---
_id: '15001'
abstract:
- lang: eng
text: "Self-replication of amyloid fibrils via secondary nucleation is an intriguing
physicochemical phenomenon in which existing fibrils catalyze the formation of
their own copies. The molecular events behind this fibril surface-mediated process
remain largely inaccessible to current structural and imaging techniques. Using
statistical mechanics, computer modeling, and chemical kinetics, we show that
the catalytic structure of the fibril surface can be inferred from the aggregation
behavior in the presence and absence of a fibril-binding inhibitor. We apply our
approach to the case of Alzheimer’s A\r\n amyloid fibrils formed in the presence
of proSP-C Brichos inhibitors. We find that self-replication of A\r\n fibrils
occurs on small catalytic sites on the fibril surface, which are far apart from
each other, and each of which can be covered by a single Brichos inhibitor."
acknowledgement: We acknowledge support from the Erasmus programme and the University
College London Institute for the Physics of Living Systems (S.C., T.C.T.M., A.Š.),
the Biotechnology and Biological Sciences Research Council (T.P.J.K.), the Engineering
and Physical Sciences Research Council (D.F.), the European Research Council (T.P.J.K.,
S.L., D.F., and A.Š.), the Frances and Augustus Newman Foundation (T.P.J.K.), the
Academy of Medical Sciences and Wellcome Trust (A.Š.), and the Royal Society (S.C.
and A.Š.).
article_number: e2220075121
article_processing_charge: Yes
article_type: original
author:
- first_name: Samo
full_name: Curk, Samo
id: 031eff0d-d481-11ee-8508-cd12a7a86e5b
last_name: Curk
orcid: 0000-0001-6160-9766
- first_name: Johannes
full_name: Krausser, Johannes
last_name: Krausser
- first_name: Georg
full_name: Meisl, Georg
last_name: Meisl
- first_name: Daan
full_name: Frenkel, Daan
last_name: Frenkel
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
- first_name: Thomas C.T.
full_name: Michaels, Thomas C.T.
last_name: Michaels
- first_name: Tuomas P.J.
full_name: Knowles, Tuomas P.J.
last_name: Knowles
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Curk S, Krausser J, Meisl G, et al. Self-replication of Aβ42 aggregates occurs
on small and isolated fibril sites. Proceedings of the National Academy of
Sciences of the United States of America. 2024;121(7). doi:10.1073/pnas.2220075121
apa: Curk, S., Krausser, J., Meisl, G., Frenkel, D., Linse, S., Michaels, T. C.
T., … Šarić, A. (2024). Self-replication of Aβ42 aggregates occurs on small and
isolated fibril sites. 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.2220075121
chicago: Curk, Samo, Johannes Krausser, Georg Meisl, Daan Frenkel, Sara Linse, Thomas
C.T. Michaels, Tuomas P.J. Knowles, and Anđela Šarić. “Self-Replication of Aβ42
Aggregates Occurs on Small and Isolated Fibril Sites.” Proceedings of the National
Academy of Sciences of the United States of America. Proceedings of the National
Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2220075121.
ieee: S. Curk et al., “Self-replication of Aβ42 aggregates occurs on small
and isolated fibril sites,” Proceedings of the National Academy of Sciences
of the United States of America, vol. 121, no. 7. Proceedings of the National
Academy of Sciences, 2024.
ista: Curk S, Krausser J, Meisl G, Frenkel D, Linse S, Michaels TCT, Knowles TPJ,
Šarić A. 2024. Self-replication of Aβ42 aggregates occurs on small and isolated
fibril sites. Proceedings of the National Academy of Sciences of the United States
of America. 121(7), e2220075121.
mla: Curk, Samo, et al. “Self-Replication of Aβ42 Aggregates Occurs on Small and
Isolated Fibril Sites.” Proceedings of the National Academy of Sciences of
the United States of America, vol. 121, no. 7, e2220075121, Proceedings of
the National Academy of Sciences, 2024, doi:10.1073/pnas.2220075121.
short: S. Curk, J. Krausser, G. Meisl, D. Frenkel, S. Linse, T.C.T. Michaels, T.P.J.
Knowles, A. Šarić, Proceedings of the National Academy of Sciences of the United
States of America 121 (2024).
date_created: 2024-02-18T23:01:00Z
date_published: 2024-02-13T00:00:00Z
date_updated: 2024-02-26T08:45:56Z
day: '13'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1073/pnas.2220075121
ec_funded: 1
external_id:
pmid:
- '38335256'
file:
- access_level: open_access
checksum: 5aeb65bcc0dd829b1f9ab307c5031d4b
content_type: application/pdf
creator: dernst
date_created: 2024-02-26T08:20:00Z
date_updated: 2024-02-26T08:20:00Z
file_id: '15026'
file_name: 2024_PNAS_Curk.pdf
file_size: 7699487
relation: main_file
success: 1
file_date_updated: 2024-02-26T08:20:00Z
has_accepted_license: '1'
intvolume: ' 121'
issue: '7'
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc-nd/4.0/
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
related_material:
record:
- id: '15027'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Self-replication of Aβ42 aggregates occurs on small and isolated fibril sites
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 121
year: '2024'
...
---
_id: '14442'
abstract:
- lang: eng
text: In the presence of an obstacle, active particles condensate into a surface
“wetting” layer due to persistent motion. If the obstacle is asymmetric, a rectification
current arises in addition to wetting. Asymmetric geometries are therefore commonly
used to concentrate microorganisms like bacteria and sperms. However, most studies
neglect the fact that biological active matter is diverse, composed of individuals
with distinct self-propulsions. Using simulations, we study a mixture of “fast”
and “slow” active Brownian disks in two dimensions interacting with large half-disk
obstacles. With this prototypical obstacle geometry, we analyze how the stationary
collective behavior depends on the degree of self-propulsion “diversity,” defined
as proportional to the difference between the self-propulsion speeds, while keeping
the average self-propulsion speed fixed. A wetting layer rich in fast particles
arises. The rectification current is amplified by speed diversity due to a superlinear
dependence of rectification on self-propulsion speed, which arises from cooperative
effects. Thus, the total rectification current cannot be obtained from an effective
one-component active fluid with the same average self-propulsion speed, highlighting
the importance of considering diversity in active matter.
acknowledgement: MR-V and RS are supported by Fondecyt Grant No. 1220536 and Millennium
Science Initiative Program NCN19_170D of ANID, Chile. P.d.C. was supported by Scholarships
Nos. 2021/10139-2 and 2022/13872-5 and ICTP-SAIFR Grant No. 2021/14335-0, all granted
by São Paulo Research Foundation (FAPESP), Brazil.
article_number: '95'
article_processing_charge: No
article_type: original
author:
- first_name: Mauricio Nicolas
full_name: Rojas Vega, Mauricio Nicolas
id: 441e7207-f91f-11ec-b67c-9e6fe3d8fd6d
last_name: Rojas Vega
- first_name: Pablo
full_name: De Castro, Pablo
last_name: De Castro
- first_name: Rodrigo
full_name: Soto, Rodrigo
last_name: Soto
citation:
ama: Rojas Vega MN, De Castro P, Soto R. Mixtures of self-propelled particles interacting
with asymmetric obstacles. The European Physical Journal E. 2023;46(10).
doi:10.1140/epje/s10189-023-00354-y
apa: Rojas Vega, M. N., De Castro, P., & Soto, R. (2023). Mixtures of self-propelled
particles interacting with asymmetric obstacles. The European Physical Journal
E. Springer Nature. https://doi.org/10.1140/epje/s10189-023-00354-y
chicago: Rojas Vega, Mauricio Nicolas, Pablo De Castro, and Rodrigo Soto. “Mixtures
of Self-Propelled Particles Interacting with Asymmetric Obstacles.” The European
Physical Journal E. Springer Nature, 2023. https://doi.org/10.1140/epje/s10189-023-00354-y.
ieee: M. N. Rojas Vega, P. De Castro, and R. Soto, “Mixtures of self-propelled particles
interacting with asymmetric obstacles,” The European Physical Journal E,
vol. 46, no. 10. Springer Nature, 2023.
ista: Rojas Vega MN, De Castro P, Soto R. 2023. Mixtures of self-propelled particles
interacting with asymmetric obstacles. The European Physical Journal E. 46(10),
95.
mla: Rojas Vega, Mauricio Nicolas, et al. “Mixtures of Self-Propelled Particles
Interacting with Asymmetric Obstacles.” The European Physical Journal E,
vol. 46, no. 10, 95, Springer Nature, 2023, doi:10.1140/epje/s10189-023-00354-y.
short: M.N. Rojas Vega, P. De Castro, R. Soto, The European Physical Journal E 46
(2023).
date_created: 2023-10-22T22:01:13Z
date_published: 2023-10-01T00:00:00Z
date_updated: 2023-10-31T11:16:41Z
day: '01'
department:
- _id: AnSa
doi: 10.1140/epje/s10189-023-00354-y
external_id:
pmid:
- '37819444'
intvolume: ' 46'
issue: '10'
language:
- iso: eng
month: '10'
oa_version: None
pmid: 1
publication: The European Physical Journal E
publication_identifier:
eissn:
- 1292-895X
issn:
- 1292-8941
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mixtures of self-propelled particles interacting with asymmetric obstacles
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 46
year: '2023'
...
---
_id: '14472'
abstract:
- lang: eng
text: "Data related to the following paper:\r\n\"Stress granules plug and stabilize
damaged endolysosomal membranes\" (https://doi.org/10.1038/s41586-023-06726-w)\r\n\r\nAbstract:
\r\nEndomembrane damage represents a form of stress that is detrimental for eukaryotic
cells. To cope with this threat, cells possess mechanisms that repair the damage
and restore cellular homeostasis. Endomembrane damage also results in organelle
instability and the mechanisms by which cells stabilize damaged endomembranes
to enable membrane repair remains unknown. In this work we use a minimal coarse-grained
molecular dynamics system to explore how lipid vesicles undergoing poration in
a protein-rich medium can be plugged and stabilised by condensate formation. The
solution of proteins in and out of the vesicle is described by beads dispersed
in implicit solvent. The membrane is described as a one-bead-thick fluid elastic
layer of mechanical properties that mimic biological membranes. We tune the interactions
between solution beads in the different compartments to capture the differences
between the cytoplasmic and endosomal protein solutions and explore how the system
responds to different degrees of membrane poration. We find that, in the right
interaction regime, condensates form rapidly at the damage site upon solution
mixing and act as a plug that prevents futher mixing and destabilisation of the
vesicle. Further, when the condensate can interact with the membrane (wetting
interactions) we find that it mediates pore sealing and membrane repair. This
research is part of the work published in \"Stress granules plug and stabilize
damaged endolysosomal membranes\", Bussi et al, Nature, 2023 - 10.1038/s41586-023-06726-w."
article_processing_charge: No
author:
- first_name: Christian Eduardo
full_name: Vanhille-Campos, Christian Eduardo
id: 3adeca52-9313-11ed-b1ac-c170b2505714
last_name: Vanhille-Campos
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Vanhille-Campos CE, Šarić A. Stress granules plug and stabilize damaged endolysosomal
membranes. 2023. doi:10.15479/AT:ISTA:14472
apa: Vanhille-Campos, C. E., & Šarić, A. (2023). Stress granules plug and stabilize
damaged endolysosomal membranes. Institute of Science and Technology Austria.
https://doi.org/10.15479/AT:ISTA:14472
chicago: Vanhille-Campos, Christian Eduardo, and Anđela Šarić. “Stress Granules
Plug and Stabilize Damaged Endolysosomal Membranes.” Institute of Science and
Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14472.
ieee: C. E. Vanhille-Campos and A. Šarić, “Stress granules plug and stabilize damaged
endolysosomal membranes.” Institute of Science and Technology Austria, 2023.
ista: Vanhille-Campos CE, Šarić A. 2023. Stress granules plug and stabilize damaged
endolysosomal membranes, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14472.
mla: Vanhille-Campos, Christian Eduardo, and Anđela Šarić. Stress Granules Plug
and Stabilize Damaged Endolysosomal Membranes. Institute of Science and Technology
Austria, 2023, doi:10.15479/AT:ISTA:14472.
short: C.E. Vanhille-Campos, A. Šarić, (2023).
date_created: 2023-10-30T16:38:32Z
date_published: 2023-10-31T00:00:00Z
date_updated: 2023-11-27T09:05:07Z
day: '31'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.15479/AT:ISTA:14472
file:
- access_level: open_access
checksum: a18706e952e8660c51ede52a167270b7
content_type: application/zip
creator: ipalaia
date_created: 2023-10-30T16:31:08Z
date_updated: 2023-10-30T16:31:08Z
file_id: '14473'
file_name: SGporecondensation-main.zip
file_size: 62821432
relation: main_file
success: 1
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checksum: 389eab31c6509dbc05795017fb618758
content_type: text/plain
creator: dernst
date_created: 2023-10-31T08:57:50Z
date_updated: 2023-10-31T08:57:50Z
file_id: '14474'
file_name: README.txt
file_size: 1697
relation: main_file
success: 1
file_date_updated: 2023-10-31T08:57:50Z
has_accepted_license: '1'
license: https://creativecommons.org/publicdomain/zero/1.0/
month: '10'
oa: 1
oa_version: Published Version
publisher: Institute of Science and Technology Austria
related_material:
record:
- id: '14610'
relation: used_in_publication
status: public
status: public
title: Stress granules plug and stabilize damaged endolysosomal membranes
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14610'
abstract:
- lang: eng
text: AbstractEndomembrane damage represents a
form of stress that is detrimental for eukaryotic cells1,2.
To cope with this threat, cells possess mechanisms that repair the damage and
restore cellular homeostasis3–7. Endomembrane damage also
results in organelle instability and the mechanisms by which cells stabilize damaged
endomembranes to enable membrane repair remains unknown. Here, by combining in
vitro and in cellulo studies with computational modelling we uncover a biological
function for stress granules whereby these biomolecular condensates form rapidly
at endomembrane damage sites and act as a plug that stabilizes the ruptured membrane.
Functionally, we demonstrate that stress granule formation and membrane stabilization
enable efficient repair of damaged endolysosomes, through both ESCRT (endosomal
sorting complex required for transport)-dependent and independent mechanisms.
We also show that blocking stress granule formation in human macrophages creates
a permissive environment for Mycobacterium tuberculosis,
a human pathogen that exploits endomembrane damage to survive within the host.
acknowledgement: "We thank the Human Embryonic Stem Cell Unit, Advanced Light Microscopy
and High-throughput Screening facilities at the Crick for their support in various
aspects of the work. We thank the laboratory of P. Anderson for providing the G3BP-DKO
U2OS cells. The authors thank N. Chen for providing the purified glycinin protein;
Z. Zhao for providing the microfluidic chip wafers; and M. Amaral and F. Frey for
helpful discussions and valuable input regarding analysis methods. This work was
supported by the Francis Crick Institute (to M.G.G.), which receives its core funding
from Cancer Research UK (FC001092), the UK Medical Research Council (FC001092) and
the Wellcome Trust (FC001092). This project has received funding from the European
Research Council (ERC) under the European Union’s Horizon 2020 research and innovation
programme (grant agreement no. 772022 to M.G.G.). C.B. has received funding from
the European Respiratory Society and the European Union’s H2020 research and innovation
programme under the Marie Sklodowska-Curie grant agreement no. 713406. A.M. acknowledges
support from Alexander von Humboldt Foundation and C.V.-C. acknowledges funding
by the Royal Society and the European Research Council under the European Union’s
Horizon 2020 Research and Innovation Programme (grant no. 802960 to A.S.). All simulations
were carried out on the high-performance computing cluster at the Institute of Science
and Technology Austria. For the purpose of Open Access, the author has applied a
CC BY public copyright licence to any Author Accepted Manuscript version arising
from this submission.\r\nOpen Access funding provided by The Francis Crick Institute."
article_processing_charge: Yes (via OA deal)
article_type: original
author:
- first_name: Claudio
full_name: Bussi, Claudio
last_name: Bussi
- first_name: Agustín
full_name: Mangiarotti, Agustín
last_name: Mangiarotti
- first_name: Christian Eduardo
full_name: Vanhille-Campos, Christian Eduardo
id: 3adeca52-9313-11ed-b1ac-c170b2505714
last_name: Vanhille-Campos
- first_name: Beren
full_name: Aylan, Beren
last_name: Aylan
- first_name: Enrica
full_name: Pellegrino, Enrica
last_name: Pellegrino
- first_name: Natalia
full_name: Athanasiadi, Natalia
last_name: Athanasiadi
- first_name: Antony
full_name: Fearns, Antony
last_name: Fearns
- first_name: Angela
full_name: Rodgers, Angela
last_name: Rodgers
- first_name: Titus M.
full_name: Franzmann, Titus M.
last_name: Franzmann
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Rumiana
full_name: Dimova, Rumiana
last_name: Dimova
- first_name: Maximiliano G.
full_name: Gutierrez, Maximiliano G.
last_name: Gutierrez
citation:
ama: Bussi C, Mangiarotti A, Vanhille-Campos CE, et al. Stress granules plug and
stabilize damaged endolysosomal membranes. Nature. 2023. doi:10.1038/s41586-023-06726-w
apa: Bussi, C., Mangiarotti, A., Vanhille-Campos, C. E., Aylan, B., Pellegrino,
E., Athanasiadi, N., … Gutierrez, M. G. (2023). Stress granules plug and stabilize
damaged endolysosomal membranes. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-06726-w
chicago: Bussi, Claudio, Agustín Mangiarotti, Christian Eduardo Vanhille-Campos,
Beren Aylan, Enrica Pellegrino, Natalia Athanasiadi, Antony Fearns, et al. “Stress
Granules Plug and Stabilize Damaged Endolysosomal Membranes.” Nature. Springer
Nature, 2023. https://doi.org/10.1038/s41586-023-06726-w.
ieee: C. Bussi et al., “Stress granules plug and stabilize damaged endolysosomal
membranes,” Nature. Springer Nature, 2023.
ista: Bussi C, Mangiarotti A, Vanhille-Campos CE, Aylan B, Pellegrino E, Athanasiadi
N, Fearns A, Rodgers A, Franzmann TM, Šarić A, Dimova R, Gutierrez MG. 2023. Stress
granules plug and stabilize damaged endolysosomal membranes. Nature.
mla: Bussi, Claudio, et al. “Stress Granules Plug and Stabilize Damaged Endolysosomal
Membranes.” Nature, Springer Nature, 2023, doi:10.1038/s41586-023-06726-w.
short: C. Bussi, A. Mangiarotti, C.E. Vanhille-Campos, B. Aylan, E. Pellegrino,
N. Athanasiadi, A. Fearns, A. Rodgers, T.M. Franzmann, A. Šarić, R. Dimova, M.G.
Gutierrez, Nature (2023).
date_created: 2023-11-27T07:56:37Z
date_published: 2023-11-15T00:00:00Z
date_updated: 2023-11-27T09:05:08Z
day: '15'
department:
- _id: AnSa
doi: 10.1038/s41586-023-06726-w
external_id:
pmid:
- '37968398'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41586-023-06726-w
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: epub_ahead
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41586-023-06882-z
record:
- id: '14472'
relation: research_data
status: public
status: public
title: Stress granules plug and stabilize damaged endolysosomal membranes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '14655'
abstract:
- lang: eng
text: The kinetics of the assembly of semiflexible filaments through end-to-end
annealing is key to the structure of the cytoskeleton, but is not understood.
We analyze this problem through scaling theory and simulations, and uncover a
regime where filaments’ ends find each other through bending fluctuations without
the need for the whole filament to diffuse. This results in a very substantial
speedup of assembly in physiological regimes, and could help with understanding
the dynamics of actin and intermediate filaments in biological processes such
as wound healing and cell division.
acknowledgement: The authors thank C´ecile Leduc and Duc-Quang Tran for invaluable
help with understanding the experimental behavior of intermediate filaments, and
Raphael Voituriez, Nicolas Levernier, and Alexander Grosberg for fruitful discussion
on the theoretical model. V. S. also thanks Davide Michieletto, Maria Panoukidou,
and Lorenzo Rovigatti for very helpful suggestions on the simulation model. M. L.
was supported by Marie Curie Integration Grant No. PCIG12-GA-2012-334053, “Investissements
d’Avenir” LabEx PALM (ANR-10-LABX- 0039-PALM), ANR Grants No. ANR-15-CE13-0004-03,
No. ANR-21-CE11-0004-02 and No. ANR-22-CE30-0024, as well as ERC Starting Grant
No. 677532. M.L.’s group belongs to the CNRS consortium AQV. Part of this work was
performed using HPC resources from GENCI–IDRIS (Grants No. 2020-A0090712066 and
No. 2021-A0110712066).
article_number: '228401'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Valerio
full_name: Sorichetti, Valerio
id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b
last_name: Sorichetti
orcid: 0000-0002-9645-6576
- first_name: Martin
full_name: Lenz, Martin
last_name: Lenz
citation:
ama: Sorichetti V, Lenz M. Transverse fluctuations control the assembly of semiflexible
filaments. Physical Review Letters. 2023;131(22). doi:10.1103/PhysRevLett.131.228401
apa: Sorichetti, V., & Lenz, M. (2023). Transverse fluctuations control the
assembly of semiflexible filaments. Physical Review Letters. American Physical
Society. https://doi.org/10.1103/PhysRevLett.131.228401
chicago: Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control
the Assembly of Semiflexible Filaments.” Physical Review Letters. American
Physical Society, 2023. https://doi.org/10.1103/PhysRevLett.131.228401.
ieee: V. Sorichetti and M. Lenz, “Transverse fluctuations control the assembly of
semiflexible filaments,” Physical Review Letters, vol. 131, no. 22. American
Physical Society, 2023.
ista: Sorichetti V, Lenz M. 2023. Transverse fluctuations control the assembly of
semiflexible filaments. Physical Review Letters. 131(22), 228401.
mla: Sorichetti, Valerio, and Martin Lenz. “Transverse Fluctuations Control the
Assembly of Semiflexible Filaments.” Physical Review Letters, vol. 131,
no. 22, 228401, American Physical Society, 2023, doi:10.1103/PhysRevLett.131.228401.
short: V. Sorichetti, M. Lenz, Physical Review Letters 131 (2023).
date_created: 2023-12-10T23:00:57Z
date_published: 2023-12-01T00:00:00Z
date_updated: 2023-12-11T07:59:25Z
day: '01'
department:
- _id: AnSa
doi: 10.1103/PhysRevLett.131.228401
external_id:
arxiv:
- '2303.03088'
intvolume: ' 131'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2303.03088
month: '12'
oa: 1
oa_version: Preprint
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Transverse fluctuations control the assembly of semiflexible filaments
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 131
year: '2023'
...
---
_id: '14782'
abstract:
- lang: eng
text: The actin cortex is a complex cytoskeletal machinery that drives and responds
to changes in cell shape. It must generate or adapt to plasma membrane curvature
to facilitate diverse functions such as cell division, migration, and phagocytosis.
Due to the complex molecular makeup of the actin cortex, it remains unclear whether
actin networks are inherently able to sense and generate membrane curvature, or
whether they rely on their diverse binding partners to accomplish this. Here,
we show that curvature sensing is an inherent capability of branched actin networks
nucleated by Arp2/3 and VCA. We develop a robust method to encapsulate actin inside
giant unilamellar vesicles (GUVs) and assemble an actin cortex at the inner surface
of the GUV membrane. We show that actin forms a uniform and thin cortical layer
when present at high concentration and distinct patches associated with negative
membrane curvature at low concentration. Serendipitously, we find that the GUV
production method also produces dumbbell-shaped GUVs, which we explain using mathematical
modeling in terms of membrane hemifusion of nested GUVs. We find that branched
actin networks preferentially assemble at the neck of the dumbbells, which possess
a micrometer-range convex curvature comparable with the curvature of the actin
patches found in spherical GUVs. Minimal branched actin networks can thus sense
membrane curvature, which may help mammalian cells to robustly recruit actin to
curved membranes to facilitate diverse cellular functions such as cytokinesis
and migration.
acknowledgement: We thank Jeffrey den Haan for protein purification, Kristina Ganzinger
(AMOLF) for providing the 10xHis VCA construct, David Kovar (University of Chicago)
for the CP constructs, and Michael Way (Crick Institute) for providing purified
human Arp2/3 proteins. We are grateful to Iris Lambert for early actin encapsulation
experiments that formed the basis for establishing the eDICE method, to Federico
Fanalista for acquiring images of dumbbell-shaped GUVs in samples produced by cDICE,
and to Tom Aarts for images of dumbbell-shaped GUVs produced by gel-assisted swelling.
Lennard van Buren is thanked for his help with image analysis to quantify actin
concentrations in GUVs. We thank Kristina Ganzinger (AMOLF) for hosting us to perform
pyrene assays in her lab, and Balász Antalicz (AMOLF) for technical assistance with
the spectrophotometer. The authors also thank Matthieu Piel and Daniel Fletcher
for insightful and inspiring discussions. We acknowledge financial support from
The Netherlands Organization of Scientific Research (NWO/OCW) Gravitation program
Building a Synthetic Cell (BaSyC) (024.003.019). F.F. gratefully acknowledges funding
from the Kavli Synergy program of the Kavli Institute of Nanoscience Delft.
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Lucia
full_name: Baldauf, Lucia
last_name: Baldauf
- first_name: Felix F
full_name: Frey, Felix F
id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3
last_name: Frey
- first_name: Marcos
full_name: Arribas Perez, Marcos
last_name: Arribas Perez
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
- first_name: Gijsje H.
full_name: Koenderink, Gijsje H.
last_name: Koenderink
citation:
ama: Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. Branched actin
cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal.
2023;122(11):2311-2324. doi:10.1016/j.bpj.2023.02.018
apa: Baldauf, L., Frey, F. F., Arribas Perez, M., Idema, T., & Koenderink, G.
H. (2023). Branched actin cortices reconstituted in vesicles sense membrane curvature.
Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2023.02.018
chicago: Baldauf, Lucia, Felix F Frey, Marcos Arribas Perez, Timon Idema, and Gijsje
H. Koenderink. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane
Curvature.” Biophysical Journal. Elsevier, 2023. https://doi.org/10.1016/j.bpj.2023.02.018.
ieee: L. Baldauf, F. F. Frey, M. Arribas Perez, T. Idema, and G. H. Koenderink,
“Branched actin cortices reconstituted in vesicles sense membrane curvature,”
Biophysical Journal, vol. 122, no. 11. Elsevier, pp. 2311–2324, 2023.
ista: Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. 2023. Branched
actin cortices reconstituted in vesicles sense membrane curvature. Biophysical
Journal. 122(11), 2311–2324.
mla: Baldauf, Lucia, et al. “Branched Actin Cortices Reconstituted in Vesicles Sense
Membrane Curvature.” Biophysical Journal, vol. 122, no. 11, Elsevier, 2023,
pp. 2311–24, doi:10.1016/j.bpj.2023.02.018.
short: L. Baldauf, F.F. Frey, M. Arribas Perez, T. Idema, G.H. Koenderink, Biophysical
Journal 122 (2023) 2311–2324.
date_created: 2024-01-10T09:45:48Z
date_published: 2023-06-06T00:00:00Z
date_updated: 2024-01-16T09:20:03Z
day: '06'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1016/j.bpj.2023.02.018
external_id:
isi:
- '001016792600001'
pmid:
- '36806830'
file:
- access_level: open_access
checksum: 70566e54cd95ea6df340909ad44c5cd5
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T09:09:29Z
date_updated: 2024-01-16T09:09:29Z
file_id: '14807'
file_name: 2023_BiophysicalJournal_Baldauf.pdf
file_size: 3285810
relation: main_file
success: 1
file_date_updated: 2024-01-16T09:09:29Z
has_accepted_license: '1'
intvolume: ' 122'
isi: 1
issue: '11'
keyword:
- Biophysics
language:
- iso: eng
month: '06'
oa: 1
oa_version: Published Version
page: 2311-2324
pmid: 1
publication: Biophysical Journal
publication_identifier:
issn:
- 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
link:
- relation: software
url: https://github.com/BioSoftMatterGroup/actin-curvature-sensing
status: public
title: Branched actin cortices reconstituted in vesicles sense membrane curvature
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 122
year: '2023'
...
---
_id: '14788'
abstract:
- lang: eng
text: "Eukaryotic cells use clathrin-mediated endocytosis to take up a large range
of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma
membrane, but it remains controversial when and how it is remodeled into a spherical
vesicle.\r\nHere, we use 3D superresolution microscopy to determine the precise
geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal
sorting, we determine the average trajectory of clathrin remodeling during endocytosis.
We find that clathrin coats assemble first on flat membranes to 50% of the coat
area before they become rapidly and continuously bent, and this mechanism is confirmed
in three cell lines. We introduce the cooperative curvature model, which is based
on positive feedback for curvature generation. It accurately describes the measured
shapes and dynamics of the clathrin coat and could represent a general mechanism
for clathrin coat remodeling on the plasma membrane."
acknowledgement: We thank the entire Ries and Kaksonen labs for fruitful discussions
and support. This work was supported by the European Research Council (ERC CoG-724489
to J. Ries), the National Institutes of Health Common Fund 4D Nucleome Program (Grant
U01 to J. Ries), the Human Frontier Science Program (RGY0065/2017 to J. Ries), the
EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Curie Actions COFUND
(Grant 229597 to O. Avinoam), the European Molecular Biology Laboratory (M. Mund,
A. Tschanz, Y.-L. Wu and J. Ries), and the Swiss National Science Foundation (grant
310030B_182825 and NCCR Chemical Biology to M. Kaksonen). O. Avinoam is an incumbent
of the Miriam Berman Presidential Development Chair.
article_number: e202206038
article_processing_charge: No
article_type: original
author:
- first_name: Markus
full_name: Mund, Markus
last_name: Mund
- first_name: Aline
full_name: Tschanz, Aline
last_name: Tschanz
- first_name: Yu-Le
full_name: Wu, Yu-Le
last_name: Wu
- first_name: Felix F
full_name: Frey, Felix F
id: a0270b37-8f1a-11ec-95c7-8e710c59a4f3
last_name: Frey
orcid: 0000-0001-8501-6017
- first_name: Johanna L.
full_name: Mehl, Johanna L.
last_name: Mehl
- first_name: Marko
full_name: Kaksonen, Marko
last_name: Kaksonen
- first_name: Ori
full_name: Avinoam, Ori
last_name: Avinoam
- first_name: Ulrich S.
full_name: Schwarz, Ulrich S.
last_name: Schwarz
- first_name: Jonas
full_name: Ries, Jonas
last_name: Ries
citation:
ama: Mund M, Tschanz A, Wu Y-L, et al. Clathrin coats partially preassemble and
subsequently bend during endocytosis. Journal of Cell Biology. 2023;222(3).
doi:10.1083/jcb.202206038
apa: Mund, M., Tschanz, A., Wu, Y.-L., Frey, F. F., Mehl, J. L., Kaksonen, M., …
Ries, J. (2023). Clathrin coats partially preassemble and subsequently bend during
endocytosis. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202206038
chicago: Mund, Markus, Aline Tschanz, Yu-Le Wu, Felix F Frey, Johanna L. Mehl, Marko
Kaksonen, Ori Avinoam, Ulrich S. Schwarz, and Jonas Ries. “Clathrin Coats Partially
Preassemble and Subsequently Bend during Endocytosis.” Journal of Cell Biology.
Rockefeller University Press, 2023. https://doi.org/10.1083/jcb.202206038.
ieee: M. Mund et al., “Clathrin coats partially preassemble and subsequently
bend during endocytosis,” Journal of Cell Biology, vol. 222, no. 3. Rockefeller
University Press, 2023.
ista: Mund M, Tschanz A, Wu Y-L, Frey FF, Mehl JL, Kaksonen M, Avinoam O, Schwarz
US, Ries J. 2023. Clathrin coats partially preassemble and subsequently bend during
endocytosis. Journal of Cell Biology. 222(3), e202206038.
mla: Mund, Markus, et al. “Clathrin Coats Partially Preassemble and Subsequently
Bend during Endocytosis.” Journal of Cell Biology, vol. 222, no. 3, e202206038,
Rockefeller University Press, 2023, doi:10.1083/jcb.202206038.
short: M. Mund, A. Tschanz, Y.-L. Wu, F.F. Frey, J.L. Mehl, M. Kaksonen, O. Avinoam,
U.S. Schwarz, J. Ries, Journal of Cell Biology 222 (2023).
date_created: 2024-01-10T10:45:55Z
date_published: 2023-02-03T00:00:00Z
date_updated: 2024-01-16T10:17:05Z
day: '03'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1083/jcb.202206038
external_id:
isi:
- '000978065000001'
pmid:
- '36734980'
file:
- access_level: open_access
checksum: 505d5cac36c14b073b68c7fed1a92bd3
content_type: application/pdf
creator: dernst
date_created: 2024-01-16T10:15:09Z
date_updated: 2024-01-16T10:15:09Z
file_id: '14811'
file_name: 2023_JCB_Mund.pdf
file_size: 5678069
relation: main_file
success: 1
file_date_updated: 2024-01-16T10:15:09Z
has_accepted_license: '1'
intvolume: ' 222'
isi: 1
issue: '3'
keyword:
- Cell Biology
language:
- iso: eng
license: https://creativecommons.org/licenses/by/4.0/
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Journal of Cell Biology
publication_identifier:
eissn:
- 1540-8140
issn:
- 0021-9525
publication_status: published
publisher: Rockefeller University Press
quality_controlled: '1'
status: public
title: Clathrin coats partially preassemble and subsequently bend during endocytosis
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: 222
year: '2023'
...
---
_id: '14831'
abstract:
- lang: eng
text: Catalysis, the acceleration of product formation by a substance that is left
unchanged, typically results from multiple elementary processes, including diffusion
of the reactants toward the catalyst, chemical steps, and release of the products.
While efforts to design catalysts are often focused on accelerating the chemical
reaction on the catalyst, catalysis is a global property of the catalytic cycle
that involves all processes. These are controlled by both intrinsic parameters
such as the composition and shape of the catalyst and extrinsic parameters such
as the concentration of the chemical species at play. We examine here the conditions
that catalysis imposes on the different steps of a reaction cycle and the respective
role of intrinsic and extrinsic parameters of the system on the emergence of catalysis
by using an approach based on first-passage times. We illustrate this approach
for various decompositions of a catalytic cycle into elementary steps, including
non-Markovian decompositions, which are useful when the presence and nature of
intermediate states are a priori unknown. Our examples cover different types of
reactions and clarify the constraints on elementary steps and the impact of species
concentrations on catalysis.
acknowledgement: We acknowledge funding from ANR-22-CE06-0037-02. This work has received
funding from the European Unions Horizon 2020 research and innovation program under
the Marie Sklodowska-Curie grant agreement No. 754387.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Yann
full_name: Sakref, Yann
last_name: Sakref
- first_name: Maitane
full_name: Muñoz Basagoiti, Maitane
id: 1a8a7950-82cd-11ed-bd4f-9624c913a607
last_name: Muñoz Basagoiti
orcid: 0000-0003-1483-1457
- first_name: Zorana
full_name: Zeravcic, Zorana
last_name: Zeravcic
- first_name: Olivier
full_name: Rivoire, Olivier
last_name: Rivoire
citation:
ama: Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. On kinetic constraints
that catalysis imposes on elementary processes. The Journal of Physical Chemistry
B. 2023;127(51):10950-10959. doi:10.1021/acs.jpcb.3c04627
apa: Sakref, Y., Muñoz Basagoiti, M., Zeravcic, Z., & Rivoire, O. (2023). On
kinetic constraints that catalysis imposes on elementary processes. The Journal
of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.3c04627
chicago: Sakref, Yann, Maitane Muñoz Basagoiti, Zorana Zeravcic, and Olivier Rivoire.
“On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” The
Journal of Physical Chemistry B. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpcb.3c04627.
ieee: Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, and O. Rivoire, “On kinetic constraints
that catalysis imposes on elementary processes,” The Journal of Physical Chemistry
B, vol. 127, no. 51. American Chemical Society, pp. 10950–10959, 2023.
ista: Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. 2023. On kinetic constraints
that catalysis imposes on elementary processes. The Journal of Physical Chemistry
B. 127(51), 10950–10959.
mla: Sakref, Yann, et al. “On Kinetic Constraints That Catalysis Imposes on Elementary
Processes.” The Journal of Physical Chemistry B, vol. 127, no. 51, American
Chemical Society, 2023, pp. 10950–59, doi:10.1021/acs.jpcb.3c04627.
short: Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, O. Rivoire, The Journal of Physical
Chemistry B 127 (2023) 10950–10959.
date_created: 2024-01-18T07:47:11Z
date_published: 2023-12-13T00:00:00Z
date_updated: 2024-01-23T07:58:27Z
day: '13'
department:
- _id: AnSa
doi: 10.1021/acs.jpcb.3c04627
external_id:
arxiv:
- '2312.15940'
isi:
- '001134068000001'
intvolume: ' 127'
isi: 1
issue: '51'
keyword:
- Materials Chemistry
- Surfaces
- Coatings and Films
- Physical and Theoretical Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2312.15940
month: '12'
oa: 1
oa_version: Preprint
page: 10950-10959
publication: The Journal of Physical Chemistry B
publication_identifier:
eissn:
- 1520-5207
issn:
- 1520-6106
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: On kinetic constraints that catalysis imposes on elementary processes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 127
year: '2023'
...
---
_id: '14844'
abstract:
- lang: eng
text: 'Many cell functions require a concerted effort from multiple membrane proteins,
for example, for signaling, cell division, and endocytosis. One contribution to
their successful self-organization stems from the membrane deformations that these
proteins induce. While the pairwise interaction potential of two membrane-deforming
spheres has recently been measured, membrane-deformation-induced interactions
have been predicted to be nonadditive, and hence their collective behavior cannot
be deduced from this measurement. We here employ a colloidal model system consisting
of adhesive spheres and giant unilamellar vesicles to test these predictions by
measuring the interaction potential of the simplest case of three membrane-deforming,
spherical particles. We quantify their interactions and arrangements and, for
the first time, experimentally confirm and quantify the nonadditive nature of
membrane-deformation-induced interactions. We furthermore conclude that there
exist two favorable configurations on the membrane: (1) a linear and (2) a triangular
arrangement of the three spheres. Using Monte Carlo simulations, we corroborate
the experimentally observed energy minima and identify a lowering of the membrane
deformation as the cause for the observed configurations. The high symmetry of
the preferred arrangements for three particles suggests that arrangements of many
membrane-deforming objects might follow simple rules.'
acknowledgement: We gratefully acknowledge useful discussions with Casper van der
Wel, help by Yogesh Shelke with PAA coverslip preparation, and support by Rachel
Doherty with particle functionalization. A.A. and D.J.K. would like to thank Timon
Idema and George Dadunashvili for initial attempts to simulate the experimental
system. D.J.K. would like to thank the physics department at Leiden University for
funding the PhD position of A.A. B.M. and A.Š. acknowledge funding by the European
Union’s Horizon 2020 research and innovation programme (ERC starting grant no. 802960).
article_processing_charge: No
article_type: original
author:
- first_name: Ali
full_name: Azadbakht, Ali
last_name: Azadbakht
- first_name: Billie
full_name: Meadowcroft, Billie
id: a4725fd6-932b-11ed-81e2-c098c7f37ae1
last_name: Meadowcroft
orcid: 0000-0003-3441-1337
- first_name: Juraj
full_name: Majek, Juraj
id: 3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1
last_name: Majek
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Daniela J.
full_name: Kraft, Daniela J.
last_name: Kraft
citation:
ama: Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions
between three membrane-wrapped colloidal spheres. Biophysical Journal.
doi:10.1016/j.bpj.2023.12.020
apa: Azadbakht, A., Meadowcroft, B., Majek, J., Šarić, A., & Kraft, D. J. (n.d.).
Nonadditivity in interactions between three membrane-wrapped colloidal spheres.
Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2023.12.020
chicago: Azadbakht, Ali, Billie Meadowcroft, Juraj Majek, Anđela Šarić, and Daniela
J. Kraft. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal
Spheres.” Biophysical Journal. Elsevier, n.d. https://doi.org/10.1016/j.bpj.2023.12.020.
ieee: A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, and D. J. Kraft, “Nonadditivity
in interactions between three membrane-wrapped colloidal spheres,” Biophysical
Journal. Elsevier.
ista: Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions
between three membrane-wrapped colloidal spheres. Biophysical Journal.
mla: Azadbakht, Ali, et al. “Nonadditivity in Interactions between Three Membrane-Wrapped
Colloidal Spheres.” Biophysical Journal, Elsevier, doi:10.1016/j.bpj.2023.12.020.
short: A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, D.J. Kraft, Biophysical
Journal (n.d.).
date_created: 2024-01-21T23:00:56Z
date_published: 2023-12-29T00:00:00Z
date_updated: 2024-01-23T09:26:35Z
day: '29'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1016/j.bpj.2023.12.020
ec_funded: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.bpj.2023.12.020
month: '12'
oa: 1
oa_version: Published Version
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Biophysical Journal
publication_identifier:
eissn:
- 1542-0086
issn:
- 0006-3495
publication_status: inpress
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nonadditivity in interactions between three membrane-wrapped colloidal spheres
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '15027'
abstract:
- lang: eng
text: 'This data repository underpins the paper, published in PNAS (doi pending)
and bioarxiv (doi: https://doi.org/10.1101/2023.07.05.547777).'
article_processing_charge: No
author:
- first_name: Samo
full_name: Curk, Samo
id: 031eff0d-d481-11ee-8508-cd12a7a86e5b
last_name: Curk
orcid: 0000-0001-6160-9766
citation:
ama: Curk S. aggregation_data. 2023.
apa: Curk, S. (2023). aggregation_data. Figshare.
chicago: Curk, Samo. “Aggregation_data.” Figshare, 2023.
ieee: S. Curk, “aggregation_data.” Figshare, 2023.
ista: Curk S. 2023. aggregation_data, Figshare.
mla: Curk, Samo. Aggregation_data. Figshare, 2023.
short: S. Curk, (2023).
date_created: 2024-02-26T08:37:57Z
date_published: 2023-12-13T00:00:00Z
date_updated: 2024-02-26T08:45:55Z
day: '13'
ddc:
- '570'
department:
- _id: AnSa
has_accepted_license: '1'
main_file_link:
- open_access: '1'
url: https://figshare.com/s/85798bba4ebc68d822ed
month: '12'
oa: 1
oa_version: Published Version
publisher: Figshare
related_material:
record:
- id: '15001'
relation: used_in_publication
status: public
status: public
title: aggregation_data
tmp:
image: /images/cc_0.png
legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode
name: Creative Commons Public Domain Dedication (CC0 1.0)
short: CC0 (1.0)
type: research_data_reference
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
year: '2023'
...
---
_id: '13094'
abstract:
- lang: eng
text: 'Endocytosis is a key cellular process involved in the uptake of nutrients,
pathogens, or the therapy of diseases. Most studies have focused on spherical
objects, whereas biologically relevant shapes can be highly anisotropic. In this
letter, we use an experimental model system based on Giant Unilamellar Vesicles
(GUVs) and dumbbell-shaped colloidal particles to mimic and investigate the first
stage of the passive endocytic process: engulfment of an anisotropic object by
the membrane. Our model has specific ligand–receptor interactions realized by
mobile receptors on the vesicles and immobile ligands on the particles. Through
a series of experiments, theory, and molecular dynamics simulations, we quantify
the wrapping process of anisotropic dumbbells by GUVs and identify distinct stages
of the wrapping pathway. We find that the strong curvature variation in the neck
of the dumbbell as well as membrane tension are crucial in determining both the
speed of wrapping and the final states.'
acknowledgement: We sincerely thank Casper van der Wel for providing open-source packages
for tracking, as well as Yogesh Shelke for his assistance with PAA coverslip preparation
and Rachel Doherty for her assistance with particle functionalization. We are grateful
to Felix Frey for useful discussions on the theory of membrane wrapping. B.M. and
A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation
programme (ERC Starting Grant No. 802960).
article_processing_charge: No
article_type: letter_note
author:
- first_name: Ali
full_name: Azadbakht, Ali
last_name: Azadbakht
- first_name: Billie
full_name: Meadowcroft, Billie
id: a4725fd6-932b-11ed-81e2-c098c7f37ae1
last_name: Meadowcroft
- first_name: Thijs
full_name: Varkevisser, Thijs
last_name: Varkevisser
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Daniela J.
full_name: Kraft, Daniela J.
last_name: Kraft
citation:
ama: Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. Wrapping pathways
of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano Letters.
2023;23(10):4267–4273. doi:10.1021/acs.nanolett.3c00375
apa: Azadbakht, A., Meadowcroft, B., Varkevisser, T., Šarić, A., & Kraft, D.
J. (2023). Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar
Vesicles. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.3c00375
chicago: Azadbakht, Ali, Billie Meadowcroft, Thijs Varkevisser, Anđela Šarić, and
Daniela J. Kraft. “Wrapping Pathways of Anisotropic Dumbbell Particles by Giant
Unilamellar Vesicles.” Nano Letters. American Chemical Society, 2023. https://doi.org/10.1021/acs.nanolett.3c00375.
ieee: A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, and D. J. Kraft, “Wrapping
pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles,” Nano
Letters, vol. 23, no. 10. American Chemical Society, pp. 4267–4273, 2023.
ista: Azadbakht A, Meadowcroft B, Varkevisser T, Šarić A, Kraft DJ. 2023. Wrapping
pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles. Nano
Letters. 23(10), 4267–4273.
mla: Azadbakht, Ali, et al. “Wrapping Pathways of Anisotropic Dumbbell Particles
by Giant Unilamellar Vesicles.” Nano Letters, vol. 23, no. 10, American
Chemical Society, 2023, pp. 4267–4273, doi:10.1021/acs.nanolett.3c00375.
short: A. Azadbakht, B. Meadowcroft, T. Varkevisser, A. Šarić, D.J. Kraft, Nano
Letters 23 (2023) 4267–4273.
date_created: 2023-05-28T22:01:03Z
date_published: 2023-05-04T00:00:00Z
date_updated: 2023-08-01T14:51:25Z
day: '04'
ddc:
- '540'
department:
- _id: AnSa
doi: 10.1021/acs.nanolett.3c00375
ec_funded: 1
external_id:
isi:
- '000985481400001'
pmid:
- '37141427'
file:
- access_level: open_access
checksum: 9734d4c617bab3578ef62916b764547a
content_type: application/pdf
creator: dernst
date_created: 2023-05-30T07:55:31Z
date_updated: 2023-05-30T07:55:31Z
file_id: '13100'
file_name: 2023_NanoLetters_Azadbakht.pdf
file_size: 3654910
relation: main_file
success: 1
file_date_updated: 2023-05-30T07:55:31Z
has_accepted_license: '1'
intvolume: ' 23'
isi: 1
issue: '10'
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
page: 4267–4273
pmid: 1
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Nano Letters
publication_identifier:
eissn:
- 1530-6992
issn:
- 1530-6984
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Wrapping pathways of anisotropic dumbbell particles by Giant Unilamellar Vesicles
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 23
year: '2023'
...
---
_id: '13237'
abstract:
- lang: eng
text: The formation of amyloid fibrils is a general class of protein self-assembly
behaviour, which is associated with both functional biology and the development
of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review,
we discuss how general physical concepts from the study of phase transitions can
be used to illuminate the fundamental mechanisms of amyloid self-assembly. We
summarize progress in the efforts to describe the essential biophysical features
of amyloid self-assembly as a nucleation-and-growth process and discuss how master
equation approaches can reveal the key molecular pathways underlying this process,
including the role of secondary nucleation. Additionally, we outline how non-classical
aspects of aggregate formation involving oligomers or biomolecular condensates
have emerged, inspiring developments in understanding, modelling and modulating
complex protein assembly pathways. Finally, we consider how these concepts can
be applied to kinetics-based drug discovery and therapeutic design to develop
treatments for protein aggregation diseases.
acknowledgement: The authors acknowledge support from the Institute for the Physics
of Living Systems, University College London (T.C.T.M.), the Swedish Research Council
(2015-00143) (S.L.), the European Research Council under the European Union’s Seventh
Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no.
337969) (T.P.J.K.), the BBSRC (T.P.J.K.), the Newman Foundation (T.P.J.K.) and the
Wellcome Trust Collaborative Award 203249/Z/16/Z (T.P.J.K.). The authors thank C.
Flandoli for help with illustrations.
article_processing_charge: No
article_type: original
author:
- first_name: Thomas C.T.
full_name: Michaels, Thomas C.T.
last_name: Michaels
- first_name: Daoyuan
full_name: Qian, Daoyuan
last_name: Qian
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Sara
full_name: Linse, Sara
last_name: Linse
- first_name: Tuomas P.J.
full_name: Knowles, Tuomas P.J.
last_name: Knowles
citation:
ama: Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. Amyloid
formation as a protein phase transition. Nature Reviews Physics. 2023;5:379–397.
doi:10.1038/s42254-023-00598-9
apa: Michaels, T. C. T., Qian, D., Šarić, A., Vendruscolo, M., Linse, S., &
Knowles, T. P. J. (2023). Amyloid formation as a protein phase transition. Nature
Reviews Physics. Springer Nature. https://doi.org/10.1038/s42254-023-00598-9
chicago: Michaels, Thomas C.T., Daoyuan Qian, Anđela Šarić, Michele Vendruscolo,
Sara Linse, and Tuomas P.J. Knowles. “Amyloid Formation as a Protein Phase Transition.”
Nature Reviews Physics. Springer Nature, 2023. https://doi.org/10.1038/s42254-023-00598-9.
ieee: T. C. T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, and T. P.
J. Knowles, “Amyloid formation as a protein phase transition,” Nature Reviews
Physics, vol. 5. Springer Nature, pp. 379–397, 2023.
ista: Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. 2023.
Amyloid formation as a protein phase transition. Nature Reviews Physics. 5, 379–397.
mla: Michaels, Thomas C. T., et al. “Amyloid Formation as a Protein Phase Transition.”
Nature Reviews Physics, vol. 5, Springer Nature, 2023, pp. 379–397, doi:10.1038/s42254-023-00598-9.
short: T.C.T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, T.P.J. Knowles,
Nature Reviews Physics 5 (2023) 379–397.
date_created: 2023-07-16T22:01:12Z
date_published: 2023-07-01T00:00:00Z
date_updated: 2023-08-02T06:28:38Z
day: '01'
department:
- _id: AnSa
doi: 10.1038/s42254-023-00598-9
external_id:
isi:
- '001017539800001'
intvolume: ' 5'
isi: 1
language:
- iso: eng
month: '07'
oa_version: None
page: 379–397
publication: Nature Reviews Physics
publication_identifier:
eissn:
- 2522-5820
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Amyloid formation as a protein phase transition
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 5
year: '2023'
...
---
_id: '13971'
abstract:
- lang: eng
text: When in equilibrium, thermal forces agitate molecules, which then diffuse,
collide and bind to form materials. However, the space of accessible structures
in which micron-scale particles can be organized by thermal forces is limited,
owing to the slow dynamics and metastable states. Active agents in a passive fluid
generate forces and flows, forming a bath with active fluctuations. Two unanswered
questions are whether those active agents can drive the assembly of passive components
into unconventional states and which material properties they will exhibit. Here
we show that passive, sticky beads immersed in a bath of swimming Escherichia
coli bacteria aggregate into unconventional clusters and gels that are controlled
by the activity of the bath. We observe a slow but persistent rotation of the
aggregates that originates in the chirality of the E. coli flagella and directs
aggregation into structures that are not accessible thermally. We elucidate the
aggregation mechanism with a numerical model of spinning, sticky beads and reproduce
quantitatively the experimental results. We show that internal activity controls
the phase diagram and the structure of the aggregates. Overall, our results highlight
the promising role of active baths in designing the structural and mechanical
properties of materials with unconventional phases.
acknowledgement: D.G. and J.P. thank E. Krasnopeeva, C. Guet, G. Guessous and T. Hwa
for providing the E. coli strains. This material is based upon work supported by
the US Department of Energy under award DE-SC0019769. I.P. acknowledges funding
by the European Union’s Horizon 2020 research and innovation programme under Marie
Skłodowska-Curie Grant Agreement No. 101034413. A.Š. acknowledges funding from the
European Research Council under the European Union’s Horizon 2020 research and innovation
programme (Grant No. 802960). M.C.U. acknowledges funding from the European Union’s
Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant
Agreement No. 754411.
article_processing_charge: Yes
article_type: original
author:
- first_name: Daniel
full_name: Grober, Daniel
id: abdfc56f-34fb-11ee-bd33-fd766fce5a99
last_name: Grober
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Mehmet C
full_name: Ucar, Mehmet C
id: 50B2A802-6007-11E9-A42B-EB23E6697425
last_name: Ucar
orcid: 0000-0003-0506-4217
- first_name: Edouard B
full_name: Hannezo, Edouard B
id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
last_name: Hannezo
orcid: 0000-0001-6005-1561
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. Unconventional
colloidal aggregation in chiral bacterial baths. Nature Physics. 2023;19:1680-1688.
doi:10.1038/s41567-023-02136-x
apa: Grober, D., Palaia, I., Ucar, M. C., Hannezo, E. B., Šarić, A., & Palacci,
J. A. (2023). Unconventional colloidal aggregation in chiral bacterial baths.
Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02136-x
chicago: Grober, Daniel, Ivan Palaia, Mehmet C Ucar, Edouard B Hannezo, Anđela Šarić,
and Jérémie A Palacci. “Unconventional Colloidal Aggregation in Chiral Bacterial
Baths.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02136-x.
ieee: D. Grober, I. Palaia, M. C. Ucar, E. B. Hannezo, A. Šarić, and J. A. Palacci,
“Unconventional colloidal aggregation in chiral bacterial baths,” Nature Physics,
vol. 19. Springer Nature, pp. 1680–1688, 2023.
ista: Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. 2023. Unconventional
colloidal aggregation in chiral bacterial baths. Nature Physics. 19, 1680–1688.
mla: Grober, Daniel, et al. “Unconventional Colloidal Aggregation in Chiral Bacterial
Baths.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1680–88, doi:10.1038/s41567-023-02136-x.
short: D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature
Physics 19 (2023) 1680–1688.
date_created: 2023-08-06T22:01:11Z
date_published: 2023-11-01T00:00:00Z
date_updated: 2024-01-30T12:26:55Z
day: '01'
ddc:
- '530'
department:
- _id: EdHa
- _id: AnSa
- _id: JePa
doi: 10.1038/s41567-023-02136-x
ec_funded: 1
external_id:
isi:
- '001037346400005'
file:
- access_level: open_access
checksum: 7e282c2ebc0ac82125a04f6b4742d4c1
content_type: application/pdf
creator: dernst
date_created: 2024-01-30T12:26:08Z
date_updated: 2024-01-30T12:26:08Z
file_id: '14906'
file_name: 2023_NaturePhysics_Grober.pdf
file_size: 6365607
relation: main_file
success: 1
file_date_updated: 2024-01-30T12:26:08Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
language:
- iso: eng
month: '11'
oa: 1
oa_version: Published Version
page: 1680-1688
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: 260C2330-B435-11E9-9278-68D0E5697425
call_identifier: H2020
grant_number: '754411'
name: ISTplus - Postdoctoral Fellowships
publication: Nature Physics
publication_identifier:
eissn:
- 1745-2481
issn:
- 1745-2473
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Unconventional colloidal aggregation in chiral bacterial baths
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: 19
year: '2023'
...
---
_id: '12705'
abstract:
- lang: eng
text: The elasticity of disordered and polydisperse polymer networks is a fundamental
problem of soft matter physics that is still open. Here, we self-assemble polymer
networks via simulations of a mixture of bivalent and tri- or tetravalent patchy
particles, which result in an exponential strand length distribution analogous
to that of experimental randomly cross-linked systems. After assembly, the network
connectivity and topology are frozen and the resulting system is characterized.
We find that the fractal structure of the network depends on the number density
at which the assembly has been carried out, but that systems with the same mean
valence and same assembly density have the same structural properties. Moreover,
we compute the long-time limit of the mean-squared displacement, also known as
the (squared) localization length, of the cross-links and of the middle monomers
of the strands, showing that the dynamics of long strands is well described by
the tube model. Finally, we find a relation connecting these two localization
lengths at high density and connect the cross-link localization length to the
shear modulus of the system.
acknowledgement: We thank Michael Lang for helpful discussions. We acknowledge financial
support from the European Research Council (ERC Consolidator Grant No. 681597, MIMIC)
and from LabEx NUMEV (Grant No. ANR-10-LABX-20) funded by the “Investissements d’Avenir”
French Government program, managed by the French National Research Agency (ANR).
W.K. is a senior member of the Institut Universitaire de France.
article_number: '074905'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Valerio
full_name: Sorichetti, Valerio
id: ef8a92cb-c7b6-11ec-8bea-e1fd5847bc5b
last_name: Sorichetti
orcid: 0000-0002-9645-6576
- first_name: Andrea
full_name: Ninarello, Andrea
last_name: Ninarello
- first_name: José
full_name: Ruiz-Franco, José
last_name: Ruiz-Franco
- first_name: Virginie
full_name: Hugouvieux, Virginie
last_name: Hugouvieux
- first_name: Emanuela
full_name: Zaccarelli, Emanuela
last_name: Zaccarelli
- first_name: Cristian
full_name: Micheletti, Cristian
last_name: Micheletti
- first_name: Walter
full_name: Kob, Walter
last_name: Kob
- first_name: Lorenzo
full_name: Rovigatti, Lorenzo
last_name: Rovigatti
citation:
ama: Sorichetti V, Ninarello A, Ruiz-Franco J, et al. Structure and elasticity of
model disordered, polydisperse, and defect-free polymer networks. Journal of
Chemical Physics. 2023;158(7). doi:10.1063/5.0134271
apa: Sorichetti, V., Ninarello, A., Ruiz-Franco, J., Hugouvieux, V., Zaccarelli,
E., Micheletti, C., … Rovigatti, L. (2023). Structure and elasticity of model
disordered, polydisperse, and defect-free polymer networks. Journal of Chemical
Physics. American Institute of Physics. https://doi.org/10.1063/5.0134271
chicago: Sorichetti, Valerio, Andrea Ninarello, José Ruiz-Franco, Virginie Hugouvieux,
Emanuela Zaccarelli, Cristian Micheletti, Walter Kob, and Lorenzo Rovigatti. “Structure
and Elasticity of Model Disordered, Polydisperse, and Defect-Free Polymer Networks.”
Journal of Chemical Physics. American Institute of Physics, 2023. https://doi.org/10.1063/5.0134271.
ieee: V. Sorichetti et al., “Structure and elasticity of model disordered,
polydisperse, and defect-free polymer networks,” Journal of Chemical Physics,
vol. 158, no. 7. American Institute of Physics, 2023.
ista: Sorichetti V, Ninarello A, Ruiz-Franco J, Hugouvieux V, Zaccarelli E, Micheletti
C, Kob W, Rovigatti L. 2023. Structure and elasticity of model disordered, polydisperse,
and defect-free polymer networks. Journal of Chemical Physics. 158(7), 074905.
mla: Sorichetti, Valerio, et al. “Structure and Elasticity of Model Disordered,
Polydisperse, and Defect-Free Polymer Networks.” Journal of Chemical Physics,
vol. 158, no. 7, 074905, American Institute of Physics, 2023, doi:10.1063/5.0134271.
short: V. Sorichetti, A. Ninarello, J. Ruiz-Franco, V. Hugouvieux, E. Zaccarelli,
C. Micheletti, W. Kob, L. Rovigatti, Journal of Chemical Physics 158 (2023).
date_created: 2023-03-05T23:01:05Z
date_published: 2023-02-21T00:00:00Z
date_updated: 2023-10-03T11:31:51Z
day: '21'
department:
- _id: AnSa
doi: 10.1063/5.0134271
external_id:
arxiv:
- '2211.04810'
isi:
- '000936943800002'
pmid:
- '36813705'
intvolume: ' 158'
isi: 1
issue: '7'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.48550/arXiv.2211.04810
month: '02'
oa: 1
oa_version: Preprint
pmid: 1
publication: Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: American Institute of Physics
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure and elasticity of model disordered, polydisperse, and defect-free
polymer networks
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 158
year: '2023'
...
---
_id: '12708'
abstract:
- lang: eng
text: Self-organisation is the spontaneous emergence of spatio-temporal structures
and patterns from the interaction of smaller individual units. Examples are found
across many scales in very different systems and scientific disciplines, from
physics, materials science and robotics to biology, geophysics and astronomy.
Recent research has highlighted how self-organisation can be both mediated and
controlled by confinement. Confinement is an action over a system that limits
its units’ translational and rotational degrees of freedom, thus also influencing
the system's phase space probability density; it can function as either a catalyst
or inhibitor of self-organisation. Confinement can then become a means to actively
steer the emergence or suppression of collective phenomena in space and time.
Here, to provide a common framework and perspective for future research, we examine
the role of confinement in the self-organisation of soft-matter systems and identify
overarching scientific challenges that need to be addressed to harness its full
scientific and technological potential in soft matter and related fields. By drawing
analogies with other disciplines, this framework will accelerate a common deeper
understanding of self-organisation and trigger the development of innovative strategies
to steer it using confinement, with impact on, e.g., the design of smarter materials,
tissue engineering for biomedicine and in guiding active matter.
acknowledgement: 'All authors are grateful to the Lorentz Center for providing a venue
for stimulating scientific discussions and to sponsor a workshop on the topic of
“Self-organisation under confinement” along with the 4TU Federation, the J. M. Burgers
Center for Fluid Dynamics and the MESA+ Institute for Nanotechnology at the University
of Twente. The authors are also grateful to Paolo Malgaretti, Federico Toschi, Twan
Wilting and Jaap den Toonder for valuable feedback. N. A. acknowledges financial
support from the Portuguese Foundation for Science and Technology (FCT) under Contracts
no. PTDC/FIS-MAC/28146/2017 (LISBOA-01-0145-FEDER-028146), UIDB/00618/2020, and
UIDP/00618/2020. L. M. C. J. acknowledges financial support from the Netherlands
Organisation for Scientific Research (NWO) through a START-UP, Physics Projectruimte,
and Vidi grant. I. C. was supported in part by a grant from by the Army Research
Office (ARO W911NF-18-1-0032) and the Cornell Center for Materials Research (DMR-1719875).
O. D. acknowledges funding by the Agence Nationale pour la Recherche under Grant
No ANR-18-CE33-0006 MSR. M. D. acknowledges financial support from the European
Research Council (Grant No. ERC-2019-ADV-H2020 884902 SoftML). W. M. D. acknowledges
funding from a BBSRC New Investigator Grant (BB/R018383/1). S. G. was supported
by DARPA Young Faculty Award # D19AP00046, and NSF IIS grant # 1955210. H. G. acknowledges
financial support from the Netherlands Organisation for Scientific Research (NWO)
through Veni Grant No. 680-47-451. R. G. acknowledges support from the Max Planck
School Matter to Life and the MaxSynBio Consortium, which are jointly funded by
the Federal Ministry of Education and Research (BMBF) of Germany, and the Max Planck
Society. L. I. acknowledges funding from the Horizon Europe ERC Consolidator Grant
ACTIVE_ ADAPTIVE (Grant No. 101001514). G. H. K. gratefully acknowledges the NWO
Talent Programme which is financed by the Dutch Research Council (project number
VI.C.182.004). H. L. and N. V. acknowledge funding from the Deutsche Forschungsgemeinschaft
(DFG) under grant numbers VO 1824/8-1 and LO 418/22-1. R. M. acknowledges funding
from the Deutsche Forschungsgemeinschaft (DFG) under grant number ME 1535/13-1 and
ME 1535/16-1. M. P. acknowledges funding from the Ramón y Cajal Program, grant no.
RYC-2018-02534, and the Leverhulme Trust, grant no. RPG-2018-345. A. Š. acknowledges
financial support from the European Research Council (Grant No. ERC-2018-STG-H2020
802960 NEPA). A. S. acknowledges funding from an ATTRACT Investigator Grant (No.
A17/MS/11572821/MBRACE) from the Luxembourg National Research Fund. C. S. acknowledges
funding from the French Agence Nationale pour la Recherche (ANR), grant ANR-14-CE090006
and ANR-12-BSV5001401, by the Fondation pour la Recherche Médicale (FRM), grant
DEQ20120323737, and from the PIC3I of Institut Curie, France. I. T. acknowledges
funding from grant IED2019-00058I/AEI/10.13039/501100011033. M. P. and I. T. also
acknowledge funding from grant PID2019-104232B-I00/AEI/10.13039/501100011033 and
from the H2020 MSCA ITN PHYMOT (Grant agreement No 95591). I. Z. acknowledges funding
from Project PID2020-114839GB-I00 MINECO/AEI/FEDER, UE. A. M. acknowledges funding
from the European Research Council, Starting Grant No. 678573 NanoPacks. G. V. acknowledges
sponsorship for this work by the US Office of Naval Research Global (Award No. N62909-18-1-2170).'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Nuno A.M.
full_name: Araújo, Nuno A.M.
last_name: Araújo
- first_name: Liesbeth M.C.
full_name: Janssen, Liesbeth M.C.
last_name: Janssen
- first_name: Thomas
full_name: Barois, Thomas
last_name: Barois
- first_name: Guido
full_name: Boffetta, Guido
last_name: Boffetta
- first_name: Itai
full_name: Cohen, Itai
last_name: Cohen
- first_name: Alessandro
full_name: Corbetta, Alessandro
last_name: Corbetta
- first_name: Olivier
full_name: Dauchot, Olivier
last_name: Dauchot
- first_name: Marjolein
full_name: Dijkstra, Marjolein
last_name: Dijkstra
- first_name: William M.
full_name: Durham, William M.
last_name: Durham
- first_name: Audrey
full_name: Dussutour, Audrey
last_name: Dussutour
- first_name: Simon
full_name: Garnier, Simon
last_name: Garnier
- first_name: Hanneke
full_name: Gelderblom, Hanneke
last_name: Gelderblom
- first_name: Ramin
full_name: Golestanian, Ramin
last_name: Golestanian
- first_name: Lucio
full_name: Isa, Lucio
last_name: Isa
- first_name: Gijsje H.
full_name: Koenderink, Gijsje H.
last_name: Koenderink
- first_name: Hartmut
full_name: Löwen, Hartmut
last_name: Löwen
- first_name: Ralf
full_name: Metzler, Ralf
last_name: Metzler
- first_name: Marco
full_name: Polin, Marco
last_name: Polin
- first_name: C. Patrick
full_name: Royall, C. Patrick
last_name: Royall
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Anupam
full_name: Sengupta, Anupam
last_name: Sengupta
- first_name: Cécile
full_name: Sykes, Cécile
last_name: Sykes
- first_name: Vito
full_name: Trianni, Vito
last_name: Trianni
- first_name: Idan
full_name: Tuval, Idan
last_name: Tuval
- first_name: Nicolas
full_name: Vogel, Nicolas
last_name: Vogel
- first_name: Julia M.
full_name: Yeomans, Julia M.
last_name: Yeomans
- first_name: Iker
full_name: Zuriguel, Iker
last_name: Zuriguel
- first_name: Alvaro
full_name: Marin, Alvaro
last_name: Marin
- first_name: Giorgio
full_name: Volpe, Giorgio
last_name: Volpe
citation:
ama: Araújo NAM, Janssen LMC, Barois T, et al. Steering self-organisation through
confinement. Soft Matter. 2023;19:1695-1704. doi:10.1039/d2sm01562e
apa: Araújo, N. A. M., Janssen, L. M. C., Barois, T., Boffetta, G., Cohen, I., Corbetta,
A., … Volpe, G. (2023). Steering self-organisation through confinement. Soft
Matter. Royal Society of Chemistry. https://doi.org/10.1039/d2sm01562e
chicago: Araújo, Nuno A.M., Liesbeth M.C. Janssen, Thomas Barois, Guido Boffetta,
Itai Cohen, Alessandro Corbetta, Olivier Dauchot, et al. “Steering Self-Organisation
through Confinement.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d2sm01562e.
ieee: N. A. M. Araújo et al., “Steering self-organisation through confinement,”
Soft Matter, vol. 19. Royal Society of Chemistry, pp. 1695–1704, 2023.
ista: Araújo NAM, Janssen LMC, Barois T, Boffetta G, Cohen I, Corbetta A, Dauchot
O, Dijkstra M, Durham WM, Dussutour A, Garnier S, Gelderblom H, Golestanian R,
Isa L, Koenderink GH, Löwen H, Metzler R, Polin M, Royall CP, Šarić A, Sengupta
A, Sykes C, Trianni V, Tuval I, Vogel N, Yeomans JM, Zuriguel I, Marin A, Volpe
G. 2023. Steering self-organisation through confinement. Soft Matter. 19, 1695–1704.
mla: Araújo, Nuno A. M., et al. “Steering Self-Organisation through Confinement.”
Soft Matter, vol. 19, Royal Society of Chemistry, 2023, pp. 1695–704, doi:10.1039/d2sm01562e.
short: N.A.M. Araújo, L.M.C. Janssen, T. Barois, G. Boffetta, I. Cohen, A. Corbetta,
O. Dauchot, M. Dijkstra, W.M. Durham, A. Dussutour, S. Garnier, H. Gelderblom,
R. Golestanian, L. Isa, G.H. Koenderink, H. Löwen, R. Metzler, M. Polin, C.P.
Royall, A. Šarić, A. Sengupta, C. Sykes, V. Trianni, I. Tuval, N. Vogel, J.M.
Yeomans, I. Zuriguel, A. Marin, G. Volpe, Soft Matter 19 (2023) 1695–1704.
date_created: 2023-03-05T23:01:06Z
date_published: 2023-02-06T00:00:00Z
date_updated: 2023-08-01T13:28:39Z
day: '06'
ddc:
- '540'
department:
- _id: AnSa
doi: 10.1039/d2sm01562e
ec_funded: 1
external_id:
arxiv:
- '2204.10059'
isi:
- '000940388100001'
file:
- access_level: open_access
checksum: af95aa18b9b01e32fb8f13477c0e2687
content_type: application/pdf
creator: cchlebak
date_created: 2023-03-07T09:19:41Z
date_updated: 2023-03-07T09:19:41Z
file_id: '12711'
file_name: 2023_SoftMatter_Araujo.pdf
file_size: 3581939
relation: main_file
success: 1
file_date_updated: 2023-03-07T09:19:41Z
has_accepted_license: '1'
intvolume: ' 19'
isi: 1
language:
- iso: eng
month: '02'
oa: 1
oa_version: Published Version
page: 1695-1704
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Soft Matter
publication_identifier:
eissn:
- 1744-6848
issn:
- 1744-683X
publication_status: published
publisher: Royal Society of Chemistry
quality_controlled: '1'
scopus_import: '1'
status: public
title: Steering self-organisation through confinement
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 19
year: '2023'
...
---
_id: '12756'
abstract:
- lang: eng
text: ESCRT-III family proteins form composite polymers that deform and cut membrane
tubes in the context of a wide range of cell biological processes across the tree
of life. In reconstituted systems, sequential changes in the composition of ESCRT-III
polymers induced by the AAA–adenosine triphosphatase Vps4 have been shown to remodel
membranes. However, it is not known how composite ESCRT-III polymers are organized
and remodeled in space and time in a cellular context. Taking advantage of the
relative simplicity of the ESCRT-III–dependent division system in Sulfolobus acidocaldarius,
one of the closest experimentally tractable prokaryotic relatives of eukaryotes,
we use super-resolution microscopy, electron microscopy, and computational modeling
to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III
division ring, which undergoes stepwise Vps4-dependent disassembly and contracts
to cut cells into two. These observations lead us to suggest sequential changes
in a patterned composite polymer as a general mechanism of ESCRT-III–dependent
membrane remodeling.
acknowledgement: "We thank Y. Liu and V. Hale for help with electron cryotomography;
the Medical Research Council (MRC) LMB Electron Microscopy Facility for access,
training, and support; and T. Darling and J. Grimmett at the MRC LMB for help with
computing infrastructure. We also thank the Flow Cytometry Facility and the MRC
LMB for training and support.\r\n F.H. and G.T.-R. were supported by a grant from
the Wellcome Trust (203276/Z/16/Z). A.C. was supported by an EMBO long-term fellowship:
ALTF_1041-2021. J.T. was supported by a grant from the VW Foundation (94933). A.A.P.
was supported by the Wellcome Trust (203276/Z/16/Z) and the HFSP (LT001027/2019).
B.B. received support from the MRC LMB, the Wellcome Trust (203276/Z/16/Z), the
VW Foundation (94933), the Life Sciences–Moore-Simons Foundation (735929LPI), and
a Gordon and Betty Moore Foundation’s Symbiosis in Aquatic Systems Initiative (9346).
A.Š. and X.J. acknowledge funding from the European Research Council (ERC) under
the European Union’s Horizon 2020 research and innovation programme (grant no. 802960).
L.H.-K. acknowledges support from Biotechnology and Biological Sciences Research
Council LIDo Programme. T.N. and J.L. were supported by the MRC (U105184326) and
the Wellcome Trust (203276/Z/16/Z)."
article_number: eade5224
article_processing_charge: No
article_type: original
author:
- first_name: Fredrik
full_name: Hurtig, Fredrik
last_name: Hurtig
- first_name: Thomas C.Q.
full_name: Burgers, Thomas C.Q.
last_name: Burgers
- first_name: Alice
full_name: Cezanne, Alice
last_name: Cezanne
- first_name: Xiuyun
full_name: Jiang, Xiuyun
last_name: Jiang
- first_name: Frank N.
full_name: Mol, Frank N.
last_name: Mol
- first_name: Jovan
full_name: Traparić, Jovan
last_name: Traparić
- first_name: Andre Arashiro
full_name: Pulschen, Andre Arashiro
last_name: Pulschen
- first_name: Tim
full_name: Nierhaus, Tim
last_name: Nierhaus
- first_name: Gabriel
full_name: Tarrason-Risa, Gabriel
last_name: Tarrason-Risa
- first_name: Lena
full_name: Harker-Kirschneck, Lena
last_name: Harker-Kirschneck
- first_name: Jan
full_name: Löwe, Jan
last_name: Löwe
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Rifka
full_name: Vlijm, Rifka
last_name: Vlijm
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
citation:
ama: Hurtig F, Burgers TCQ, Cezanne A, et al. The patterned assembly and stepwise
Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell
division. Science Advances. 2023;9(11). doi:10.1126/sciadv.ade5224
apa: Hurtig, F., Burgers, T. C. Q., Cezanne, A., Jiang, X., Mol, F. N., Traparić,
J., … Baum, B. (2023). The patterned assembly and stepwise Vps4-mediated disassembly
of composite ESCRT-III polymers drives archaeal cell division. Science Advances.
American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.ade5224
chicago: Hurtig, Fredrik, Thomas C.Q. Burgers, Alice Cezanne, Xiuyun Jiang, Frank
N. Mol, Jovan Traparić, Andre Arashiro Pulschen, et al. “The Patterned Assembly
and Stepwise Vps4-Mediated Disassembly of Composite ESCRT-III Polymers Drives
Archaeal Cell Division.” Science Advances. American Association for the
Advancement of Science, 2023. https://doi.org/10.1126/sciadv.ade5224.
ieee: F. Hurtig et al., “The patterned assembly and stepwise Vps4-mediated
disassembly of composite ESCRT-III polymers drives archaeal cell division,” Science
Advances, vol. 9, no. 11. American Association for the Advancement of Science,
2023.
ista: Hurtig F, Burgers TCQ, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA,
Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum
B. 2023. The patterned assembly and stepwise Vps4-mediated disassembly of composite
ESCRT-III polymers drives archaeal cell division. Science Advances. 9(11), eade5224.
mla: Hurtig, Fredrik, et al. “The Patterned Assembly and Stepwise Vps4-Mediated
Disassembly of Composite ESCRT-III Polymers Drives Archaeal Cell Division.” Science
Advances, vol. 9, no. 11, eade5224, American Association for the Advancement
of Science, 2023, doi:10.1126/sciadv.ade5224.
short: F. Hurtig, T.C.Q. Burgers, A. Cezanne, X. Jiang, F.N. Mol, J. Traparić, A.A.
Pulschen, T. Nierhaus, G. Tarrason-Risa, L. Harker-Kirschneck, J. Löwe, A. Šarić,
R. Vlijm, B. Baum, Science Advances 9 (2023).
date_created: 2023-03-26T22:01:06Z
date_published: 2023-03-17T00:00:00Z
date_updated: 2023-08-01T13:45:54Z
day: '17'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1126/sciadv.ade5224
ec_funded: 1
external_id:
isi:
- '000968083500010'
file:
- access_level: open_access
checksum: 6d7dbe9ed86a116c8a002d62971202c5
content_type: application/pdf
creator: dernst
date_created: 2023-03-27T06:24:49Z
date_updated: 2023-03-27T06:24:49Z
file_id: '12768'
file_name: 2023_ScienceAdvances_Hurtig.pdf
file_size: 1826471
relation: main_file
success: 1
file_date_updated: 2023-03-27T06:24:49Z
has_accepted_license: '1'
intvolume: ' 9'
isi: 1
issue: '11'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Science Advances
publication_identifier:
eissn:
- 2375-2548
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: The patterned assembly and stepwise Vps4-mediated disassembly of composite
ESCRT-III polymers drives archaeal cell division
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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 9
year: '2023'
...
---
_id: '11340'
abstract:
- lang: eng
text: Like-charge attraction, driven by ionic correlations, challenges our understanding
of electrostatics both in soft and hard matter. For two charged planar surfaces
confining counterions and water, we prove that, even at relatively low correlation
strength, the relevant physics is the ground-state one, oblivious of fluctuations.
Based on this, we derive a simple and accurate interaction pressure that fulfills
known exact requirements and can be used as an effective potential. We test this
equation against implicit-solvent Monte Carlo simulations and against explicit-solvent
simulations of cement and several types of clays. We argue that water destructuring
under nanometric confinement drastically reduces dielectric screening, enhancing
ionic correlations. Our equation of state at reduced permittivity therefore explains
the exotic attractive regime reported for these materials, even in the absence
of multivalent counterions.
acknowledgement: We thank Martin Trulsson for useful discussions and for providing
us with simulation data. This work has received funding from the European Union’s
Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie
grant agreement 674979-NANOTRANS. The support received from VEGA Grant No. 2/0092/21
is acknowledged.
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Abhay
full_name: Goyal, Abhay
last_name: Goyal
- first_name: Emanuela
full_name: Del Gado, Emanuela
last_name: Del Gado
- first_name: Ladislav
full_name: Šamaj, Ladislav
last_name: Šamaj
- first_name: Emmanuel
full_name: Trizac, Emmanuel
last_name: Trizac
citation:
ama: 'Palaia I, Goyal A, Del Gado E, Šamaj L, Trizac E. Like-charge attraction at
the nanoscale: Ground-state correlations and water destructuring. Journal of
Physical Chemistry B. 2022;126(16):3143-3149. doi:10.1021/acs.jpcb.2c00028'
apa: 'Palaia, I., Goyal, A., Del Gado, E., Šamaj, L., & Trizac, E. (2022). Like-charge
attraction at the nanoscale: Ground-state correlations and water destructuring.
Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.2c00028'
chicago: 'Palaia, Ivan, Abhay Goyal, Emanuela Del Gado, Ladislav Šamaj, and Emmanuel
Trizac. “Like-Charge Attraction at the Nanoscale: Ground-State Correlations and
Water Destructuring.” Journal of Physical Chemistry B. American Chemical
Society, 2022. https://doi.org/10.1021/acs.jpcb.2c00028.'
ieee: 'I. Palaia, A. Goyal, E. Del Gado, L. Šamaj, and E. Trizac, “Like-charge attraction
at the nanoscale: Ground-state correlations and water destructuring,” Journal
of Physical Chemistry B, vol. 126, no. 16. American Chemical Society, pp.
3143–3149, 2022.'
ista: 'Palaia I, Goyal A, Del Gado E, Šamaj L, Trizac E. 2022. Like-charge attraction
at the nanoscale: Ground-state correlations and water destructuring. Journal of
Physical Chemistry B. 126(16), 3143–3149.'
mla: 'Palaia, Ivan, et al. “Like-Charge Attraction at the Nanoscale: Ground-State
Correlations and Water Destructuring.” Journal of Physical Chemistry B,
vol. 126, no. 16, American Chemical Society, 2022, pp. 3143–49, doi:10.1021/acs.jpcb.2c00028.'
short: I. Palaia, A. Goyal, E. Del Gado, L. Šamaj, E. Trizac, Journal of Physical
Chemistry B 126 (2022) 3143–3149.
date_created: 2022-05-01T22:01:42Z
date_published: 2022-04-14T00:00:00Z
date_updated: 2023-08-03T06:42:50Z
day: '14'
department:
- _id: AnSa
doi: 10.1021/acs.jpcb.2c00028
external_id:
arxiv:
- '2203.10524'
isi:
- '000796953700022'
intvolume: ' 126'
isi: 1
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: ' https://doi.org/10.48550/arXiv.2203.10524'
month: '04'
oa: 1
oa_version: Preprint
page: 3143-3149
publication: Journal of Physical Chemistry B
publication_identifier:
eissn:
- 1520-5207
issn:
- 1520-6106
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Like-charge attraction at the nanoscale: Ground-state correlations and water
destructuring'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 126
year: '2022'
...
---
_id: '11400'
abstract:
- lang: eng
text: By varying the concentration of molecules in the cytoplasm or on the membrane,
cells can induce the formation of condensates and liquid droplets, similar to
phase separation. Their thermodynamics, much studied, depends on the mutual interactions
between microscopic constituents. Here, we focus on the kinetics and size control
of 2D clusters, forming on membranes. Using molecular dynamics of patchy colloids,
we model a system of two species of proteins, giving origin to specific heterotypic
bonds. We find that concentrations, together with valence and bond strength, control
both the size and the growth time rate of the clusters. In particular, if one
species is in large excess, it gradually saturates the binding sites of the other
species; the system then becomes kinetically arrested and cluster coarsening slows
down or stops, thus yielding effective size selection. This phenomenology is observed
both in solid and fluid clusters, which feature additional generic homotypic interactions
and are reminiscent of the ones observed on biological membranes.
acknowledgement: "The authors thank Longhui Zeng and Xiaolei Su (Yale University)
for bringing the topic to their attention and for useful comments. This work has
received funding from the European Research Council under the European Union’s Horizon\r\n2020
research and innovation program (ERC Grant No. 802960 and Marie Skłodowska-Curie
Grant No. 101034413). The authors are grateful to the UK Materials and Molecular
Modeling Hub for computational resources, which is partially funded by EPSRC (Grant
Nos. EP/P020194/1 and EP/T022213/1). The authors acknowledge support from ISTA and
from the Royal Society (Grant No. UF160266)."
article_number: '194902'
article_processing_charge: No
article_type: original
author:
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Palaia I, Šarić A. Controlling cluster size in 2D phase-separating binary mixtures
with specific interactions. The Journal of Chemical Physics. 2022;156(19).
doi:10.1063/5.0087769
apa: Palaia, I., & Šarić, A. (2022). Controlling cluster size in 2D phase-separating
binary mixtures with specific interactions. The Journal of Chemical Physics.
AIP Publishing. https://doi.org/10.1063/5.0087769
chicago: Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating
Binary Mixtures with Specific Interactions.” The Journal of Chemical Physics.
AIP Publishing, 2022. https://doi.org/10.1063/5.0087769.
ieee: I. Palaia and A. Šarić, “Controlling cluster size in 2D phase-separating binary
mixtures with specific interactions,” The Journal of Chemical Physics,
vol. 156, no. 19. AIP Publishing, 2022.
ista: Palaia I, Šarić A. 2022. Controlling cluster size in 2D phase-separating binary
mixtures with specific interactions. The Journal of Chemical Physics. 156(19),
194902.
mla: Palaia, Ivan, and Anđela Šarić. “Controlling Cluster Size in 2D Phase-Separating
Binary Mixtures with Specific Interactions.” The Journal of Chemical Physics,
vol. 156, no. 19, 194902, AIP Publishing, 2022, doi:10.1063/5.0087769.
short: I. Palaia, A. Šarić, The Journal of Chemical Physics 156 (2022).
date_created: 2022-05-22T17:04:48Z
date_published: 2022-05-16T00:00:00Z
date_updated: 2023-09-05T11:59:00Z
day: '16'
ddc:
- '540'
department:
- _id: AnSa
doi: 10.1063/5.0087769
ec_funded: 1
external_id:
isi:
- '000797236000004'
file:
- access_level: open_access
checksum: 7fada58059676a4bb0944b82247af740
content_type: application/pdf
creator: dernst
date_created: 2022-05-23T07:45:33Z
date_updated: 2022-05-23T07:45:33Z
file_id: '11405'
file_name: 2022_JourChemPhysics_Palaia.pdf
file_size: 6387208
relation: main_file
success: 1
file_date_updated: 2022-05-23T07:45:33Z
has_accepted_license: '1'
intvolume: ' 156'
isi: 1
issue: '19'
keyword:
- Physical and Theoretical Chemistry
- General Physics and Astronomy
language:
- iso: eng
month: '05'
oa: 1
oa_version: Published Version
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
publication: The Journal of Chemical Physics
publication_identifier:
eissn:
- 1089-7690
issn:
- 0021-9606
publication_status: published
publisher: AIP Publishing
quality_controlled: '1'
status: public
title: Controlling cluster size in 2D phase-separating binary mixtures with specific
interactions
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: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 156
year: '2022'
...
---
_id: '11841'
abstract:
- lang: eng
text: Primary nucleation is the fundamental event that initiates the conversion
of proteins from their normal physiological forms into pathological amyloid aggregates
associated with the onset and development of disorders including systemic amyloidosis,
as well as the neurodegenerative conditions Alzheimer’s and Parkinson’s diseases.
It has become apparent that the presence of surfaces can dramatically modulate
nucleation. However, the underlying physicochemical parameters governing this
process have been challenging to elucidate, with interfaces in some cases having
been found to accelerate aggregation, while in others they can inhibit the kinetics
of this process. Here we show through kinetic analysis that for three different
fibril-forming proteins, interfaces affect the aggregation reaction mainly through
modulating the primary nucleation step. Moreover, we show through direct measurements
of the Gibbs free energy of adsorption, combined with theory and coarse-grained
computer simulations, that overall nucleation rates are suppressed at high and
at low surface interaction strengths but significantly enhanced at intermediate
strengths, and we verify these regimes experimentally. Taken together, these results
provide a quantitative description of the fundamental process which triggers amyloid
formation and shed light on the key factors that control this process.
acknowledgement: "The research leading to these results has received funding from
the European Research Council (ERC) under the European Union’s Seventh Framework
Programme (FP7/2007-2013) through the ERC grant PhysProt\r\n(agreement 337969).
We are grateful for financial support from the Biotechnology and Biological Sciences
Research Council (BBSRC) (T.P.J.K.), the Newman\r\nFoundation (T.P.J.K.), the Wellcome
Trust (T.P.J.K. and M.V.), Peterhouse College\r\nCambridge (T.C.T.M.), the ERC Starting
Grant (StG) Non-Equilibrium Protein Assembly (NEPA) (A.S.), the Royal Society (A.S.),
the Academy of Medical Sciences\r\n(A.S. and J.K.), and the Cambridge Centre for
Misfolding Diseases (CMD)."
article_number: e2109718119
article_processing_charge: No
article_type: original
author:
- first_name: Zenon
full_name: Toprakcioglu, Zenon
last_name: Toprakcioglu
- first_name: Ayaka
full_name: Kamada, Ayaka
last_name: Kamada
- first_name: Thomas C.T.
full_name: Michaels, Thomas C.T.
last_name: Michaels
- first_name: Mengqi
full_name: Xie, Mengqi
last_name: Xie
- first_name: Johannes
full_name: Krausser, Johannes
last_name: Krausser
- first_name: Jiapeng
full_name: Wei, Jiapeng
last_name: Wei
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Michele
full_name: Vendruscolo, Michele
last_name: Vendruscolo
- first_name: Tuomas P.J.
full_name: Knowles, Tuomas P.J.
last_name: Knowles
citation:
ama: Toprakcioglu Z, Kamada A, Michaels TCT, et al. Adsorption free energy predicts
amyloid protein nucleation rates. Proceedings of the National Academy of Sciences
of the United States of America. 2022;119(31). doi:10.1073/pnas.2109718119
apa: Toprakcioglu, Z., Kamada, A., Michaels, T. C. T., Xie, M., Krausser, J., Wei,
J., … Knowles, T. P. J. (2022). Adsorption free energy predicts amyloid protein
nucleation rates. 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.2109718119
chicago: Toprakcioglu, Zenon, Ayaka Kamada, Thomas C.T. Michaels, Mengqi Xie, Johannes
Krausser, Jiapeng Wei, Anđela Šarić, Michele Vendruscolo, and Tuomas P.J. Knowles.
“Adsorption Free Energy Predicts Amyloid Protein Nucleation Rates.” 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.2109718119.
ieee: Z. Toprakcioglu et al., “Adsorption free energy predicts amyloid protein
nucleation rates,” Proceedings of the National Academy of Sciences of the United
States of America, vol. 119, no. 31. Proceedings of the National Academy of
Sciences, 2022.
ista: Toprakcioglu Z, Kamada A, Michaels TCT, Xie M, Krausser J, Wei J, Šarić A,
Vendruscolo M, Knowles TPJ. 2022. Adsorption free energy predicts amyloid protein
nucleation rates. Proceedings of the National Academy of Sciences of the United
States of America. 119(31), e2109718119.
mla: Toprakcioglu, Zenon, et al. “Adsorption Free Energy Predicts Amyloid Protein
Nucleation Rates.” Proceedings of the National Academy of Sciences of the United
States of America, vol. 119, no. 31, e2109718119, Proceedings of the National
Academy of Sciences, 2022, doi:10.1073/pnas.2109718119.
short: Z. Toprakcioglu, A. Kamada, T.C.T. Michaels, M. Xie, J. Krausser, J. Wei,
A. Šarić, M. Vendruscolo, T.P.J. Knowles, Proceedings of the National Academy
of Sciences of the United States of America 119 (2022).
date_created: 2022-08-14T22:01:45Z
date_published: 2022-07-28T00:00:00Z
date_updated: 2023-10-04T09:06:52Z
day: '28'
ddc:
- '570'
department:
- _id: AnSa
doi: 10.1073/pnas.2109718119
ec_funded: 1
external_id:
isi:
- '000903753500002'
file:
- access_level: open_access
checksum: 0fe3878896cbeb6c44e29222ec2f336a
content_type: application/pdf
creator: dernst
date_created: 2023-10-04T09:05:44Z
date_updated: 2023-10-04T09:05:44Z
file_id: '14386'
file_name: 2022_PNAS_Toprakcioglu.pdf
file_size: 2476021
relation: main_file
success: 1
file_date_updated: 2023-10-04T09:05:44Z
has_accepted_license: '1'
intvolume: ' 119'
isi: 1
issue: '31'
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
project:
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
publication: Proceedings of the National Academy of Sciences of the United States
of America
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Adsorption free energy predicts amyloid protein nucleation rates
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: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 119
year: '2022'
...
---
_id: '12108'
abstract:
- lang: eng
text: The sequential exchange of filament composition to increase filament curvature
was proposed as a mechanism for how some biological polymers deform and cut membranes.
The relationship between the filament composition and its mechanical effect is
lacking. We develop a kinetic model for the assembly of composite filaments that
includes protein–membrane adhesion, filament mechanics and membrane mechanics.
We identify the physical conditions for such a membrane remodeling and show this
mechanism of sequential polymer assembly lowers the energetic barrier for membrane
deformation.
acknowledgement: "We thank T. C. T. Michaels and J. Palacci for useful discussions.
We thank Claudia Flandoli for the illustrations in Fig. 1(b) and Fig. 2. We acknowledge
funding by the European Union’s Horizon 2020 Research and Innovation Programme under
the Marie Skłodowska-Curie Grant\r\nAgreement No. 101034413 (I. P.), the Royal Society
Grant No. UF160266 (A. Š.), the European Research Council under the European Union’s
Horizon 2020 Research and Innovation Programme (Grant No. 802960; B. M., I. P.,
and A. Š.), and the Volkswagen Foundation\r\nLife Grant (B. B. and A. Š). "
article_number: '268101'
article_processing_charge: No
article_type: original
author:
- first_name: Billie
full_name: Meadowcroft, Billie
id: a4725fd6-932b-11ed-81e2-c098c7f37ae1
last_name: Meadowcroft
- first_name: Ivan
full_name: Palaia, Ivan
id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa
last_name: Palaia
orcid: ' 0000-0002-8843-9485 '
- first_name: Anna Katharina
full_name: Pfitzner, Anna Katharina
last_name: Pfitzner
- first_name: Aurélien
full_name: Roux, Aurélien
last_name: Roux
- first_name: Buzz
full_name: Baum, Buzz
last_name: Baum
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
citation:
ama: Meadowcroft B, Palaia I, Pfitzner AK, Roux A, Baum B, Šarić A. Mechanochemical
rules for shape-shifting filaments that remodel membranes. Physical Review
Letters. 2022;129(26). doi:10.1103/PhysRevLett.129.268101
apa: Meadowcroft, B., Palaia, I., Pfitzner, A. K., Roux, A., Baum, B., & Šarić,
A. (2022). Mechanochemical rules for shape-shifting filaments that remodel membranes.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.129.268101
chicago: Meadowcroft, Billie, Ivan Palaia, Anna Katharina Pfitzner, Aurélien Roux,
Buzz Baum, and Anđela Šarić. “Mechanochemical Rules for Shape-Shifting Filaments
That Remodel Membranes.” Physical Review Letters. American Physical Society,
2022. https://doi.org/10.1103/PhysRevLett.129.268101.
ieee: B. Meadowcroft, I. Palaia, A. K. Pfitzner, A. Roux, B. Baum, and A. Šarić,
“Mechanochemical rules for shape-shifting filaments that remodel membranes,” Physical
Review Letters, vol. 129, no. 26. American Physical Society, 2022.
ista: Meadowcroft B, Palaia I, Pfitzner AK, Roux A, Baum B, Šarić A. 2022. Mechanochemical
rules for shape-shifting filaments that remodel membranes. Physical Review Letters.
129(26), 268101.
mla: Meadowcroft, Billie, et al. “Mechanochemical Rules for Shape-Shifting Filaments
That Remodel Membranes.” Physical Review Letters, vol. 129, no. 26, 268101,
American Physical Society, 2022, doi:10.1103/PhysRevLett.129.268101.
short: B. Meadowcroft, I. Palaia, A.K. Pfitzner, A. Roux, B. Baum, A. Šarić, Physical
Review Letters 129 (2022).
date_created: 2023-01-08T23:00:53Z
date_published: 2022-12-23T00:00:00Z
date_updated: 2023-08-03T14:10:59Z
day: '23'
department:
- _id: AnSa
doi: 10.1103/PhysRevLett.129.268101
ec_funded: 1
external_id:
isi:
- '000906721500001'
pmid:
- '36608212'
intvolume: ' 129'
isi: 1
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: 'https://doi.org/10.1101/2022.05.10.490642 '
month: '12'
oa: 1
oa_version: Preprint
pmid: 1
project:
- _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c
call_identifier: H2020
grant_number: '101034413'
name: 'IST-BRIDGE: International postdoctoral program'
- _id: eba2549b-77a9-11ec-83b8-a81e493eae4e
call_identifier: H2020
grant_number: '802960'
name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines'
- _id: eba0f67c-77a9-11ec-83b8-cc8501b3e222
grant_number: '96752'
name: 'The evolution of trafficking: from archaea to eukaryotes'
publication: Physical Review Letters
publication_identifier:
eissn:
- 1079-7114
issn:
- 0031-9007
publication_status: published
publisher: American Physical Society
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanochemical rules for shape-shifting filaments that remodel membranes
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 129
year: '2022'
...