[{"OA_place":"publisher","OA_type":"hybrid","language":[{"iso":"eng"}],"publication":"Molecular Biology of the Cell","issue":"3","scopus_import":"1","acknowledgement":"We thank Professor José Paulo Leal, Department of Computer Science − Faculdade de Ciências da Universidade do Porto, for his invaluable help during the Implementation of NAGPKin. This work is part of a project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement no. 952334 (PhasAGE). This research was funded by the Portuguese Foundation for Science and Technology (FCT) in the framework of project PTDC/QUI-COL/2444/2021.","publication_identifier":{"issn":["1059-1524"],"eissn":["1939-4586"]},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","citation":{"chicago":"Sárkány, Zsuzsa, Francisco Figueiredo, Sandra Macedo-Ribeiro, and Pedro M. Martins. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein Phase Separation.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2024. <a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">https://doi.org/10.1091/mbc.e23-07-0289</a>.","apa":"Sárkány, Z., Figueiredo, F., Macedo-Ribeiro, S., &#38; Martins, P. M. (2024). NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">https://doi.org/10.1091/mbc.e23-07-0289</a>","mla":"Sárkány, Zsuzsa, et al. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein Phase Separation.” <i>Molecular Biology of the Cell</i>, vol. 35, no. 3, mr1, American Society for Cell Biology, 2024, doi:<a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">10.1091/mbc.e23-07-0289</a>.","ama":"Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. <i>Molecular Biology of the Cell</i>. 2024;35(3). doi:<a href=\"https://doi.org/10.1091/mbc.e23-07-0289\">10.1091/mbc.e23-07-0289</a>","ieee":"Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, and P. M. Martins, “NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation,” <i>Molecular Biology of the Cell</i>, vol. 35, no. 3. American Society for Cell Biology, 2024.","ista":"Sárkány Z, Figueiredo F, Macedo-Ribeiro S, Martins PM. 2024. NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation. Molecular Biology of the Cell. 35(3), mr1.","short":"Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, P.M. Martins, Molecular Biology of the Cell 35 (2024)."},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_updated":"2026-10-01T11:22:53Z","supplementarymaterial":"no","_id":"18934","title":"NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation","date_created":"2025-01-29T07:58:40Z","author":[{"last_name":"Sárkány","first_name":"Zsuzsa","full_name":"Sárkány, Zsuzsa"},{"full_name":"Figueiredo, Francisco","last_name":"Figueiredo","first_name":"Francisco","id":"8125cbe2-9661-11ed-a754-afe96018f37d"},{"full_name":"Macedo-Ribeiro, Sandra","first_name":"Sandra","last_name":"Macedo-Ribeiro"},{"full_name":"Martins, Pedro M.","first_name":"Pedro M.","last_name":"Martins"}],"status":"public","article_type":"original","oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"The assembly of biomolecular condensate in eukaryotic cells and the accumulation of amyloid deposits in neurons are processes involving the nucleation and growth (NAG) of new protein phases. To therapeutically target protein phase separation, drug candidates are tested in in vitro assays that monitor the increase in the mass or size of the new phase. Limited mechanistic insight is, however, provided if empirical or untestable kinetic models are fitted to these progress curves. Here we present the web server NAGPKin that quantifies NAG rates using mass-based or size-based progress curves as the input data. A report is generated containing the fitted NAG parameters and elucidating the phase separation mechanisms at play. The NAG parameters can be used to predict particle size distributions of, for example, protein droplets formed by liquid-liquid phase separation (LLPS) or amyloid fibrils formed by protein aggregation. Because minimal intervention is required from the user, NAGPKin is a good platform for standardized reporting of LLPS and protein self-assembly data. NAGPKin is useful for drug discovery as well as for fundamental studies on protein phase separation. NAGPKin is freely available (no login required) at https://nagpkin.i3s.up.pt ."}],"article_number":"mr1","volume":35,"file":[{"file_id":"18935","file_size":1699180,"file_name":"2024_MolecularBioCell_Sarkany.pdf","date_updated":"2025-01-29T08:12:11Z","content_type":"application/pdf","checksum":"d7deb6390f294da69321cfbe352ed611","date_created":"2025-01-29T08:12:11Z","success":1,"creator":"dernst","relation":"main_file","access_level":"open_access"}],"researchdata_availability":"yes","doi":"10.1091/mbc.e23-07-0289","day":"01","oa":1,"external_id":{"pmid":["38117593"]},"month":"03","department":[{"_id":"FlSc"}],"publisher":"American Society for Cell Biology","file_date_updated":"2025-01-29T08:12:11Z","date_published":"2024-03-01T00:00:00Z","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","fulldoi":"https://doi.org/10.1091/mbc.e23-07-0289","das_tickbox":"0","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"ddc":["570"],"pmid":1,"year":"2024","quality_controlled":"1","publication_status":"published","intvolume":"        35"},{"main_file_link":[{"open_access":"1","url":"https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723"}],"fulldoi":"https://doi.org/10.1091/MBC.E20-11-0723","article_processing_charge":"No","date_published":"2021-04-19T00:00:00Z","intvolume":"        32","publication_status":"published","pmid":1,"year":"2021","quality_controlled":"1","ddc":["570"],"tmp":{"short":"CC BY-NC-SA (3.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode","image":"/images/cc_by_nc_sa.png"},"doi":"10.1091/MBC.E20-11-0723","volume":32,"isi":1,"publisher":"American Society for Cell Biology","department":[{"_id":"MaLo"}],"month":"04","external_id":{"isi":["000641574700005"],"pmid":["33439671"]},"oa":1,"day":"19","date_updated":"2026-06-18T19:52:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule depolymerization in large asters. <i>Molecular Biology of the Cell</i>. 2021;32(9):869-879. doi:<a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">10.1091/MBC.E20-11-0723</a>","mla":"Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization in Large Asters.” <i>Molecular Biology of the Cell</i>, vol. 32, no. 9, American Society for Cell Biology, 2021, pp. 869–79, doi:<a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">10.1091/MBC.E20-11-0723</a>.","ista":"Ishihara K, Decker F, Dos Santos Caldas PR, Pelletier JF, Loose M, Brugués J, Mitchison TJ. 2021. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 32(9), 869–879.","short":"K. Ishihara, F. Decker, P.R. Dos Santos Caldas, J.F. Pelletier, M. Loose, J. Brugués, T.J. Mitchison, Molecular Biology of the Cell 32 (2021) 869–879.","ieee":"K. Ishihara <i>et al.</i>, “Spatial variation of microtubule depolymerization in large asters,” <i>Molecular Biology of the Cell</i>, vol. 32, no. 9. American Society for Cell Biology, pp. 869–879, 2021.","chicago":"Ishihara, Keisuke, Franziska Decker, Paulo R Dos Santos Caldas, James F. Pelletier, Martin Loose, Jan Brugués, and Timothy J. Mitchison. “Spatial Variation of Microtubule Depolymerization in Large Asters.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2021. <a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">https://doi.org/10.1091/MBC.E20-11-0723</a>.","apa":"Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose, M., Brugués, J., &#38; Mitchison, T. J. (2021). Spatial variation of microtubule depolymerization in large asters. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">https://doi.org/10.1091/MBC.E20-11-0723</a>"},"page":"869-879","project":[{"grant_number":"679239","call_identifier":"H2020","name":"Self-Organization of the Bacterial Cell","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"_id":"260D98C8-B435-11E9-9278-68D0E5697425","name":"Reconstitution of Bacterial Cell Division Using Purified Components"}],"license":"https://creativecommons.org/licenses/by-nc-sa/3.0/","abstract":[{"lang":"eng","text":"Microtubule plus-end depolymerization rate is a potentially important target of physiological regulation, but it has been challenging to measure, so its role in spatial organization is poorly understood. Here we apply a method for tracking plus ends based on time difference imaging to measure depolymerization rates in large interphase asters growing in Xenopus egg extract. We observed strong spatial regulation of depolymerization rates, which were higher in the aster interior compared with the periphery, and much less regulation of polymerization or catastrophe rates. We interpret these data in terms of a limiting component model, where aster growth results in lower levels of soluble tubulin and microtubule-associated proteins (MAPs) in the interior cytosol compared with that at the periphery. The steady-state polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the aster interior. We propose that the limiting component for microtubule assembly is a MAP that inhibits depolymerization, and that egg asters are tuned to low microtubule density."}],"oa_version":"Published Version","type":"journal_article","article_type":"original","author":[{"full_name":"Ishihara, Keisuke","first_name":"Keisuke","last_name":"Ishihara"},{"full_name":"Decker, Franziska","first_name":"Franziska","last_name":"Decker"},{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","first_name":"Paulo R","last_name":"Dos Santos Caldas","orcid":"0000-0001-6730-4461","full_name":"Dos Santos Caldas, Paulo R"},{"full_name":"Pelletier, James F.","last_name":"Pelletier","first_name":"James F."},{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Brugués, Jan","first_name":"Jan","last_name":"Brugués"},{"full_name":"Mitchison, Timothy J.","first_name":"Timothy J.","last_name":"Mitchison"}],"status":"public","date_created":"2021-05-23T22:01:45Z","title":"Spatial variation of microtubule depolymerization in large asters","_id":"9414","language":[{"iso":"eng"}],"acknowledgement":"The authors thank the members of Mitchison, Brugués, and Jay Gatlin groups (University of Wyoming) for discussions. We thank Heino Andreas (MPI-CBG) for frog maintenance. We thank Nikon for microscopy support at Marine Biological Laboratory (MBL). K.I. was supported by fellowships from the Honjo International Scholarship Foundation and Center of Systems Biology Dresden. F.D. was supported by the DIGGS-BB fellowship provided by the German Research Foundation (DFG). P.C. is supported by a Boehringer Ingelheim Fonds PhD fellowship. J.F.P. was supported by a fellowship from the Fannie and John Hertz Foundation. M.L.’s research is supported by European Research Council (ERC) Grant no. ERC-2015-StG-679239. J.B.’s research is supported by the Human Frontiers Science Program (CDA00074/2014). T.J.M.’s research is supported by National Institutes of Health Grant no. R35GM131753.","publication_identifier":{"eissn":["1939-4586"],"issn":["1059-1524"]},"ec_funded":1,"scopus_import":"1","issue":"9","publication":"Molecular Biology of the Cell"},{"external_id":{"pmid":["30156465"],"isi":["000455641000011"]},"publisher":"American Society for Cell Biology","month":"11","department":[{"_id":"MiSi"}],"day":"01","oa":1,"volume":29,"doi":"10.1091/mbc.e18-02-0082","file":[{"creator":"kschuh","relation":"main_file","access_level":"open_access","date_created":"2019-02-14T12:34:29Z","checksum":"e98465b4416b3e804c47f40086932af2","file_size":6668971,"date_updated":"2020-07-14T12:47:15Z","content_type":"application/pdf","file_name":"2018_ASCB_Dolati.pdf","file_id":"5994"}],"isi":1,"publication_status":"published","pmid":1,"quality_controlled":"1","year":"2018","intvolume":"        29","ddc":["570"],"tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"das_tickbox":"1","fulldoi":"https://doi.org/10.1091/mbc.e18-02-0082","has_accepted_license":"1","date_published":"2018-11-01T00:00:00Z","file_date_updated":"2020-07-14T12:47:15Z","article_processing_charge":"No","publication_identifier":{"eissn":["1939-4586"]},"publication":"Molecular Biology of the Cell","scopus_import":"1","issue":"22","language":[{"iso":"eng"}],"type":"journal_article","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Lamellipodia are flat membrane protrusions formed during mesenchymal motion. Polymerization at the leading edge assembles the actin filament network and generates protrusion force. How this force is supported by the network and how the assembly rate is shared between protrusion and network retrograde flow determines the protrusion rate. We use mathematical modeling to understand experiments changing the F-actin density in lamellipodia of B16-F1 melanoma cells by modulation of Arp2/3 complex activity or knockout of the formins FMNL2 and FMNL3. Cells respond to a reduction of density with a decrease of protrusion velocity, an increase in the ratio of force to filament number, but constant network assembly rate. The relation between protrusion force and tension gradient in the F-actin network and the density dependency of friction, elasticity, and viscosity of the network explain the experimental observations. The formins act as filament nucleators and elongators with differential rates. Modulation of their activity suggests an effect on network assembly rate. Contrary to these expectations, the effect of changes in elongator composition is much weaker than the consequences of the density change. We conclude that the force acting on the leading edge membrane is the force required to drive F-actin network retrograde flow."}],"title":"On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility","_id":"5992","status":"public","author":[{"full_name":"Dolati, Setareh","last_name":"Dolati","first_name":"Setareh"},{"last_name":"Kage","first_name":"Frieda","full_name":"Kage, Frieda"},{"last_name":"Mueller","first_name":"Jan","full_name":"Mueller, Jan"},{"full_name":"Müsken, Mathias","last_name":"Müsken","first_name":"Mathias"},{"full_name":"Kirchner, Marieluise","last_name":"Kirchner","first_name":"Marieluise"},{"full_name":"Dittmar, Gunnar","first_name":"Gunnar","last_name":"Dittmar"},{"orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"},{"last_name":"Falcke","first_name":"Martin","full_name":"Falcke, Martin"}],"date_created":"2019-02-14T12:25:47Z","date_updated":"2026-07-06T12:25:34Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"2674-2686","citation":{"apa":"Dolati, S., Kage, F., Mueller, J., Müsken, M., Kirchner, M., Dittmar, G., … Falcke, M. (2018). On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/mbc.e18-02-0082\">https://doi.org/10.1091/mbc.e18-02-0082</a>","chicago":"Dolati, Setareh, Frieda Kage, Jan Mueller, Mathias Müsken, Marieluise Kirchner, Gunnar Dittmar, Michael K Sixt, Klemens Rottner, and Martin Falcke. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2018. <a href=\"https://doi.org/10.1091/mbc.e18-02-0082\">https://doi.org/10.1091/mbc.e18-02-0082</a>.","short":"S. Dolati, F. Kage, J. Mueller, M. Müsken, M. Kirchner, G. Dittmar, M.K. Sixt, K. Rottner, M. Falcke, Molecular Biology of the Cell 29 (2018) 2674–2686.","ieee":"S. Dolati <i>et al.</i>, “On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility,” <i>Molecular Biology of the Cell</i>, vol. 29, no. 22. American Society for Cell Biology, pp. 2674–2686, 2018.","ista":"Dolati S, Kage F, Mueller J, Müsken M, Kirchner M, Dittmar G, Sixt MK, Rottner K, Falcke M. 2018. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. 29(22), 2674–2686.","mla":"Dolati, Setareh, et al. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” <i>Molecular Biology of the Cell</i>, vol. 29, no. 22, American Society for Cell Biology, 2018, pp. 2674–86, doi:<a href=\"https://doi.org/10.1091/mbc.e18-02-0082\">10.1091/mbc.e18-02-0082</a>.","ama":"Dolati S, Kage F, Mueller J, et al. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. <i>Molecular Biology of the Cell</i>. 2018;29(22):2674-2686. doi:<a href=\"https://doi.org/10.1091/mbc.e18-02-0082\">10.1091/mbc.e18-02-0082</a>"}}]