---
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. Molecular Biology
of the Cell. 2024;35(3). doi:10.1091/mbc.e23-07-0289'
apa: 'Sárkány, Z., Figueiredo, F., Macedo-Ribeiro, S., & Martins, P. M. (2024).
NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation.
Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.e23-07-0289'
chicago: 'Sárkány, Zsuzsa, Francisco Figueiredo, Sandra Macedo-Ribeiro, and Pedro
M. Martins. “NAGPKin: Nucleation-and-Growth Parameters from the Kinetics of Protein
Phase Separation.” Molecular Biology of the Cell. American Society for
Cell Biology, 2024. https://doi.org/10.1091/mbc.e23-07-0289.'
ieee: 'Z. Sárkány, F. Figueiredo, S. Macedo-Ribeiro, and P. M. Martins, “NAGPKin:
Nucleation-and-growth parameters from the kinetics of protein phase separation,”
Molecular Biology of the Cell, 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.” Molecular Biology of the Cell, vol.
35, no. 3, mr1, American Society for Cell Biology, 2024, doi:10.1091/mbc.e23-07-0289.'
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:
- access_level: open_access
checksum: d7deb6390f294da69321cfbe352ed611
content_type: application/pdf
creator: dernst
date_created: 2025-01-29T08:12:11Z
date_updated: 2025-01-29T08:12:11Z
file_id: '18935'
file_name: 2024_MolecularBioCell_Sarkany.pdf
file_size: 1699180
relation: main_file
success: 1
file_date_updated: 2025-01-29T08:12:11Z
has_accepted_license: '1'
intvolume: ' 35'
issue: '3'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/4.0/
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'
...
---
_id: '9414'
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.
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.
article_processing_charge: No
article_type: original
author:
- first_name: Keisuke
full_name: Ishihara, Keisuke
last_name: Ishihara
- first_name: Franziska
full_name: Decker, Franziska
last_name: Decker
- first_name: Paulo R
full_name: Dos Santos Caldas, Paulo R
id: 38FCDB4C-F248-11E8-B48F-1D18A9856A87
last_name: Dos Santos Caldas
orcid: 0000-0001-6730-4461
- first_name: James F.
full_name: Pelletier, James F.
last_name: Pelletier
- first_name: Martin
full_name: Loose, Martin
id: 462D4284-F248-11E8-B48F-1D18A9856A87
last_name: Loose
orcid: 0000-0001-7309-9724
- first_name: Jan
full_name: Brugués, Jan
last_name: Brugués
- first_name: Timothy J.
full_name: Mitchison, Timothy J.
last_name: Mitchison
citation:
ama: Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule
depolymerization in large asters. Molecular Biology of the Cell. 2021;32(9):869-879.
doi:10.1091/MBC.E20-11-0723
apa: Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose,
M., Brugués, J., & Mitchison, T. J. (2021). Spatial variation of microtubule
depolymerization in large asters. Molecular Biology of the Cell. American
Society for Cell Biology. https://doi.org/10.1091/MBC.E20-11-0723
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.” Molecular Biology of the
Cell. American Society for Cell Biology, 2021. https://doi.org/10.1091/MBC.E20-11-0723.
ieee: K. Ishihara et al., “Spatial variation of microtubule depolymerization
in large asters,” Molecular Biology of the Cell, vol. 32, no. 9. American
Society for Cell Biology, pp. 869–879, 2021.
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.
mla: Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization
in Large Asters.” Molecular Biology of the Cell, vol. 32, no. 9, American
Society for Cell Biology, 2021, pp. 869–79, doi:10.1091/MBC.E20-11-0723.
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.
date_created: 2021-05-23T22:01:45Z
date_published: 2021-04-19T00:00:00Z
date_updated: 2025-04-14T07:21:30Z
day: '19'
department:
- _id: MaLo
doi: 10.1091/MBC.E20-11-0723
ec_funded: 1
external_id:
isi:
- '000641574700005'
pmid:
- '33439671'
intvolume: ' 32'
isi: 1
issue: '9'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-sa/3.0/
main_file_link:
- open_access: '1'
url: https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723
month: '04'
oa: 1
oa_version: Published Version
page: 869-879
pmid: 1
project:
- _id: 2595697A-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '679239'
name: Self-Organization of the Bacterial Cell
- _id: 260D98C8-B435-11E9-9278-68D0E5697425
name: Reconstitution of Bacterial Cell Division Using Purified Components
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: Spatial variation of microtubule depolymerization in large asters
tmp:
image: /images/cc_by_nc_sa.png
legal_code_url: https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode
name: Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA
3.0)
short: CC BY-NC-SA (3.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2021'
...
---
_id: '698'
abstract:
- lang: eng
text: 'Extracellular matrix signals from the microenvironment regulate gene expression
patterns and cell behavior. Using a combination of experiments and geometric models,
we demonstrate correlations between cell geometry, three-dimensional (3D) organization
of chromosome territories, and gene expression. Fluorescence in situ hybridization
experiments showed that micropatterned fibroblasts cultured on anisotropic versus
isotropic substrates resulted in repositioning of specific chromosomes, which
contained genes that were differentially regulated by cell geometries. Experiments
combined with ellipsoid packing models revealed that the mechanosensitivity of
chromosomes was correlated with their orientation in the nucleus. Transcription
inhibition experiments suggested that the intermingling degree was more sensitive
to global changes in transcription than to chromosome radial positioning and its
orientations. These results suggested that cell geometry modulated 3D chromosome
arrangement, and their neighborhoods correlated with gene expression patterns
in a predictable manner. This is central to understanding geometric control of
genetic programs involved in cellular homeostasis and the associated diseases. '
article_processing_charge: No
author:
- first_name: Yejun
full_name: Wang, Yejun
last_name: Wang
- first_name: Mallika
full_name: Nagarajan, Mallika
last_name: Nagarajan
- first_name: Caroline
full_name: Uhler, Caroline
id: 49ADD78E-F248-11E8-B48F-1D18A9856A87
last_name: Uhler
orcid: 0000-0002-7008-0216
- first_name: Gv
full_name: Shivashankar, Gv
last_name: Shivashankar
citation:
ama: Wang Y, Nagarajan M, Uhler C, Shivashankar G. Orientation and repositioning
of chromosomes correlate with cell geometry dependent gene expression. Molecular
Biology of the Cell. 2017;28(14):1997-2009. doi:10.1091/mbc.E16-12-0825
apa: Wang, Y., Nagarajan, M., Uhler, C., & Shivashankar, G. (2017). Orientation
and repositioning of chromosomes correlate with cell geometry dependent gene expression.
Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.E16-12-0825
chicago: Wang, Yejun, Mallika Nagarajan, Caroline Uhler, and Gv Shivashankar. “Orientation
and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.”
Molecular Biology of the Cell. American Society for Cell Biology, 2017.
https://doi.org/10.1091/mbc.E16-12-0825.
ieee: Y. Wang, M. Nagarajan, C. Uhler, and G. Shivashankar, “Orientation and repositioning
of chromosomes correlate with cell geometry dependent gene expression,” Molecular
Biology of the Cell, vol. 28, no. 14. American Society for Cell Biology, pp.
1997–2009, 2017.
ista: Wang Y, Nagarajan M, Uhler C, Shivashankar G. 2017. Orientation and repositioning
of chromosomes correlate with cell geometry dependent gene expression. Molecular
Biology of the Cell. 28(14), 1997–2009.
mla: Wang, Yejun, et al. “Orientation and Repositioning of Chromosomes Correlate
with Cell Geometry Dependent Gene Expression.” Molecular Biology of the Cell,
vol. 28, no. 14, American Society for Cell Biology, 2017, pp. 1997–2009, doi:10.1091/mbc.E16-12-0825.
short: Y. Wang, M. Nagarajan, C. Uhler, G. Shivashankar, Molecular Biology of the
Cell 28 (2017) 1997–2009.
date_created: 2018-12-11T11:47:59Z
date_published: 2017-07-07T00:00:00Z
date_updated: 2025-09-10T11:09:13Z
day: '07'
ddc:
- '519'
department:
- _id: CaUh
doi: 10.1091/mbc.E16-12-0825
external_id:
isi:
- '000406471600019'
file:
- access_level: open_access
checksum: de01dac9e30970cfa6ae902480a4e04d
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:10:53Z
date_updated: 2020-07-14T12:47:46Z
file_id: '4844'
file_name: IST-2017-892-v1+1_Mol._Biol._Cell-2017-Wang-1997-2009.pdf
file_size: 1086097
relation: main_file
file_date_updated: 2020-07-14T12:47:46Z
has_accepted_license: '1'
intvolume: ' 28'
isi: 1
issue: '14'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
page: 1997 - 2009
project:
- _id: 2530CA10-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: Y 903-N35
name: 'Gaussian Graphical Models: Theory and Applications'
publication: Molecular Biology of the Cell
publication_identifier:
issn:
- 1059-1524
publication_status: published
publisher: American Society for Cell Biology
publist_id: '7001'
pubrep_id: '892'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Orientation and repositioning of chromosomes correlate with cell geometry dependent
gene expression
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: 317138e5-6ab7-11ef-aa6d-ffef3953e345
volume: 28
year: '2017'
...
---
_id: '11082'
abstract:
- lang: eng
text: The nuclear pore complex (NPC) plays a critical role in gene expression by
mediating import of transcription regulators into the nucleus and export of RNA
transcripts to the cytoplasm. Emerging evidence suggests that in addition to mediating
transport, a subset of nucleoporins (Nups) engage in transcriptional activation
and elongation at genomic loci that are not associated with NPCs. The underlying
mechanism and regulation of Nup mobility on and off nuclear pores remain unclear.
Here we show that Nup50 is a mobile Nup with a pronounced presence both at the
NPC and in the nucleoplasm that can move between these different localizations.
Strikingly, the dynamic behavior of Nup50 in both locations is dependent on active
transcription by RNA polymerase II and requires the N-terminal half of the protein,
which contains importin α– and Nup153-binding domains. However, Nup50 dynamics
are independent of importin α, Nup153, and Nup98, even though the latter two proteins
also exhibit transcription-dependent mobility. Of interest, depletion of Nup50
from C2C12 myoblasts does not affect cell proliferation but inhibits differentiation
into myotubes. Taken together, our results suggest a transport-independent role
for Nup50 in chromatin biology that occurs away from the NPC.
article_processing_charge: No
article_type: original
author:
- first_name: Abigail L.
full_name: Buchwalter, Abigail L.
last_name: Buchwalter
- first_name: Yun
full_name: Liang, Yun
last_name: Liang
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Buchwalter AL, Liang Y, Hetzer M. Nup50 is required for cell differentiation
and exhibits transcription-dependent dynamics. Molecular Biology of the Cell.
2014;25(16):2472-2484. doi:10.1091/mbc.e14-04-0865
apa: Buchwalter, A. L., Liang, Y., & Hetzer, M. (2014). Nup50 is required for
cell differentiation and exhibits transcription-dependent dynamics. Molecular
Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.e14-04-0865
chicago: Buchwalter, Abigail L., Yun Liang, and Martin Hetzer. “Nup50 Is Required
for Cell Differentiation and Exhibits Transcription-Dependent Dynamics.” Molecular
Biology of the Cell. American Society for Cell Biology, 2014. https://doi.org/10.1091/mbc.e14-04-0865.
ieee: A. L. Buchwalter, Y. Liang, and M. Hetzer, “Nup50 is required for cell differentiation
and exhibits transcription-dependent dynamics,” Molecular Biology of the Cell,
vol. 25, no. 16. American Society for Cell Biology, pp. 2472–2484, 2014.
ista: Buchwalter AL, Liang Y, Hetzer M. 2014. Nup50 is required for cell differentiation
and exhibits transcription-dependent dynamics. Molecular Biology of the Cell.
25(16), 2472–2484.
mla: Buchwalter, Abigail L., et al. “Nup50 Is Required for Cell Differentiation
and Exhibits Transcription-Dependent Dynamics.” Molecular Biology of the Cell,
vol. 25, no. 16, American Society for Cell Biology, 2014, pp. 2472–84, doi:10.1091/mbc.e14-04-0865.
short: A.L. Buchwalter, Y. Liang, M. Hetzer, Molecular Biology of the Cell 25 (2014)
2472–2484.
date_created: 2022-04-07T07:50:24Z
date_published: 2014-08-15T00:00:00Z
date_updated: 2024-10-14T11:23:34Z
day: '15'
doi: 10.1091/mbc.e14-04-0865
extern: '1'
intvolume: ' 25'
issue: '16'
keyword:
- Cell Biology
- Molecular Biology
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1091/mbc.e14-04-0865
month: '08'
oa: 1
oa_version: Published Version
page: 2472-2484
publication: Molecular Biology of the Cell
publication_identifier:
issn:
- 1059-1524
- 1939-4586
publication_status: published
publisher: American Society for Cell Biology
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nup50 is required for cell differentiation and exhibits transcription-dependent
dynamics
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 25
year: '2014'
...