 22, 228401, American Physical Society, 2023, doi:10.1103/PhysRevLett.131.228401."},"month":"12","intvolume":" 131","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2303.03088"}],"oa_version":"Preprint","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."}],"volume":131,"issue":"22","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"14655","department":[{"_id":"AnSa"}],"date_updated":"2023-12-11T07:59:25Z"},{"ddc":["570"],"date_updated":"2024-01-16T09:20:03Z","file_date_updated":"2024-01-16T09:09:29Z","department":[{"_id":"AnSa"}],"_id":"14782","keyword":["Biophysics"],"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"file":[{"file_name":"2023_BiophysicalJournal_Baldauf.pdf","date_created":"2024-01-16T09:09:29Z","file_size":3285810,"date_updated":"2024-01-16T09:09:29Z","creator":"dernst","success":1,"file_id":"14807","checksum":"70566e54cd95ea6df340909ad44c5cd5","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","publication_identifier":{"issn":["0006-3495"]},"related_material":{"link":[{"relation":"software","url":"https://github.com/BioSoftMatterGroup/actin-curvature-sensing"}]},"issue":"11","volume":122,"oa_version":"Published Version","pmid":1,"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","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","chicago":"Baldauf, Lucia, Felix F Frey, Marcos Arribas Perez, Timon Idema, and Gijsje H. Koenderink. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” Biophysical Journal. Elsevier, 2023. https://doi.org/10.1016/j.bpj.2023.02.018.","ieee":"L. Baldauf, F. F. Frey, M. Arribas Perez, T. Idema, and G. H. Koenderink, “Branched actin cortices reconstituted in vesicles sense membrane curvature,” Biophysical Journal, vol. 122, no. 11. Elsevier, pp. 2311–2324, 2023.","short":"L. Baldauf, F.F. Frey, M. Arribas Perez, T. Idema, G.H. Koenderink, Biophysical Journal 122 (2023) 2311–2324.","ama":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. 2023;122(11):2311-2324. doi:10.1016/j.bpj.2023.02.018","apa":"Baldauf, L., Frey, F. F., Arribas Perez, M., Idema, T., & Koenderink, G. H. (2023). Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2023.02.018","mla":"Baldauf, Lucia, et al. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” Biophysical Journal, vol. 122, no. 11, Elsevier, 2023, pp. 2311–24, doi:10.1016/j.bpj.2023.02.018."},"title":"Branched actin cortices reconstituted in vesicles sense membrane curvature","article_processing_charge":"Yes (in subscription journal)","external_id":{"isi":["001016792600001"],"pmid":["36806830"]},"author":[{"first_name":"Lucia","full_name":"Baldauf, Lucia","last_name":"Baldauf"},{"full_name":"Frey, Felix F","last_name":"Frey","first_name":"Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3"},{"first_name":"Marcos","full_name":"Arribas Perez, Marcos","last_name":"Arribas Perez"},{"first_name":"Timon","full_name":"Idema, Timon","last_name":"Idema"},{"full_name":"Koenderink, Gijsje H.","last_name":"Koenderink","first_name":"Gijsje H."}],"publication":"Biophysical Journal","day":"06","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2024-01-10T09:45:48Z","doi":"10.1016/j.bpj.2023.02.018","date_published":"2023-06-06T00:00:00Z","page":"2311-2324","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.","oa":1,"publisher":"Elsevier","quality_controlled":"1"},{"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."}],"oa_version":"Published Version","pmid":1,"intvolume":" 222","month":"02","publication_status":"published","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"language":[{"iso":"eng"}],"file":[{"file_id":"14811","checksum":"505d5cac36c14b073b68c7fed1a92bd3","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2024-01-16T10:15:09Z","file_name":"2023_JCB_Mund.pdf","creator":"dernst","date_updated":"2024-01-16T10:15:09Z","file_size":5678069}],"issue":"3","volume":222,"_id":"14788","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["Cell Biology"],"status":"public","date_updated":"2024-01-16T10:17:05Z","ddc":["570"],"department":[{"_id":"AnSa"}],"file_date_updated":"2024-01-16T10:15:09Z","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.","oa":1,"publisher":"Rockefeller University Press","quality_controlled":"1","year":"2023","has_accepted_license":"1","isi":1,"publication":"Journal of Cell Biology","day":"03","date_created":"2024-01-10T10:45:55Z","date_published":"2023-02-03T00:00:00Z","doi":"10.1083/jcb.202206038","article_number":"e202206038","citation":{"mla":"Mund, Markus, et al. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” Journal of Cell Biology, vol. 222, no. 3, e202206038, Rockefeller University Press, 2023, doi:10.1083/jcb.202206038.","ama":"Mund M, Tschanz A, Wu Y-L, et al. Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. 2023;222(3). doi:10.1083/jcb.202206038","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. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202206038","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).","ieee":"M. Mund et al., “Clathrin coats partially preassemble and subsequently bend during endocytosis,” Journal of Cell Biology, vol. 222, no. 3. Rockefeller University Press, 2023.","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.” Journal of Cell Biology. Rockefeller University Press, 2023. https://doi.org/10.1083/jcb.202206038.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000978065000001"],"pmid":["36734980"]},"article_processing_charge":"No","author":[{"first_name":"Markus","full_name":"Mund, Markus","last_name":"Mund"},{"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","full_name":"Frey, Felix F","last_name":"Frey","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","first_name":"Felix F"},{"first_name":"Johanna L.","full_name":"Mehl, Johanna L.","last_name":"Mehl"},{"last_name":"Kaksonen","full_name":"Kaksonen, Marko","first_name":"Marko"},{"first_name":"Ori","full_name":"Avinoam, Ori","last_name":"Avinoam"},{"last_name":"Schwarz","full_name":"Schwarz, Ulrich S.","first_name":"Ulrich S."},{"full_name":"Ries, Jonas","last_name":"Ries","first_name":"Jonas"}],"title":"Clathrin coats partially preassemble and subsequently bend during endocytosis"},{"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.","publisher":"American Chemical Society","quality_controlled":"1","oa":1,"isi":1,"year":"2023","day":"13","publication":"The Journal of Physical Chemistry B","page":"10950-10959","doi":"10.1021/acs.jpcb.3c04627","date_published":"2023-12-13T00:00:00Z","date_created":"2024-01-18T07:47:11Z","citation":{"chicago":"Sakref, Yann, Maitane Muñoz Basagoiti, Zorana Zeravcic, and Olivier Rivoire. “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” The Journal of Physical Chemistry B. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpcb.3c04627.","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.","mla":"Sakref, Yann, et al. “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” The Journal of Physical Chemistry B, vol. 127, no. 51, American Chemical Society, 2023, pp. 10950–59, doi:10.1021/acs.jpcb.3c04627.","short":"Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, O. Rivoire, The Journal of Physical Chemistry B 127 (2023) 10950–10959.","ieee":"Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, and O. Rivoire, “On kinetic constraints that catalysis imposes on elementary processes,” The Journal of Physical Chemistry B, vol. 127, no. 51. American Chemical Society, pp. 10950–10959, 2023.","ama":"Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. On kinetic constraints that catalysis imposes on elementary processes. The Journal of Physical Chemistry B. 2023;127(51):10950-10959. doi:10.1021/acs.jpcb.3c04627","apa":"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. American Chemical Society. https://doi.org/10.1021/acs.jpcb.3c04627"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Yann","full_name":"Sakref, Yann","last_name":"Sakref"},{"full_name":"Muñoz Basagoiti, Maitane","orcid":"0000-0003-1483-1457","last_name":"Muñoz Basagoiti","first_name":"Maitane","id":"1a8a7950-82cd-11ed-bd4f-9624c913a607"},{"first_name":"Zorana","full_name":"Zeravcic, Zorana","last_name":"Zeravcic"},{"first_name":"Olivier","full_name":"Rivoire, Olivier","last_name":"Rivoire"}],"external_id":{"isi":["001134068000001"],"arxiv":["2312.15940"]},"article_processing_charge":"No","title":"On kinetic constraints that catalysis imposes on elementary processes","abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2312.15940"}],"month":"12","intvolume":" 127","publication_identifier":{"eissn":["1520-5207"],"issn":["1520-6106"]},"publication_status":"published","language":[{"iso":"eng"}],"volume":127,"issue":"51","_id":"14831","article_type":"original","type":"journal_article","status":"public","keyword":["Materials Chemistry","Surfaces","Coatings and Films","Physical and Theoretical Chemistry"],"date_updated":"2024-01-23T07:58:27Z","department":[{"_id":"AnSa"}]},{"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).","quality_controlled":"1","publisher":"Elsevier","oa":1,"day":"29","publication":"Biophysical Journal","year":"2023","date_published":"2023-12-29T00:00:00Z","doi":"10.1016/j.bpj.2023.12.020","date_created":"2024-01-21T23:00:56Z","project":[{"grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Azadbakht, Ali, et al. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” Biophysical Journal, Elsevier, doi:10.1016/j.bpj.2023.12.020.","ama":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal. doi:10.1016/j.bpj.2023.12.020","apa":"Azadbakht, A., Meadowcroft, B., Majek, J., Šarić, A., & Kraft, D. J. (n.d.). Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2023.12.020","short":"A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, D.J. Kraft, Biophysical Journal (n.d.).","ieee":"A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, and D. J. Kraft, “Nonadditivity in interactions between three membrane-wrapped colloidal spheres,” Biophysical Journal. Elsevier.","chicago":"Azadbakht, Ali, Billie Meadowcroft, Juraj Majek, Anđela Šarić, and Daniela J. Kraft. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” Biophysical Journal. Elsevier, n.d. https://doi.org/10.1016/j.bpj.2023.12.020.","ista":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal."},"title":"Nonadditivity in interactions between three membrane-wrapped colloidal spheres","author":[{"full_name":"Azadbakht, Ali","last_name":"Azadbakht","first_name":"Ali"},{"id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1","first_name":"Billie","orcid":"0000-0003-3441-1337","full_name":"Meadowcroft, Billie","last_name":"Meadowcroft"},{"id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1","first_name":"Juraj","last_name":"Majek","full_name":"Majek, Juraj"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"full_name":"Kraft, Daniela J.","last_name":"Kraft","first_name":"Daniela J."}],"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"month":"12","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.bpj.2023.12.020","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1542-0086"],"issn":["0006-3495"]},"publication_status":"inpress","ec_funded":1,"_id":"14844","status":"public","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"ddc":["570"],"date_updated":"2024-01-23T09:26:35Z","department":[{"_id":"AnSa"}]},{"year":"2023","has_accepted_license":"1","isi":1,"publication":"Nature Physics","day":"01","page":"1680-1688","date_created":"2023-08-06T22:01:11Z","date_published":"2023-11-01T00:00:00Z","doi":"10.1038/s41567-023-02136-x","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.","oa":1,"quality_controlled":"1","publisher":"Springer Nature","citation":{"mla":"Grober, Daniel, et al. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1680–88, doi:10.1038/s41567-023-02136-x.","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,” Nature Physics, vol. 19. Springer Nature, pp. 1680–1688, 2023.","ama":"Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. Unconventional colloidal aggregation in chiral bacterial baths. Nature Physics. 2023;19:1680-1688. doi:10.1038/s41567-023-02136-x","apa":"Grober, D., Palaia, I., Ucar, M. C., Hannezo, E. B., Šarić, A., & Palacci, J. A. (2023). Unconventional colloidal aggregation in chiral bacterial baths. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02136-x","chicago":"Grober, Daniel, Ivan Palaia, Mehmet C Ucar, Edouard B Hannezo, Anđela Šarić, and Jérémie A Palacci. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02136-x.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","external_id":{"isi":["001037346400005"]},"author":[{"last_name":"Grober","full_name":"Grober, Daniel","id":"abdfc56f-34fb-11ee-bd33-fd766fce5a99","first_name":"Daniel"},{"id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa","first_name":"Ivan","full_name":"Palaia, Ivan","orcid":" 0000-0002-8843-9485 ","last_name":"Palaia"},{"last_name":"Ucar","orcid":"0000-0003-0506-4217","full_name":"Ucar, Mehmet C","id":"50B2A802-6007-11E9-A42B-EB23E6697425","first_name":"Mehmet C"},{"last_name":"Hannezo","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","first_name":"Jérémie A","last_name":"Palacci","orcid":"0000-0002-7253-9465","full_name":"Palacci, Jérémie A"}],"title":"Unconventional colloidal aggregation in chiral bacterial baths","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program"},{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication_status":"published","publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2024-01-30T12:26:08Z","file_size":6365607,"creator":"dernst","date_created":"2024-01-30T12:26:08Z","file_name":"2023_NaturePhysics_Grober.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"7e282c2ebc0ac82125a04f6b4742d4c1","file_id":"14906","success":1}],"ec_funded":1,"volume":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"}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 19","month":"11","date_updated":"2024-01-30T12:26:55Z","ddc":["530"],"department":[{"_id":"EdHa"},{"_id":"AnSa"},{"_id":"JePa"}],"file_date_updated":"2024-01-30T12:26:08Z","_id":"13971","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","status":"public"},{"_id":"15027","tmp":{"image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)"},"type":"research_data_reference","status":"public","citation":{"chicago":"Curk, Samo. “Aggregation_data.” Figshare, 2023.","ista":"Curk S. 2023. aggregation_data, Figshare.","mla":"Curk, Samo. Aggregation_data. Figshare, 2023.","short":"S. Curk, (2023).","ieee":"S. Curk, “aggregation_data.” Figshare, 2023.","apa":"Curk, S. (2023). aggregation_data. Figshare.","ama":"Curk S. aggregation_data. 2023."},"date_updated":"2024-02-26T08:45:55Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"full_name":"Curk, Samo","orcid":"0000-0001-6160-9766","last_name":"Curk","id":"031eff0d-d481-11ee-8508-cd12a7a86e5b","first_name":"Samo"}],"department":[{"_id":"AnSa"}],"title":"aggregation_data","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"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://figshare.com/s/85798bba4ebc68d822ed"}],"oa":1,"publisher":"Figshare","month":"12","year":"2023","has_accepted_license":"1","day":"13","date_created":"2024-02-26T08:37:57Z","related_material":{"record":[{"id":"15001","status":"public","relation":"used_in_publication"}]},"date_published":"2023-12-13T00:00:00Z"},{"title":"Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring","external_id":{"arxiv":["2203.10524"],"isi":["000796953700022"]},"article_processing_charge":"No","author":[{"last_name":"Palaia","full_name":"Palaia, Ivan","orcid":" 0000-0002-8843-9485 ","first_name":"Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa"},{"last_name":"Goyal","full_name":"Goyal, Abhay","first_name":"Abhay"},{"first_name":"Emanuela","last_name":"Del Gado","full_name":"Del Gado, Emanuela"},{"full_name":"Šamaj, Ladislav","last_name":"Šamaj","first_name":"Ladislav"},{"full_name":"Trizac, Emmanuel","last_name":"Trizac","first_name":"Emmanuel"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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.” Journal of Physical Chemistry B. American Chemical Society, 2022. https://doi.org/10.1021/acs.jpcb.2c00028.","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.","mla":"Palaia, Ivan, et al. “Like-Charge Attraction at the Nanoscale: Ground-State Correlations and Water Destructuring.” Journal of Physical Chemistry B, vol. 126, no. 16, American Chemical Society, 2022, pp. 3143–49, doi:10.1021/acs.jpcb.2c00028.","ama":"Palaia I, Goyal A, Del Gado E, Šamaj L, Trizac E. Like-charge attraction at the nanoscale: Ground-state correlations and water destructuring. Journal of Physical Chemistry B. 2022;126(16):3143-3149. doi:10.1021/acs.jpcb.2c00028","apa":"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. American Chemical Society. https://doi.org/10.1021/acs.jpcb.2c00028","short":"I. Palaia, A. Goyal, E. Del Gado, L. Šamaj, E. Trizac, Journal of Physical Chemistry B 126 (2022) 3143–3149.","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,” Journal of Physical Chemistry B, vol. 126, no. 16. American Chemical Society, pp. 3143–3149, 2022."},"date_created":"2022-05-01T22:01:42Z","date_published":"2022-04-14T00:00:00Z","doi":"10.1021/acs.jpcb.2c00028","page":"3143-3149","publication":"Journal of Physical Chemistry B","day":"14","year":"2022","isi":1,"oa":1,"publisher":"American Chemical Society","quality_controlled":"1","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.","department":[{"_id":"AnSa"}],"date_updated":"2023-08-03T06:42:50Z","status":"public","article_type":"original","type":"journal_article","_id":"11340","volume":126,"issue":"16","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1520-6106"],"eissn":["1520-5207"]},"intvolume":" 126","month":"04","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.2203.10524","open_access":"1"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"lang":"eng","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."}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Meadowcroft, Billie, et al. “Mechanochemical Rules for Shape-Shifting Filaments That Remodel Membranes.” Physical Review Letters, vol. 129, no. 26, 268101, American Physical Society, 2022, doi:10.1103/PhysRevLett.129.268101.","apa":"Meadowcroft, B., Palaia, I., Pfitzner, A. K., Roux, A., Baum, B., & Šarić, A. (2022). Mechanochemical rules for shape-shifting filaments that remodel membranes. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.129.268101","ama":"Meadowcroft B, Palaia I, Pfitzner AK, Roux A, Baum B, Šarić A. Mechanochemical rules for shape-shifting filaments that remodel membranes. Physical Review Letters. 2022;129(26). doi:10.1103/PhysRevLett.129.268101","short":"B. Meadowcroft, I. Palaia, A.K. Pfitzner, A. Roux, B. Baum, A. Šarić, Physical Review Letters 129 (2022).","ieee":"B. Meadowcroft, I. Palaia, A. K. Pfitzner, A. Roux, B. Baum, and A. Šarić, “Mechanochemical rules for shape-shifting filaments that remodel membranes,” Physical Review Letters, vol. 129, no. 26. American Physical Society, 2022.","chicago":"Meadowcroft, Billie, Ivan Palaia, Anna Katharina Pfitzner, Aurélien Roux, Buzz Baum, and Anđela Šarić. “Mechanochemical Rules for Shape-Shifting Filaments That Remodel Membranes.” Physical Review Letters. American Physical Society, 2022. https://doi.org/10.1103/PhysRevLett.129.268101.","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."},"title":"Mechanochemical rules for shape-shifting filaments that remodel membranes","article_processing_charge":"No","external_id":{"pmid":["36608212"],"isi":["000906721500001"]},"author":[{"full_name":"Meadowcroft, Billie","last_name":"Meadowcroft","first_name":"Billie","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1"},{"orcid":" 0000-0002-8843-9485 ","full_name":"Palaia, Ivan","last_name":"Palaia","first_name":"Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa"},{"first_name":"Anna Katharina","full_name":"Pfitzner, Anna Katharina","last_name":"Pfitzner"},{"last_name":"Roux","full_name":"Roux, Aurélien","first_name":"Aurélien"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić"}],"article_number":"268101","project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"},{"_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"}],"publication":"Physical Review Letters","day":"23","year":"2022","isi":1,"date_created":"2023-01-08T23:00:53Z","date_published":"2022-12-23T00:00:00Z","doi":"10.1103/PhysRevLett.129.268101","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). ","oa":1,"publisher":"American Physical Society","quality_controlled":"1","date_updated":"2023-08-03T14:10:59Z","department":[{"_id":"AnSa"}],"_id":"12108","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"ec_funded":1,"volume":129,"issue":"26","oa_version":"Preprint","pmid":1,"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","month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.05.10.490642 "}],"scopus_import":"1"},{"scopus_import":"1","month":"10","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"}],"oa_version":"Published Version","related_material":{"link":[{"relation":"software","url":"https://github.com/sharonJXY/3-filament-model"}]},"issue":"10","volume":18,"ec_funded":1,"publication_identifier":{"issn":["1553-7358"]},"publication_status":"published","file":[{"file_id":"12359","checksum":"bada6a7865e470cf42bbdfa67dd471d2","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2023-01-24T10:45:01Z","file_name":"2022_PLoSCompBio_Jiang.pdf","date_updated":"2023-01-24T10:45:01Z","file_size":2641067,"creator":"dernst"}],"language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Computational Theory and Mathematics","Cellular and Molecular Neuroscience","Genetics","Molecular Biology","Ecology","Modeling and Simulation","Ecology","Evolution","Behavior and Systematics"],"_id":"12152","department":[{"_id":"AnSa"}],"file_date_updated":"2023-01-24T10:45:01Z","date_updated":"2023-08-04T09:03:21Z","ddc":["570"],"quality_controlled":"1","publisher":"Public Library of Science","oa":1,"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.","doi":"10.1371/journal.pcbi.1010586","date_published":"2022-10-17T00:00:00Z","date_created":"2023-01-12T12:08:10Z","isi":1,"has_accepted_license":"1","year":"2022","day":"17","publication":"PLOS Computational Biology","project":[{"_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","call_identifier":"H2020","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"},{"_id":"eba0f67c-77a9-11ec-83b8-cc8501b3e222","name":"The evolution of trafficking: from archaea to eukaryotes","grant_number":"96752"}],"article_number":"e1010586","author":[{"first_name":"Xiuyun","full_name":"Jiang, Xiuyun","last_name":"Jiang"},{"full_name":"Harker-Kirschneck, Lena","last_name":"Harker-Kirschneck","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","full_name":"Pfitzner, Anna-Katharina","last_name":"Pfitzner"},{"last_name":"Lominadze","full_name":"Lominadze, Elene","first_name":"Elene"},{"last_name":"Roux","full_name":"Roux, Aurélien","first_name":"Aurélien"},{"first_name":"Buzz","last_name":"Baum","full_name":"Baum, Buzz"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"}],"article_processing_charge":"No","external_id":{"isi":["000924885500005"]},"title":"Modelling membrane reshaping by staged polymerization of ESCRT-III filaments","citation":{"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.” PLOS Computational Biology. Public Library of Science, 2022. https://doi.org/10.1371/journal.pcbi.1010586.","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.","mla":"Jiang, Xiuyun, et al. “Modelling Membrane Reshaping by Staged Polymerization of ESCRT-III Filaments.” PLOS Computational Biology, vol. 18, no. 10, e1010586, Public Library of Science, 2022, doi:10.1371/journal.pcbi.1010586.","ieee":"X. Jiang et al., “Modelling membrane reshaping by staged polymerization of ESCRT-III filaments,” PLOS Computational Biology, 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).","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. PLOS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1010586","ama":"Jiang X, Harker-Kirschneck L, Vanhille-Campos CE, et al. Modelling membrane reshaping by staged polymerization of ESCRT-III filaments. PLOS Computational Biology. 2022;18(10). doi:10.1371/journal.pcbi.1010586"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"article_number":"943355","citation":{"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.","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.” Frontiers in Neuroscience. Frontiers Media, 2022. https://doi.org/10.3389/fnins.2022.943355.","apa":"Weiffert, T., Meisl, G., Curk, S., Cukalevski, R., Šarić, A., Knowles, T. P. J., & Linse, S. (2022). Influence of denaturants on amyloid β42 aggregation kinetics. Frontiers in Neuroscience. Frontiers Media. https://doi.org/10.3389/fnins.2022.943355","ama":"Weiffert T, Meisl G, Curk S, et al. Influence of denaturants on amyloid β42 aggregation kinetics. Frontiers in Neuroscience. 2022;16. doi:10.3389/fnins.2022.943355","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 et al., “Influence of denaturants on amyloid β42 aggregation kinetics,” Frontiers in Neuroscience, vol. 16. Frontiers Media, 2022.","mla":"Weiffert, Tanja, et al. “Influence of Denaturants on Amyloid Β42 Aggregation Kinetics.” Frontiers in Neuroscience, vol. 16, 943355, Frontiers Media, 2022, doi:10.3389/fnins.2022.943355."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","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"},{"last_name":"Cukalevski","full_name":"Cukalevski, Risto","first_name":"Risto"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"full_name":"Knowles, Tuomas P. J.","last_name":"Knowles","first_name":"Tuomas P. J."},{"last_name":"Linse","full_name":"Linse, Sara","first_name":"Sara"}],"external_id":{"isi":["000866287100001"]},"article_processing_charge":"No","title":"Influence of denaturants on amyloid β42 aggregation kinetics","acknowledgement":"This work was supported by grants from the Swedish Research Council (grant no. 2015-00143) and the European Research Council (grant no. 340890).","quality_controlled":"1","publisher":"Frontiers Media","oa":1,"has_accepted_license":"1","isi":1,"year":"2022","day":"20","publication":"Frontiers in Neuroscience","date_published":"2022-09-20T00:00:00Z","doi":"10.3389/fnins.2022.943355","date_created":"2023-01-16T09:56:43Z","_id":"12251","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["General Neuroscience"],"date_updated":"2023-08-04T09:48:56Z","ddc":["570"],"department":[{"_id":"AnSa"}],"file_date_updated":"2023-01-30T09:15:13Z","abstract":[{"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 in vitro and in bodily fluids. A key outstanding question is how the relative stabilities of monomers, fibrils and intermediates affect each step in the fibril formation process. By monitoring the kinetics of aggregation of Aβ42, in the presence of urea or guanidinium hydrochloride (GuHCl), we here determine the rates of the underlying microscopic steps and establish the importance of changes in relative stability induced by the presence of denaturant for each individual step. Denaturants shift the equilibrium towards the unfolded state of each species. We find that a non-ionic denaturant, urea, reduces the overall aggregation rate, and that the effect on nucleation is stronger than the effect on elongation. Urea reduces the rate of secondary nucleation by decreasing the coverage of fibril surfaces and the rate of nucleus formation. It also reduces the rate of primary nucleation, increasing its reaction order. The ionic denaturant, GuHCl, accelerates the aggregation at low denaturant concentrations and decelerates the aggregation at high denaturant concentrations. Below approximately 0.25 M GuHCl, the screening of repulsive electrostatic interactions between peptides by the charged denaturant dominates, leading to an increased aggregation rate. At higher GuHCl concentrations, the electrostatic repulsion is completely screened, and the denaturing effect dominates. The results illustrate how the differential effects of denaturants on stability of monomer, oligomer and fibril translate to differential effects on microscopic steps, with the rate of nucleation being most strongly reduced.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"09","intvolume":" 16","publication_identifier":{"issn":["1662-453X"]},"publication_status":"published","file":[{"creator":"dernst","file_size":19798610,"date_updated":"2023-01-30T09:15:13Z","file_name":"2022_FrontiersNeuroscience_Weiffert2.pdf","date_created":"2023-01-30T09:15:13Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"e67d16113ffb4fb4fa38a183d169f210","file_id":"12442"}],"language":[{"iso":"eng"}],"volume":16},{"language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"11405","checksum":"7fada58059676a4bb0944b82247af740","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2022_JourChemPhysics_Palaia.pdf","date_created":"2022-05-23T07:45:33Z","creator":"dernst","file_size":6387208,"date_updated":"2022-05-23T07:45:33Z"}],"publication_status":"published","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"ec_funded":1,"issue":"19","volume":156,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"intvolume":" 156","month":"05","ddc":["540"],"date_updated":"2023-09-05T11:59:00Z","file_date_updated":"2022-05-23T07:45:33Z","department":[{"_id":"AnSa"}],"_id":"11400","keyword":["Physical and Theoretical Chemistry","General Physics and Astronomy"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","publication":"The Journal of Chemical Physics","day":"16","year":"2022","has_accepted_license":"1","isi":1,"date_created":"2022-05-22T17:04:48Z","date_published":"2022-05-16T00:00:00Z","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).","oa":1,"publisher":"AIP Publishing","quality_controlled":"1","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.” The Journal of Chemical Physics. AIP Publishing, 2022. https://doi.org/10.1063/5.0087769.","ieee":"I. Palaia and A. Šarić, “Controlling cluster size in 2D phase-separating binary mixtures with specific interactions,” The Journal of Chemical Physics, vol. 156, no. 19. AIP Publishing, 2022.","short":"I. Palaia, A. Šarić, The Journal of Chemical Physics 156 (2022).","ama":"Palaia I, Šarić A. Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. The Journal of Chemical Physics. 2022;156(19). doi:10.1063/5.0087769","apa":"Palaia, I., & Šarić, A. (2022). Controlling cluster size in 2D phase-separating binary mixtures with specific interactions. The Journal of Chemical Physics. AIP Publishing. https://doi.org/10.1063/5.0087769","mla":"Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating Binary Mixtures with Specific Interactions.” The Journal of Chemical Physics, vol. 156, no. 19, 194902, AIP Publishing, 2022, doi:10.1063/5.0087769."},"title":"Controlling cluster size in 2D phase-separating binary mixtures with specific interactions","article_processing_charge":"No","external_id":{"isi":["000797236000004"]},"author":[{"full_name":"Palaia, Ivan","orcid":" 0000-0002-8843-9485 ","last_name":"Palaia","first_name":"Ivan","id":"9c805cd2-4b75-11ec-a374-db6dd0ed57fa"},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"}],"article_number":"194902","project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","grant_number":"802960","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines"},{"grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c"}]},{"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."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 119","month":"07","publication_status":"published","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"language":[{"iso":"eng"}],"file":[{"file_size":2476021,"date_updated":"2023-10-04T09:05:44Z","creator":"dernst","file_name":"2022_PNAS_Toprakcioglu.pdf","date_created":"2023-10-04T09:05:44Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"0fe3878896cbeb6c44e29222ec2f336a","file_id":"14386"}],"ec_funded":1,"issue":"31","volume":119,"_id":"11841","tmp":{"short":"CC BY-NC-ND (4.0)","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","image":"/images/cc_by_nc_nd.png"},"article_type":"original","type":"journal_article","status":"public","date_updated":"2023-10-04T09:06:52Z","ddc":["570"],"file_date_updated":"2023-10-04T09:05:44Z","department":[{"_id":"AnSa"}],"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).","oa":1,"quality_controlled":"1","publisher":"Proceedings of the National Academy of Sciences","year":"2022","isi":1,"has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"28","date_created":"2022-08-14T22:01:45Z","date_published":"2022-07-28T00:00:00Z","doi":"10.1073/pnas.2109718119","article_number":"e2109718119","project":[{"name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960","call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e"}],"citation":{"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.","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.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2022. https://doi.org/10.1073/pnas.2109718119.","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. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2109718119","ama":"Toprakcioglu Z, Kamada A, Michaels TCT, et al. Adsorption free energy predicts amyloid protein nucleation rates. Proceedings of the National Academy of Sciences of the United States of America. 2022;119(31). doi:10.1073/pnas.2109718119","ieee":"Z. Toprakcioglu et al., “Adsorption free energy predicts amyloid protein nucleation rates,” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 31. Proceedings of the National Academy of Sciences, 2022.","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).","mla":"Toprakcioglu, Zenon, et al. “Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” Proceedings of the National Academy of Sciences of the United States of America, vol. 119, no. 31, e2109718119, Proceedings of the National Academy of Sciences, 2022, doi:10.1073/pnas.2109718119."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["000903753500002"]},"article_processing_charge":"No","author":[{"last_name":"Toprakcioglu","full_name":"Toprakcioglu, Zenon","first_name":"Zenon"},{"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"},{"last_name":"Krausser","full_name":"Krausser, Johannes","first_name":"Johannes"},{"last_name":"Wei","full_name":"Wei, Jiapeng","first_name":"Jiapeng"},{"first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"last_name":"Vendruscolo","full_name":"Vendruscolo, Michele","first_name":"Michele"},{"first_name":"Tuomas P.J.","last_name":"Knowles","full_name":"Knowles, Tuomas P.J."}],"title":"Adsorption free energy predicts amyloid protein nucleation rates"}]