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