{"author":[{"first_name":"Zsuzsa","last_name":"Sárkány","full_name":"Sárkány, Zsuzsa"},{"first_name":"Francisco","id":"8125cbe2-9661-11ed-a754-afe96018f37d","last_name":"Figueiredo","full_name":"Figueiredo, Francisco"},{"last_name":"Macedo-Ribeiro","full_name":"Macedo-Ribeiro, Sandra","first_name":"Sandra"},{"last_name":"Martins","full_name":"Martins, Pedro M.","first_name":"Pedro M."}],"OA_type":"hybrid","type":"journal_article","article_type":"original","publication":"Molecular Biology of the Cell","date_updated":"2025-01-29T08:16:20Z","issue":"3","_id":"18934","language":[{"iso":"eng"}],"oa_version":"Published Version","external_id":{"pmid":["38117593"]},"oa":1,"publication_status":"published","title":"NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation","publication_identifier":{"eissn":["1939-4586"],"issn":["1059-1524"]},"date_published":"2024-03-01T00:00:00Z","abstract":[{"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 .","lang":"eng"}],"has_accepted_license":"1","OA_place":"publisher","day":"01","quality_controlled":"1","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","volume":35,"department":[{"_id":"FlSc"}],"file_date_updated":"2025-01-29T08:12:11Z","year":"2024","pmid":1,"scopus_import":"1","article_number":"mr1","intvolume":"        35","month":"03","file":[{"date_created":"2025-01-29T08:12:11Z","creator":"dernst","success":1,"checksum":"d7deb6390f294da69321cfbe352ed611","file_id":"18935","file_size":1699180,"file_name":"2024_MolecularBioCell_Sarkany.pdf","relation":"main_file","date_updated":"2025-01-29T08:12:11Z","access_level":"open_access","content_type":"application/pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"doi":"10.1091/mbc.e23-07-0289","article_processing_charge":"Yes (in subscription journal)","status":"public","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.","date_created":"2025-01-29T07:58:40Z","tmp":{"image":"/images/cc_by_nc_sa.png","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"publisher":"American Society for Cell Biology","citation":{"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.","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>","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>","short":"Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, P.M. Martins, Molecular Biology of the Cell 35 (2024).","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>.","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."}}