---
_id: '10766'
abstract:
- lang: eng
text: Tension of the actomyosin cell cortex plays a key role in determining cell–cell
contact growth and size. The level of cortical tension outside of the cell–cell
contact, when pulling at the contact edge, scales with the total size to which
a cell–cell contact can grow [J.-L. Maître et al., Science 338, 253–256 (2012)].
Here, we show in zebrafish primary germ-layer progenitor cells that this monotonic
relationship only applies to a narrow range of cortical tension increase and that
above a critical threshold, contact size inversely scales with cortical tension.
This switch from cortical tension increasing to decreasing progenitor cell–cell
contact size is caused by cortical tension promoting E-cadherin anchoring to the
actomyosin cytoskeleton, thereby increasing clustering and stability of E-cadherin
at the contact. After tension-mediated E-cadherin stabilization at the contact
exceeds a critical threshold level, the rate by which the contact expands in response
to pulling forces from the cortex sharply drops, leading to smaller contacts at
physiologically relevant timescales of contact formation. Thus, the activity of
cortical tension in expanding cell–cell contact size is limited by tension-stabilizing
E-cadherin–actin complexes at the contact.
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: PreCl
acknowledgement: 'We thank Guillaume Salbreaux, Silvia Grigolon, Edouard Hannezo,
and Vanessa Barone for discussions and comments on the manuscript and Shayan Shamipour
and Daniel Capek for help with data analysis. We also thank the Imaging & Optics,
Electron Microscopy, and Zebrafish Facility Scientific Service Units at the Institute
of Science and Technology Austria (ISTA)Nasser Darwish-Miranda for continuous support.
We acknowledge Hitoshi Morita for the gift of VinculinB-GFP plasmid. This research
was supported by an ISTA Fellow Marie-Curie Co-funding of regional, national, and
international programmes Grant P_IST_EU01 (to J.S.), European Molecular Biology
Organization Long-Term Fellowship Grant, ALTF reference number: 187-2013 (to M.S.),
Schroedinger Fellowship J4332-B28 (to M.S.), and European Research Council Advanced
Grant (MECSPEC; to C.-P.H.).'
article_number: e2122030119
article_processing_charge: No
article_type: original
author:
- first_name: Jana
full_name: Slovakova, Jana
id: 30F3F2F0-F248-11E8-B48F-1D18A9856A87
last_name: Slovakova
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Feyza N
full_name: Arslan, Feyza N
id: 49DA7910-F248-11E8-B48F-1D18A9856A87
last_name: Arslan
orcid: 0000-0001-5809-9566
- first_name: Silvia
full_name: Caballero Mancebo, Silvia
id: 2F1E1758-F248-11E8-B48F-1D18A9856A87
last_name: Caballero Mancebo
orcid: 0000-0002-5223-3346
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Jack
full_name: Merrin, Jack
id: 4515C308-F248-11E8-B48F-1D18A9856A87
last_name: Merrin
orcid: 0000-0001-5145-4609
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Slovakova J, Sikora MK, Arslan FN, et al. Tension-dependent stabilization of
E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor
cells. Proceedings of the National Academy of Sciences of the United States
of America. 2022;119(8). doi:10.1073/pnas.2122030119
apa: Slovakova, J., Sikora, M. K., Arslan, F. N., Caballero Mancebo, S., Krens,
G., Kaufmann, W., … Heisenberg, C.-P. J. (2022). Tension-dependent stabilization
of E-cadherin limits cell-cell contact expansion in zebrafish germ-layer progenitor
cells. 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.2122030119
chicago: Slovakova, Jana, Mateusz K Sikora, Feyza N Arslan, Silvia Caballero Mancebo,
Gabriel Krens, Walter Kaufmann, Jack Merrin, and Carl-Philipp J Heisenberg. “Tension-Dependent
Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion in Zebrafish Germ-Layer
Progenitor Cells.” 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.2122030119.
ieee: J. Slovakova et al., “Tension-dependent stabilization of E-cadherin
limits cell-cell contact expansion in zebrafish germ-layer progenitor cells,”
Proceedings of the National Academy of Sciences of the United States of America,
vol. 119, no. 8. Proceedings of the National Academy of Sciences, 2022.
ista: Slovakova J, Sikora MK, Arslan FN, Caballero Mancebo S, Krens G, Kaufmann
W, Merrin J, Heisenberg C-PJ. 2022. Tension-dependent stabilization of E-cadherin
limits cell-cell contact expansion in zebrafish germ-layer progenitor cells. Proceedings
of the National Academy of Sciences of the United States of America. 119(8), e2122030119.
mla: Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits
Cell-Cell Contact Expansion in Zebrafish Germ-Layer Progenitor Cells.” Proceedings
of the National Academy of Sciences of the United States of America, vol.
119, no. 8, e2122030119, Proceedings of the National Academy of Sciences, 2022,
doi:10.1073/pnas.2122030119.
short: J. Slovakova, M.K. Sikora, F.N. Arslan, S. Caballero Mancebo, G. Krens, W.
Kaufmann, J. Merrin, C.-P.J. Heisenberg, Proceedings of the National Academy of
Sciences of the United States of America 119 (2022).
date_created: 2022-02-20T23:01:31Z
date_published: 2022-02-14T00:00:00Z
date_updated: 2023-08-02T14:26:51Z
day: '14'
ddc:
- '570'
department:
- _id: CaHe
- _id: EM-Fac
- _id: Bio
doi: 10.1073/pnas.2122030119
ec_funded: 1
external_id:
isi:
- '000766926900009'
file:
- access_level: open_access
checksum: d49f83c3580613966f71768ddb9a55a5
content_type: application/pdf
creator: dernst
date_created: 2022-02-21T08:45:11Z
date_updated: 2022-02-21T08:45:11Z
file_id: '10780'
file_name: 2022_PNAS_Slovakova.pdf
file_size: 1609678
relation: main_file
success: 1
file_date_updated: 2022-02-21T08:45:11Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '8'
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 2521E28E-B435-11E9-9278-68D0E5697425
grant_number: 187-2013
name: Modulation of adhesion function in cell-cell contact formation by cortical
tension
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- '10916490'
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '9750'
relation: earlier_version
status: public
scopus_import: '1'
status: public
title: Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion
in zebrafish germ-layer progenitor cells
tmp:
image: /images/cc_by_nc_nd.png
legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
(CC BY-NC-ND 4.0)
short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 119
year: '2022'
...
---
_id: '8680'
abstract:
- lang: eng
text: Animal development entails the organization of specific cell types in space
and time, and spatial patterns must form in a robust manner. In the zebrafish
spinal cord, neural progenitors form stereotypic patterns despite noisy morphogen
signaling and large-scale cellular rearrangements during morphogenesis and growth.
By directly measuring adhesion forces and preferences for three types of endogenous
neural progenitors, we provide evidence for the differential adhesion model in
which differences in intercellular adhesion mediate cell sorting. Cell type–specific
combinatorial expression of different classes of cadherins (N-cadherin, cadherin
11, and protocadherin 19) results in homotypic preference ex vivo and patterning
robustness in vivo. Furthermore, the differential adhesion code is regulated by
the sonic hedgehog morphogen gradient. We propose that robust patterning during
tissue morphogenesis results from interplay between adhesion-based self-organization
and morphogen-directed patterning.
acknowledgement: "We thank the members of the Megason and Heisenberg labs for critical
discussions of and technical assistance during the work and B. Appel, S. Holley,
J. Jontes, and D. Gilmour for transgenic fish. This work is supported by the Damon
Runyon Cancer Foundation, a NICHD K99 fellowship (1K99HD092623), a Travelling Fellowship
of the Company of Biologists, a Collaborative Research grant from the Burroughs
Wellcome Foundation (T.Y.-C.T.), NIH grant 01GM107733 (T.Y.-C.T. and S.G.M.), NIH
grant R01NS102322 (T.C.-C. and H.K.), and an ERC advanced grant\r\n(MECSPEC) (C.-P.H.)."
article_processing_charge: No
article_type: original
author:
- first_name: Tony Y.-C.
full_name: Tsai, Tony Y.-C.
last_name: Tsai
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Peng
full_name: Xia, Peng
id: 4AB6C7D0-F248-11E8-B48F-1D18A9856A87
last_name: Xia
orcid: 0000-0002-5419-7756
- first_name: Tugba
full_name: Colak-Champollion, Tugba
last_name: Colak-Champollion
- first_name: Holger
full_name: Knaut, Holger
last_name: Knaut
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Sean G.
full_name: Megason, Sean G.
last_name: Megason
citation:
ama: Tsai TY-C, Sikora MK, Xia P, et al. An adhesion code ensures robust pattern
formation during tissue morphogenesis. Science. 2020;370(6512):113-116.
doi:10.1126/science.aba6637
apa: Tsai, T. Y.-C., Sikora, M. K., Xia, P., Colak-Champollion, T., Knaut, H., Heisenberg,
C.-P. J., & Megason, S. G. (2020). An adhesion code ensures robust pattern
formation during tissue morphogenesis. Science. American Association for
the Advancement of Science. https://doi.org/10.1126/science.aba6637
chicago: Tsai, Tony Y.-C., Mateusz K Sikora, Peng Xia, Tugba Colak-Champollion,
Holger Knaut, Carl-Philipp J Heisenberg, and Sean G. Megason. “An Adhesion Code
Ensures Robust Pattern Formation during Tissue Morphogenesis.” Science.
American Association for the Advancement of Science, 2020. https://doi.org/10.1126/science.aba6637.
ieee: T. Y.-C. Tsai et al., “An adhesion code ensures robust pattern formation
during tissue morphogenesis,” Science, vol. 370, no. 6512. American Association
for the Advancement of Science, pp. 113–116, 2020.
ista: Tsai TY-C, Sikora MK, Xia P, Colak-Champollion T, Knaut H, Heisenberg C-PJ,
Megason SG. 2020. An adhesion code ensures robust pattern formation during tissue
morphogenesis. Science. 370(6512), 113–116.
mla: Tsai, Tony Y. C., et al. “An Adhesion Code Ensures Robust Pattern Formation
during Tissue Morphogenesis.” Science, vol. 370, no. 6512, American Association
for the Advancement of Science, 2020, pp. 113–16, doi:10.1126/science.aba6637.
short: T.Y.-C. Tsai, M.K. Sikora, P. Xia, T. Colak-Champollion, H. Knaut, C.-P.J.
Heisenberg, S.G. Megason, Science 370 (2020) 113–116.
date_created: 2020-10-19T14:09:38Z
date_published: 2020-10-02T00:00:00Z
date_updated: 2023-08-22T10:36:35Z
day: '02'
department:
- _id: CaHe
doi: 10.1126/science.aba6637
ec_funded: 1
external_id:
isi:
- '000579169000053'
intvolume: ' 370'
isi: 1
issue: '6512'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.biorxiv.org/content/10.1101/803635v1
month: '10'
oa: 1
oa_version: Preprint
page: 113-116
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
related_material:
link:
- description: News on IST Homepage
relation: press_release
url: https://ist.ac.at/en/news/sticking-together/
scopus_import: '1'
status: public
title: An adhesion code ensures robust pattern formation during tissue morphogenesis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 370
year: '2020'
...
---
_id: '9750'
abstract:
- lang: eng
text: Tension of the actomyosin cell cortex plays a key role in determining cell-cell
contact growth and size. The level of cortical tension outside of the cell-cell
contact, when pulling at the contact edge, scales with the total size to which
a cell-cell contact can grow1,2. Here we show in zebrafish primary germ layer
progenitor cells that this monotonic relationship only applies to a narrow range
of cortical tension increase, and that above a critical threshold, contact size
inversely scales with cortical tension. This switch from cortical tension increasing
to decreasing progenitor cell-cell contact size is caused by cortical tension
promoting E-cadherin anchoring to the actomyosin cytoskeleton, thereby increasing
clustering and stability of E-cadherin at the contact. Once tension-mediated E-cadherin
stabilization at the contact exceeds a critical threshold level, the rate by which
the contact expands in response to pulling forces from the cortex sharply drops,
leading to smaller contacts at physiologically relevant timescales of contact
formation. Thus, the activity of cortical tension in expanding cell-cell contact
size is limited by tension stabilizing E-cadherin-actin complexes at the contact.
acknowledged_ssus:
- _id: Bio
- _id: EM-Fac
- _id: SSU
acknowledgement: We would like to thank Edouard Hannezo for discussions, Shayan Shami
Pour and Daniel Capek for help with data analysis, Vanessa Barone and other members
of the Heisenberg laboratory for thoughtful discussions and comments on the manuscript.
We also thank Jack Merrin for preparing the microwells, and the Scientific Service
Units at IST Austria, specifically Bioimaging and Electron Microscopy, and the Zebrafish
Facility for continuous support. We acknowledge Hitoshi Morita for the kind gift
of VinculinB-GFP plasmid. This research was supported by an ERC Advanced Grant (MECSPEC)
to C.-P.H, EMBO Long Term grant (ALTF 187-2013) to M.S and IST Fellow Marie-Curie
COFUND No. P_IST_EU01 to J.S.
article_processing_charge: No
author:
- first_name: Jana
full_name: Slovakova, Jana
id: 30F3F2F0-F248-11E8-B48F-1D18A9856A87
last_name: Slovakova
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Silvia
full_name: Caballero Mancebo, Silvia
id: 2F1E1758-F248-11E8-B48F-1D18A9856A87
last_name: Caballero Mancebo
orcid: 0000-0002-5223-3346
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Walter
full_name: Kaufmann, Walter
id: 3F99E422-F248-11E8-B48F-1D18A9856A87
last_name: Kaufmann
orcid: 0000-0001-9735-5315
- first_name: Karla
full_name: Huljev, Karla
id: 44C6F6A6-F248-11E8-B48F-1D18A9856A87
last_name: Huljev
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Slovakova J, Sikora MK, Caballero Mancebo S, et al. Tension-dependent stabilization
of E-cadherin limits cell-cell contact expansion. bioRxiv. 2020. doi:10.1101/2020.11.20.391284
apa: Slovakova, J., Sikora, M. K., Caballero Mancebo, S., Krens, G., Kaufmann, W.,
Huljev, K., & Heisenberg, C.-P. J. (2020). Tension-dependent stabilization
of E-cadherin limits cell-cell contact expansion. bioRxiv. Cold Spring
Harbor Laboratory. https://doi.org/10.1101/2020.11.20.391284
chicago: Slovakova, Jana, Mateusz K Sikora, Silvia Caballero Mancebo, Gabriel Krens,
Walter Kaufmann, Karla Huljev, and Carl-Philipp J Heisenberg. “Tension-Dependent
Stabilization of E-Cadherin Limits Cell-Cell Contact Expansion.” BioRxiv.
Cold Spring Harbor Laboratory, 2020. https://doi.org/10.1101/2020.11.20.391284.
ieee: J. Slovakova et al., “Tension-dependent stabilization of E-cadherin
limits cell-cell contact expansion,” bioRxiv. Cold Spring Harbor Laboratory,
2020.
ista: Slovakova J, Sikora MK, Caballero Mancebo S, Krens G, Kaufmann W, Huljev K,
Heisenberg C-PJ. 2020. Tension-dependent stabilization of E-cadherin limits cell-cell
contact expansion. bioRxiv, 10.1101/2020.11.20.391284.
mla: Slovakova, Jana, et al. “Tension-Dependent Stabilization of E-Cadherin Limits
Cell-Cell Contact Expansion.” BioRxiv, Cold Spring Harbor Laboratory, 2020,
doi:10.1101/2020.11.20.391284.
short: J. Slovakova, M.K. Sikora, S. Caballero Mancebo, G. Krens, W. Kaufmann, K.
Huljev, C.-P.J. Heisenberg, BioRxiv (2020).
date_created: 2021-07-29T11:29:50Z
date_published: 2020-11-20T00:00:00Z
date_updated: 2024-03-25T23:30:10Z
day: '20'
department:
- _id: CaHe
- _id: EM-Fac
- _id: Bio
doi: 10.1101/2020.11.20.391284
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/2020.11.20.391284
month: '11'
oa: 1
oa_version: Preprint
page: '41'
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 260F1432-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '742573'
name: Interaction and feedback between cell mechanics and fate specification in
vertebrate gastrulation
- _id: 2521E28E-B435-11E9-9278-68D0E5697425
grant_number: 187-2013
name: Modulation of adhesion function in cell-cell contact formation by cortical
tension
publication: bioRxiv
publication_status: published
publisher: Cold Spring Harbor Laboratory
related_material:
record:
- id: '10766'
relation: later_version
status: public
- id: '9623'
relation: dissertation_contains
status: public
status: public
title: Tension-dependent stabilization of E-cadherin limits cell-cell contact expansion
type: preprint
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
year: '2020'
...
---
_id: '804'
abstract:
- lang: eng
text: Polysaccharides (carbohydrates) are key regulators of a large number of cell
biological processes. However, precise biochemical or genetic manipulation of
these often complex structures is laborious and hampers experimental structure–function
studies. Molecular Dynamics (MD) simulations provide a valuable alternative tool
to generate and test hypotheses on saccharide function. Yet, currently used MD
force fields often overestimate the aggregation propensity of polysaccharides,
affecting the usability of those simulations. Here we tested MARTINI, a popular
coarse-grained (CG) force field for biological macromolecules, for its ability
to accurately represent molecular forces between saccharides. To this end, we
calculated a thermodynamic solution property, the second virial coefficient of
the osmotic pressure (B22). Comparison with light scattering experiments revealed
a nonphysical aggregation of a prototypical polysaccharide in MARTINI, pointing
at an imbalance of the nonbonded solute–solute, solute–water, and water–water
interactions. This finding also applies to smaller oligosaccharides which were
all found to aggregate in simulations even at moderate concentrations, well below
their solubility limit. Finally, we explored the influence of the Lennard-Jones
(LJ) interaction between saccharide molecules and propose a simple scaling of
the LJ interaction strength that makes MARTINI more reliable for the simulation
of saccharides.
acknowledged_ssus:
- _id: ScienComp
acknowledgement: P.S.S. was supported by research fellowship 2811/1-1 from the German
Research Foundation (DFG), and M.S. was supported by EMBO Long Term Fellowship ALTF
187-2013 and Grant GC65-32 from the Interdisciplinary Centre for Mathematical and
Computational Modelling (ICM), University of Warsaw, Poland. The authors thank Antje
Potthast, Marek Cieplak, Tomasz Włodarski, and Damien Thompson for fruitful discussions
and the IST Austria Scientific Computing Facility for support.
article_processing_charge: No
author:
- first_name: Philipp S
full_name: Schmalhorst, Philipp S
id: 309D50DA-F248-11E8-B48F-1D18A9856A87
last_name: Schmalhorst
orcid: 0000-0002-5795-0133
- first_name: Felix
full_name: Deluweit, Felix
last_name: Deluweit
- first_name: Roger
full_name: Scherrers, Roger
last_name: Scherrers
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
citation:
ama: Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. Overcoming
the limitations of the MARTINI force field in simulations of polysaccharides.
Journal of Chemical Theory and Computation. 2017;13(10):5039-5053. doi:10.1021/acs.jctc.7b00374
apa: Schmalhorst, P. S., Deluweit, F., Scherrers, R., Heisenberg, C.-P. J., &
Sikora, M. K. (2017). Overcoming the limitations of the MARTINI force field in
simulations of polysaccharides. Journal of Chemical Theory and Computation.
American Chemical Society. https://doi.org/10.1021/acs.jctc.7b00374
chicago: Schmalhorst, Philipp S, Felix Deluweit, Roger Scherrers, Carl-Philipp J
Heisenberg, and Mateusz K Sikora. “Overcoming the Limitations of the MARTINI Force
Field in Simulations of Polysaccharides.” Journal of Chemical Theory and Computation.
American Chemical Society, 2017. https://doi.org/10.1021/acs.jctc.7b00374.
ieee: P. S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P. J. Heisenberg, and M.
K. Sikora, “Overcoming the limitations of the MARTINI force field in simulations
of polysaccharides,” Journal of Chemical Theory and Computation, vol. 13,
no. 10. American Chemical Society, pp. 5039–5053, 2017.
ista: Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg C-PJ, Sikora MK. 2017.
Overcoming the limitations of the MARTINI force field in simulations of polysaccharides.
Journal of Chemical Theory and Computation. 13(10), 5039–5053.
mla: Schmalhorst, Philipp S., et al. “Overcoming the Limitations of the MARTINI
Force Field in Simulations of Polysaccharides.” Journal of Chemical Theory
and Computation, vol. 13, no. 10, American Chemical Society, 2017, pp. 5039–53,
doi:10.1021/acs.jctc.7b00374.
short: P.S. Schmalhorst, F. Deluweit, R. Scherrers, C.-P.J. Heisenberg, M.K. Sikora,
Journal of Chemical Theory and Computation 13 (2017) 5039–5053.
date_created: 2018-12-11T11:48:35Z
date_published: 2017-10-10T00:00:00Z
date_updated: 2023-09-27T10:58:45Z
day: '10'
department:
- _id: CaHe
doi: 10.1021/acs.jctc.7b00374
external_id:
isi:
- '000412965700036'
intvolume: ' 13'
isi: 1
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1704.03773
month: '10'
oa: 1
oa_version: Submitted Version
page: 5039 - 5053
publication: Journal of Chemical Theory and Computation
publication_identifier:
issn:
- '15499618'
publication_status: published
publisher: American Chemical Society
publist_id: '6847'
quality_controlled: '1'
scopus_import: '1'
status: public
title: Overcoming the limitations of the MARTINI force field in simulations of polysaccharides
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 13
year: '2017'
...
---
_id: '735'
abstract:
- lang: eng
text: Cell-cell contact formation constitutes an essential step in evolution, leading
to the differentiation of specialized cell types. However, remarkably little is
known about whether and how the interplay between contact formation and fate specification
affects development. Here, we identify a positive feedback loop between cell-cell
contact duration, morphogen signaling, and mesendoderm cell-fate specification
during zebrafish gastrulation. We show that long-lasting cell-cell contacts enhance
the competence of prechordal plate (ppl) progenitor cells to respond to Nodal
signaling, required for ppl cell-fate specification. We further show that Nodal
signaling promotes ppl cell-cell contact duration, generating a positive feedback
loop between ppl cell-cell contact duration and cell-fate specification. Finally,
by combining mathematical modeling and experimentation, we show that this feedback
determines whether anterior axial mesendoderm cells become ppl or, instead, turn
into endoderm. Thus, the interdependent activities of cell-cell signaling and
contact formation control fate diversification within the developing embryo.
article_processing_charge: No
author:
- first_name: Vanessa
full_name: Barone, Vanessa
id: 419EECCC-F248-11E8-B48F-1D18A9856A87
last_name: Barone
orcid: 0000-0003-2676-3367
- first_name: Moritz
full_name: Lang, Moritz
id: 29E0800A-F248-11E8-B48F-1D18A9856A87
last_name: Lang
- first_name: Gabriel
full_name: Krens, Gabriel
id: 2B819732-F248-11E8-B48F-1D18A9856A87
last_name: Krens
orcid: 0000-0003-4761-5996
- first_name: Saurabh
full_name: Pradhan, Saurabh
last_name: Pradhan
- first_name: Shayan
full_name: Shamipour, Shayan
id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
last_name: Shamipour
- first_name: Keisuke
full_name: Sako, Keisuke
id: 3BED66BE-F248-11E8-B48F-1D18A9856A87
last_name: Sako
orcid: 0000-0002-6453-8075
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Calin C
full_name: Guet, Calin C
id: 47F8433E-F248-11E8-B48F-1D18A9856A87
last_name: Guet
orcid: 0000-0001-6220-2052
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Barone V, Lang M, Krens G, et al. An effective feedback loop between cell-cell
contact duration and morphogen signaling determines cell fate. Developmental
Cell. 2017;43(2):198-211. doi:10.1016/j.devcel.2017.09.014
apa: Barone, V., Lang, M., Krens, G., Pradhan, S., Shamipour, S., Sako, K., … Heisenberg,
C.-P. J. (2017). An effective feedback loop between cell-cell contact duration
and morphogen signaling determines cell fate. Developmental Cell. Cell
Press. https://doi.org/10.1016/j.devcel.2017.09.014
chicago: Barone, Vanessa, Moritz Lang, Gabriel Krens, Saurabh Pradhan, Shayan Shamipour,
Keisuke Sako, Mateusz K Sikora, Calin C Guet, and Carl-Philipp J Heisenberg. “An
Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling
Determines Cell Fate.” Developmental Cell. Cell Press, 2017. https://doi.org/10.1016/j.devcel.2017.09.014.
ieee: V. Barone et al., “An effective feedback loop between cell-cell contact
duration and morphogen signaling determines cell fate,” Developmental Cell,
vol. 43, no. 2. Cell Press, pp. 198–211, 2017.
ista: Barone V, Lang M, Krens G, Pradhan S, Shamipour S, Sako K, Sikora MK, Guet
CC, Heisenberg C-PJ. 2017. An effective feedback loop between cell-cell contact
duration and morphogen signaling determines cell fate. Developmental Cell. 43(2),
198–211.
mla: Barone, Vanessa, et al. “An Effective Feedback Loop between Cell-Cell Contact
Duration and Morphogen Signaling Determines Cell Fate.” Developmental Cell,
vol. 43, no. 2, Cell Press, 2017, pp. 198–211, doi:10.1016/j.devcel.2017.09.014.
short: V. Barone, M. Lang, G. Krens, S. Pradhan, S. Shamipour, K. Sako, M.K. Sikora,
C.C. Guet, C.-P.J. Heisenberg, Developmental Cell 43 (2017) 198–211.
date_created: 2018-12-11T11:48:13Z
date_published: 2017-10-23T00:00:00Z
date_updated: 2024-03-25T23:30:21Z
day: '23'
department:
- _id: CaHe
- _id: CaGu
- _id: GaTk
doi: 10.1016/j.devcel.2017.09.014
ec_funded: 1
external_id:
isi:
- '000413443700011'
intvolume: ' 43'
isi: 1
issue: '2'
language:
- iso: eng
month: '10'
oa_version: None
page: 198 - 211
project:
- _id: 25681D80-B435-11E9-9278-68D0E5697425
call_identifier: FP7
grant_number: '291734'
name: International IST Postdoc Fellowship Programme
- _id: 252DD2A6-B435-11E9-9278-68D0E5697425
call_identifier: FWF
grant_number: I2058
name: 'Cell segregation in gastrulation: the role of cell fate specification'
publication: Developmental Cell
publication_identifier:
issn:
- '15345807'
publication_status: published
publisher: Cell Press
publist_id: '6934'
quality_controlled: '1'
related_material:
record:
- id: '961'
relation: dissertation_contains
status: public
- id: '8350'
relation: dissertation_contains
status: public
scopus_import: '1'
status: public
title: An effective feedback loop between cell-cell contact duration and morphogen
signaling determines cell fate
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 43
year: '2017'
...
---
_id: '1096'
author:
- first_name: Cornelia
full_name: Schwayer, Cornelia
id: 3436488C-F248-11E8-B48F-1D18A9856A87
last_name: Schwayer
orcid: 0000-0001-5130-2226
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Jana
full_name: Slovakova, Jana
id: 30F3F2F0-F248-11E8-B48F-1D18A9856A87
last_name: Slovakova
- first_name: Roland
full_name: Kardos, Roland
id: 4039350E-F248-11E8-B48F-1D18A9856A87
last_name: Kardos
- first_name: Carl-Philipp J
full_name: Heisenberg, Carl-Philipp J
id: 39427864-F248-11E8-B48F-1D18A9856A87
last_name: Heisenberg
orcid: 0000-0002-0912-4566
citation:
ama: Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. Actin rings
of power. Developmental Cell. 2016;37(6):493-506. doi:10.1016/j.devcel.2016.05.024
apa: Schwayer, C., Sikora, M. K., Slovakova, J., Kardos, R., & Heisenberg, C.-P.
J. (2016). Actin rings of power. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2016.05.024
chicago: Schwayer, Cornelia, Mateusz K Sikora, Jana Slovakova, Roland Kardos, and
Carl-Philipp J Heisenberg. “Actin Rings of Power.” Developmental Cell.
Cell Press, 2016. https://doi.org/10.1016/j.devcel.2016.05.024.
ieee: C. Schwayer, M. K. Sikora, J. Slovakova, R. Kardos, and C.-P. J. Heisenberg,
“Actin rings of power,” Developmental Cell, vol. 37, no. 6. Cell Press,
pp. 493–506, 2016.
ista: Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. 2016. Actin
rings of power. Developmental Cell. 37(6), 493–506.
mla: Schwayer, Cornelia, et al. “Actin Rings of Power.” Developmental Cell,
vol. 37, no. 6, Cell Press, 2016, pp. 493–506, doi:10.1016/j.devcel.2016.05.024.
short: C. Schwayer, M.K. Sikora, J. Slovakova, R. Kardos, C.-P.J. Heisenberg, Developmental
Cell 37 (2016) 493–506.
date_created: 2018-12-11T11:50:07Z
date_published: 2016-06-20T00:00:00Z
date_updated: 2023-09-07T12:56:41Z
day: '20'
department:
- _id: CaHe
doi: 10.1016/j.devcel.2016.05.024
intvolume: ' 37'
issue: '6'
language:
- iso: eng
month: '06'
oa_version: None
page: 493 - 506
publication: Developmental Cell
publication_status: published
publisher: Cell Press
publist_id: '6279'
quality_controlled: '1'
related_material:
record:
- id: '7186'
relation: part_of_dissertation
status: public
scopus_import: 1
status: public
title: Actin rings of power
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 37
year: '2016'
...
---
_id: '1566'
abstract:
- lang: eng
text: Deposits of misfolded proteins in the human brain are associated with the
development of many neurodegenerative diseases. Recent studies show that these
proteins have common traits even at the monomer level. Among them, a polyglutamine
region that is present in huntingtin is known to exhibit a correlation between
the length of the chain and the severity as well as the earliness of the onset
of Huntington disease. Here, we apply bias exchange molecular dynamics to generate
structures of polyglutamine expansions of several lengths and characterize the
resulting independent conformations. We compare the properties of these conformations
to those of the standard proteins, as well as to other homopolymeric tracts. We
find that, similar to the previously studied polyvaline chains, the set of possible
transient folds is much broader than the set of known-to-date folds, although
the conformations have different structures. We show that the mechanical stability
is not related to any simple geometrical characteristics of the structures. We
demonstrate that long polyglutamine expansions result in higher mechanical stability
than the shorter ones. They also have a longer life span and are substantially
more prone to form knotted structures. The knotted region has an average length
of 35 residues, similar to the typical threshold for most polyglutamine-related
diseases. Similarly, changes in shape and mechanical stability appear once the
total length of the peptide exceeds this threshold of 35 glutamine residues. We
suggest that knotted conformers may also harm the cellular machinery and thus
lead to disease.
acknowledgement: 'We acknowledge the support by the EU Joint Programme in Neurodegenerative
Diseases (JPND AC14/00037) project. The project is supported through the following
funding organisations under the aegis of JPND—www.jpnd.eu: Ireland, HRB; Poland,
National Science Centre; and Spain, ISCIII. '
article_number: e1004541
author:
- first_name: Àngel
full_name: Gómez Sicilia, Àngel
last_name: Gómez Sicilia
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Marek
full_name: Cieplak, Marek
last_name: Cieplak
- first_name: Mariano
full_name: Carrión Vázquez, Mariano
last_name: Carrión Vázquez
citation:
ama: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of
the universe of polyglutamine structures. PLoS Computational Biology. 2015;11(10).
doi:10.1371/journal.pcbi.1004541
apa: Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015).
An exploration of the universe of polyglutamine structures. PLoS Computational
Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004541
chicago: Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión
Vázquez. “An Exploration of the Universe of Polyglutamine Structures.” PLoS
Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004541.
ieee: À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration
of the universe of polyglutamine structures,” PLoS Computational Biology,
vol. 11, no. 10. Public Library of Science, 2015.
ista: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration
of the universe of polyglutamine structures. PLoS Computational Biology. 11(10),
e1004541.
mla: Gómez Sicilia, Àngel, et al. “An Exploration of the Universe of Polyglutamine
Structures.” PLoS Computational Biology, vol. 11, no. 10, e1004541, Public
Library of Science, 2015, doi:10.1371/journal.pcbi.1004541.
short: À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, PLoS Computational
Biology 11 (2015).
date_created: 2018-12-11T11:52:45Z
date_published: 2015-10-23T00:00:00Z
date_updated: 2023-02-23T14:05:55Z
day: '23'
ddc:
- '570'
department:
- _id: CaHe
doi: 10.1371/journal.pcbi.1004541
file:
- access_level: open_access
checksum: 8b67d729be663bfc9af04bfd94459655
content_type: application/pdf
creator: system
date_created: 2018-12-12T10:16:21Z
date_updated: 2020-07-14T12:45:02Z
file_id: '5207'
file_name: IST-2016-478-v1+1_journal.pcbi.1004541.pdf
file_size: 1412511
relation: main_file
file_date_updated: 2020-07-14T12:45:02Z
has_accepted_license: '1'
intvolume: ' 11'
issue: '10'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
publication: PLoS Computational Biology
publication_status: published
publisher: Public Library of Science
publist_id: '5605'
pubrep_id: '478'
quality_controlled: '1'
related_material:
record:
- id: '9714'
relation: research_data
status: public
scopus_import: 1
status: public
title: An exploration of the universe of polyglutamine structures
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 11
year: '2015'
...
---
_id: '9714'
article_processing_charge: No
author:
- first_name: Àngel
full_name: Gómez Sicilia, Àngel
last_name: Gómez Sicilia
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Marek
full_name: Cieplak, Marek
last_name: Cieplak
- first_name: Mariano
full_name: Carrión Vázquez, Mariano
last_name: Carrión Vázquez
citation:
ama: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. An exploration of
the universe of polyglutamine structures - submission to PLOS journals. 2015.
doi:10.1371/journal.pcbi.1004541.s001
apa: Gómez Sicilia, À., Sikora, M. K., Cieplak, M., & Carrión Vázquez, M. (2015).
An exploration of the universe of polyglutamine structures - submission to PLOS
journals. Public Library of Science . https://doi.org/10.1371/journal.pcbi.1004541.s001
chicago: Gómez Sicilia, Àngel, Mateusz K Sikora, Marek Cieplak, and Mariano Carrión
Vázquez. “An Exploration of the Universe of Polyglutamine Structures - Submission
to PLOS Journals.” Public Library of Science , 2015. https://doi.org/10.1371/journal.pcbi.1004541.s001.
ieee: À. Gómez Sicilia, M. K. Sikora, M. Cieplak, and M. Carrión Vázquez, “An exploration
of the universe of polyglutamine structures - submission to PLOS journals.” Public
Library of Science , 2015.
ista: Gómez Sicilia À, Sikora MK, Cieplak M, Carrión Vázquez M. 2015. An exploration
of the universe of polyglutamine structures - submission to PLOS journals, Public
Library of Science , 10.1371/journal.pcbi.1004541.s001.
mla: Gómez Sicilia, Àngel, et al. An Exploration of the Universe of Polyglutamine
Structures - Submission to PLOS Journals. Public Library of Science , 2015,
doi:10.1371/journal.pcbi.1004541.s001.
short: À. Gómez Sicilia, M.K. Sikora, M. Cieplak, M. Carrión Vázquez, (2015).
date_created: 2021-07-23T12:05:28Z
date_published: 2015-10-23T00:00:00Z
date_updated: 2023-02-23T10:04:35Z
day: '23'
department:
- _id: CaHe
doi: 10.1371/journal.pcbi.1004541.s001
month: '10'
oa_version: Published Version
publisher: 'Public Library of Science '
related_material:
record:
- id: '1566'
relation: used_in_publication
status: public
status: public
title: An exploration of the universe of polyglutamine structures - submission to
PLOS journals
type: research_data_reference
user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf
year: '2015'
...
---
_id: '1891'
abstract:
- lang: eng
text: We provide theoretical tests of a novel experimental technique to determine
mechanostability of proteins based on stretching a mechanically protected protein
by single-molecule force spectroscopy. This technique involves stretching a homogeneous
or heterogeneous chain of reference proteins (single-molecule markers) in which
one of them acts as host to the guest protein under study. The guest protein is
grafted into the host through genetic engineering. It is expected that unraveling
of the host precedes the unraveling of the guest removing ambiguities in the reading
of the force-extension patterns of the guest protein. We study examples of such
systems within a coarse-grained structure-based model. We consider systems with
various ratios of mechanostability for the host and guest molecules and compare
them to experimental results involving cohesin I as the guest molecule. For a
comparison, we also study the force-displacement patterns in proteins that are
linked in a serial fashion. We find that the mechanostability of the guest is
similar to that of the isolated or serially linked protein. We also demonstrate
that the ideal configuration of this strategy would be one in which the host is
much more mechanostable than the single-molecule markers. We finally show that
it is troublesome to use the highly stable cystine knot proteins as a host to
graft a guest in stretching studies because this would involve a cleaving procedure.
acknowledgement: Grant Nr. 2011/01/N/ST3/02475
author:
- first_name: Mateusz
full_name: Chwastyk, Mateusz
last_name: Chwastyk
- first_name: Albert
full_name: Galera Prat, Albert
last_name: Galera Prat
- first_name: Mateusz K
full_name: Sikora, Mateusz K
id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87
last_name: Sikora
- first_name: Àngel
full_name: Gómez Sicilia, Àngel
last_name: Gómez Sicilia
- first_name: Mariano
full_name: Carrión Vázquez, Mariano
last_name: Carrión Vázquez
- first_name: Marek
full_name: Cieplak, Marek
last_name: Cieplak
citation:
ama: 'Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M,
Cieplak M. Theoretical tests of the mechanical protection strategy in protein
nanomechanics. Proteins: Structure, Function and Bioinformatics. 2014;82(5):717-726.
doi:10.1002/prot.24436'
apa: 'Chwastyk, M., Galera Prat, A., Sikora, M. K., Gómez Sicilia, À., Carrión Vázquez,
M., & Cieplak, M. (2014). Theoretical tests of the mechanical protection strategy
in protein nanomechanics. Proteins: Structure, Function and Bioinformatics.
Wiley-Blackwell. https://doi.org/10.1002/prot.24436'
chicago: 'Chwastyk, Mateusz, Albert Galera Prat, Mateusz K Sikora, Àngel Gómez Sicilia,
Mariano Carrión Vázquez, and Marek Cieplak. “Theoretical Tests of the Mechanical
Protection Strategy in Protein Nanomechanics.” Proteins: Structure, Function
and Bioinformatics. Wiley-Blackwell, 2014. https://doi.org/10.1002/prot.24436.'
ieee: 'M. Chwastyk, A. Galera Prat, M. K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez,
and M. Cieplak, “Theoretical tests of the mechanical protection strategy in protein
nanomechanics,” Proteins: Structure, Function and Bioinformatics, vol.
82, no. 5. Wiley-Blackwell, pp. 717–726, 2014.'
ista: 'Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M,
Cieplak M. 2014. Theoretical tests of the mechanical protection strategy in protein
nanomechanics. Proteins: Structure, Function and Bioinformatics. 82(5), 717–726.'
mla: 'Chwastyk, Mateusz, et al. “Theoretical Tests of the Mechanical Protection
Strategy in Protein Nanomechanics.” Proteins: Structure, Function and Bioinformatics,
vol. 82, no. 5, Wiley-Blackwell, 2014, pp. 717–26, doi:10.1002/prot.24436.'
short: 'M. Chwastyk, A. Galera Prat, M.K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez,
M. Cieplak, Proteins: Structure, Function and Bioinformatics 82 (2014) 717–726.'
date_created: 2018-12-11T11:54:34Z
date_published: 2014-05-01T00:00:00Z
date_updated: 2021-01-12T06:53:52Z
day: '01'
department:
- _id: CaHe
doi: 10.1002/prot.24436
intvolume: ' 82'
issue: '5'
language:
- iso: eng
month: '05'
oa_version: None
page: 717 - 726
publication: 'Proteins: Structure, Function and Bioinformatics'
publication_status: published
publisher: Wiley-Blackwell
publist_id: '5204'
scopus_import: 1
status: public
title: Theoretical tests of the mechanical protection strategy in protein nanomechanics
type: journal_article
user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87
volume: 82
year: '2014'
...