---
_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. <i>Biophysical Journal</i>.
    2023;122(11):2311-2324. doi:<a href="https://doi.org/10.1016/j.bpj.2023.02.018">10.1016/j.bpj.2023.02.018</a>
  apa: Baldauf, L., Frey, F. F., Arribas Perez, M., Idema, T., &#38; Koenderink, G.
    H. (2023). Branched actin cortices reconstituted in vesicles sense membrane curvature.
    <i>Biophysical Journal</i>. Elsevier. <a href="https://doi.org/10.1016/j.bpj.2023.02.018">https://doi.org/10.1016/j.bpj.2023.02.018</a>
  chicago: Baldauf, Lucia, Felix F Frey, Marcos Arribas Perez, Timon Idema, and Gijsje
    H. Koenderink. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane
    Curvature.” <i>Biophysical Journal</i>. Elsevier, 2023. <a href="https://doi.org/10.1016/j.bpj.2023.02.018">https://doi.org/10.1016/j.bpj.2023.02.018</a>.
  ieee: L. Baldauf, F. F. Frey, M. Arribas Perez, T. Idema, and G. H. Koenderink,
    “Branched actin cortices reconstituted in vesicles sense membrane curvature,”
    <i>Biophysical Journal</i>, 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.” <i>Biophysical Journal</i>, vol. 122, no. 11, Elsevier, 2023,
    pp. 2311–24, doi:<a href="https://doi.org/10.1016/j.bpj.2023.02.018">10.1016/j.bpj.2023.02.018</a>.
  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: '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. <i>Biophysical Journal</i>.
    doi:<a href="https://doi.org/10.1016/j.bpj.2023.12.020">10.1016/j.bpj.2023.12.020</a>
  apa: Azadbakht, A., Meadowcroft, B., Majek, J., Šarić, A., &#38; Kraft, D. J. (n.d.).
    Nonadditivity in interactions between three membrane-wrapped colloidal spheres.
    <i>Biophysical Journal</i>. Elsevier. <a href="https://doi.org/10.1016/j.bpj.2023.12.020">https://doi.org/10.1016/j.bpj.2023.12.020</a>
  chicago: Azadbakht, Ali, Billie Meadowcroft, Juraj Majek, Anđela Šarić, and Daniela
    J. Kraft. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal
    Spheres.” <i>Biophysical Journal</i>. Elsevier, n.d. <a href="https://doi.org/10.1016/j.bpj.2023.12.020">https://doi.org/10.1016/j.bpj.2023.12.020</a>.
  ieee: A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, and D. J. Kraft, “Nonadditivity
    in interactions between three membrane-wrapped colloidal spheres,” <i>Biophysical
    Journal</i>. 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.” <i>Biophysical Journal</i>, Elsevier, doi:<a href="https://doi.org/10.1016/j.bpj.2023.12.020">10.1016/j.bpj.2023.12.020</a>.
  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: '10530'
abstract:
- lang: eng
  text: "Cell dispersion from a confined area is fundamental in a number of biological
    processes,\r\nincluding cancer metastasis. To date, a quantitative understanding
    of the interplay of single\r\ncell motility, cell proliferation, and intercellular
    contacts remains elusive. In particular, the role\r\nof E- and N-Cadherin junctions,
    central components of intercellular contacts, is still\r\ncontroversial. Combining
    theoretical modeling with in vitro observations, we investigate the\r\ncollective
    spreading behavior of colonies of human cancer cells (T24). The spreading of these\r\ncolonies
    is driven by stochastic single-cell migration with frequent transient cell-cell
    contacts.\r\nWe find that inhibition of E- and N-Cadherin junctions decreases
    colony spreading and average\r\nspreading velocities, without affecting the strength
    of correlations in spreading velocities of\r\nneighboring cells. Based on a biophysical
    simulation model for cell migration, we show that the\r\nbehavioral changes upon
    disruption of these junctions can be explained by reduced repulsive\r\nexcluded
    volume interactions between cells. This suggests that in cancer cell migration,\r\ncadherin-based
    intercellular contacts sharpen cell boundaries leading to repulsive rather than\r\ncohesive
    interactions between cells, thereby promoting efficient cell spreading during
    collective\r\nmigration.\r\n"
acknowledgement: Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research
  Foundation) - Project-ID 201269156 - SFB 1032 (Projects B8 and B12). D.B.B. is supported
  in part by a DFG fellowship within the Graduate School of Quantitative Biosciences
  Munich (QBM) and by the Joachim Herz Stiftung.
article_processing_charge: No
article_type: original
author:
- first_name: Themistoklis
  full_name: Zisis, Themistoklis
  last_name: Zisis
- first_name: David
  full_name: Brückner, David
  id: e1e86031-6537-11eb-953a-f7ab92be508d
  last_name: Brückner
  orcid: 0000-0001-7205-2975
- first_name: Tom
  full_name: Brandstätter, Tom
  last_name: Brandstätter
- first_name: Wei Xiong
  full_name: Siow, Wei Xiong
  last_name: Siow
- first_name: Joseph
  full_name: d’Alessandro, Joseph
  last_name: d’Alessandro
- first_name: Angelika M.
  full_name: Vollmar, Angelika M.
  last_name: Vollmar
- first_name: Chase P.
  full_name: Broedersz, Chase P.
  last_name: Broedersz
- first_name: Stefan
  full_name: Zahler, Stefan
  last_name: Zahler
citation:
  ama: Zisis T, Brückner D, Brandstätter T, et al. Disentangling cadherin-mediated
    cell-cell interactions in collective cancer cell migration. <i>Biophysical Journal</i>.
    2022;121(1):P44-60. doi:<a href="https://doi.org/10.1016/j.bpj.2021.12.006">10.1016/j.bpj.2021.12.006</a>
  apa: Zisis, T., Brückner, D., Brandstätter, T., Siow, W. X., d’Alessandro, J., Vollmar,
    A. M., … Zahler, S. (2022). Disentangling cadherin-mediated cell-cell interactions
    in collective cancer cell migration. <i>Biophysical Journal</i>. Elsevier. <a
    href="https://doi.org/10.1016/j.bpj.2021.12.006">https://doi.org/10.1016/j.bpj.2021.12.006</a>
  chicago: Zisis, Themistoklis, David Brückner, Tom Brandstätter, Wei Xiong Siow,
    Joseph d’Alessandro, Angelika M. Vollmar, Chase P. Broedersz, and Stefan Zahler.
    “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell
    Migration.” <i>Biophysical Journal</i>. Elsevier, 2022. <a href="https://doi.org/10.1016/j.bpj.2021.12.006">https://doi.org/10.1016/j.bpj.2021.12.006</a>.
  ieee: T. Zisis <i>et al.</i>, “Disentangling cadherin-mediated cell-cell interactions
    in collective cancer cell migration,” <i>Biophysical Journal</i>, vol. 121, no.
    1. Elsevier, pp. P44-60, 2022.
  ista: Zisis T, Brückner D, Brandstätter T, Siow WX, d’Alessandro J, Vollmar AM,
    Broedersz CP, Zahler S. 2022. Disentangling cadherin-mediated cell-cell interactions
    in collective cancer cell migration. Biophysical Journal. 121(1), P44-60.
  mla: Zisis, Themistoklis, et al. “Disentangling Cadherin-Mediated Cell-Cell Interactions
    in Collective Cancer Cell Migration.” <i>Biophysical Journal</i>, vol. 121, no.
    1, Elsevier, 2022, pp. P44-60, doi:<a href="https://doi.org/10.1016/j.bpj.2021.12.006">10.1016/j.bpj.2021.12.006</a>.
  short: T. Zisis, D. Brückner, T. Brandstätter, W.X. Siow, J. d’Alessandro, A.M.
    Vollmar, C.P. Broedersz, S. Zahler, Biophysical Journal 121 (2022) P44-60.
date_created: 2021-12-10T09:48:19Z
date_published: 2022-01-04T00:00:00Z
date_updated: 2023-08-02T13:34:25Z
day: '04'
ddc:
- '570'
department:
- _id: EdHa
- _id: GaTk
doi: 10.1016/j.bpj.2021.12.006
external_id:
  isi:
  - '000740815400007'
file:
- access_level: open_access
  checksum: 1aa7c3478e0c8256b973b632efd1f6b4
  content_type: application/pdf
  creator: dernst
  date_created: 2022-07-29T10:17:10Z
  date_updated: 2022-07-29T10:17:10Z
  file_id: '11697'
  file_name: 2022_BiophysicalJour_Zisis.pdf
  file_size: 4475504
  relation: main_file
  success: 1
file_date_updated: 2022-07-29T10:17:10Z
has_accepted_license: '1'
intvolume: '       121'
isi: 1
issue: '1'
keyword:
- Biophysics
language:
- iso: eng
month: '01'
oa: 1
oa_version: Published Version
page: P44-60
project:
- _id: 9B861AAC-BA93-11EA-9121-9846C619BF3A
  name: NOMIS Fellowship Program
publication: Biophysical Journal
publication_identifier:
  issn:
  - 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Disentangling cadherin-mediated cell-cell interactions in collective cancer
  cell migration
tmp:
  image: /images/cc_by_nc_nd.png
  legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International
    (CC BY-NC-ND 4.0)
  short: CC BY-NC-ND (4.0)
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 121
year: '2022'
...
---
_id: '9350'
abstract:
- lang: eng
  text: Intercellular adhesion is the key to multicellularity, and its malfunction
    plays an important role in various developmental and disease-related processes.
    Although it has been intensively studied by both biologists and physicists, a
    commonly accepted definition of cell-cell adhesion is still being debated. Cell-cell
    adhesion has been described at the molecular scale as a function of adhesion receptors
    controlling binding affinity, at the cellular scale as resistance to detachment
    forces or modulation of surface tension, and at the tissue scale as a regulator
    of cellular rearrangements and morphogenesis. In this review, we aim to summarize
    and discuss recent advances in the molecular, cellular, and theoretical description
    of cell-cell adhesion, ranging from biomimetic models to the complexity of cells
    and tissues in an organismal context. In particular, we will focus on cadherin-mediated
    cell-cell adhesion and the role of adhesion signaling and mechanosensation therein,
    two processes central for understanding the biological and physical basis of cell-cell
    adhesion.
acknowledgement: T.S. acknowledges funding by the research program “The Active Matter
  Physics of Collective Metastasis,” which is financed by the Dutch Research Council
  (NWO).
article_processing_charge: No
article_type: original
author:
- first_name: Feyza N
  full_name: Arslan, Feyza N
  id: 49DA7910-F248-11E8-B48F-1D18A9856A87
  last_name: Arslan
  orcid: 0000-0001-5809-9566
- first_name: Julia
  full_name: Eckert, Julia
  last_name: Eckert
- first_name: Thomas
  full_name: Schmidt, Thomas
  last_name: Schmidt
- first_name: Carl-Philipp J
  full_name: Heisenberg, Carl-Philipp J
  id: 39427864-F248-11E8-B48F-1D18A9856A87
  last_name: Heisenberg
  orcid: 0000-0002-0912-4566
citation:
  ama: 'Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. Holding it together: when
    cadherin meets cadherin. <i>Biophysical Journal</i>. 2021;120:4182-4192. doi:<a
    href="https://doi.org/10.1016/j.bpj.2021.03.025">10.1016/j.bpj.2021.03.025</a>'
  apa: 'Arslan, F. N., Eckert, J., Schmidt, T., &#38; Heisenberg, C.-P. J. (2021).
    Holding it together: when cadherin meets cadherin. <i>Biophysical Journal</i>.
    Biophysical Society. <a href="https://doi.org/10.1016/j.bpj.2021.03.025">https://doi.org/10.1016/j.bpj.2021.03.025</a>'
  chicago: 'Arslan, Feyza N, Julia Eckert, Thomas Schmidt, and Carl-Philipp J Heisenberg.
    “Holding It Together: When Cadherin Meets Cadherin.” <i>Biophysical Journal</i>.
    Biophysical Society, 2021. <a href="https://doi.org/10.1016/j.bpj.2021.03.025">https://doi.org/10.1016/j.bpj.2021.03.025</a>.'
  ieee: 'F. N. Arslan, J. Eckert, T. Schmidt, and C.-P. J. Heisenberg, “Holding it
    together: when cadherin meets cadherin,” <i>Biophysical Journal</i>, vol. 120.
    Biophysical Society, pp. 4182–4192, 2021.'
  ista: 'Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. 2021. Holding it together:
    when cadherin meets cadherin. Biophysical Journal. 120, 4182–4192.'
  mla: 'Arslan, Feyza N., et al. “Holding It Together: When Cadherin Meets Cadherin.”
    <i>Biophysical Journal</i>, vol. 120, Biophysical Society, 2021, pp. 4182–92,
    doi:<a href="https://doi.org/10.1016/j.bpj.2021.03.025">10.1016/j.bpj.2021.03.025</a>.'
  short: F.N. Arslan, J. Eckert, T. Schmidt, C.-P.J. Heisenberg, Biophysical Journal
    120 (2021) 4182–4192.
date_created: 2021-04-25T22:01:30Z
date_published: 2021-10-05T00:00:00Z
date_updated: 2023-08-08T13:14:10Z
day: '05'
department:
- _id: CaHe
doi: 10.1016/j.bpj.2021.03.025
external_id:
  isi:
  - '000704646900006'
  pmid:
  - '33794149'
intvolume: '       120'
isi: 1
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://scholarlypublications.universiteitleiden.nl/access/item%3A3251048/view
month: '10'
oa: 1
oa_version: Published Version
page: 4182-4192
pmid: 1
publication: Biophysical Journal
publication_identifier:
  eissn:
  - 1542-0086
  issn:
  - 0006-3495
publication_status: published
publisher: Biophysical Society
quality_controlled: '1'
related_material:
  record:
  - id: '12368'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: 'Holding it together: when cadherin meets cadherin'
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 120
year: '2021'
...
---
_id: '10338'
abstract:
- lang: eng
  text: In the nuclear pore complex, intrinsically disordered proteins (FG Nups),
    along with their interactions with more globular proteins called nuclear transport
    receptors (NTRs), are vital to the selectivity of transport into and out of the
    cell nucleus. Although such interactions can be modeled at different levels of
    coarse graining, in vitro experimental data have been quantitatively described
    by minimal models that describe FG Nups as cohesive homogeneous polymers and NTRs
    as uniformly cohesive spheres, in which the heterogeneous effects have been smeared
    out. By definition, these minimal models do not account for the explicit heterogeneities
    in FG Nup sequences, essentially a string of cohesive and noncohesive polymer
    units, and at the NTR surface. Here, we develop computational and analytical models
    that do take into account such heterogeneity in a minimal fashion and compare
    them with experimental data on single-molecule interactions between FG Nups and
    NTRs. Overall, we find that the heterogeneous nature of FG Nups and NTRs does
    play a role in determining equilibrium binding properties but is of much greater
    significance when it comes to unbinding and binding kinetics. Using our models,
    we predict how binding equilibria and kinetics depend on the distribution of cohesive
    blocks in the FG Nup sequences and of the binding pockets at the NTR surface,
    with multivalency playing a key role. Finally, we observe that single-molecule
    binding kinetics has a rather minor influence on the diffusion of NTRs in polymer
    melts consisting of FG-Nup-like sequences.
article_processing_charge: No
article_type: original
author:
- first_name: Luke K.
  full_name: Davis, Luke K.
  last_name: Davis
- first_name: Anđela
  full_name: Šarić, Anđela
  id: bf63d406-f056-11eb-b41d-f263a6566d8b
  last_name: Šarić
  orcid: 0000-0002-7854-2139
- first_name: Bart W.
  full_name: Hoogenboom, Bart W.
  last_name: Hoogenboom
- first_name: Anton
  full_name: Zilman, Anton
  last_name: Zilman
citation:
  ama: Davis LK, Šarić A, Hoogenboom BW, Zilman A. Physical modeling of multivalent
    interactions in the nuclear pore complex. <i>Biophysical Journal</i>. 2021;120(9):1565-1577.
    doi:<a href="https://doi.org/10.1016/j.bpj.2021.01.039">10.1016/j.bpj.2021.01.039</a>
  apa: Davis, L. K., Šarić, A., Hoogenboom, B. W., &#38; Zilman, A. (2021). Physical
    modeling of multivalent interactions in the nuclear pore complex. <i>Biophysical
    Journal</i>. Elsevier. <a href="https://doi.org/10.1016/j.bpj.2021.01.039">https://doi.org/10.1016/j.bpj.2021.01.039</a>
  chicago: Davis, Luke K., Anđela Šarić, Bart W. Hoogenboom, and Anton Zilman. “Physical
    Modeling of Multivalent Interactions in the Nuclear Pore Complex.” <i>Biophysical
    Journal</i>. Elsevier, 2021. <a href="https://doi.org/10.1016/j.bpj.2021.01.039">https://doi.org/10.1016/j.bpj.2021.01.039</a>.
  ieee: L. K. Davis, A. Šarić, B. W. Hoogenboom, and A. Zilman, “Physical modeling
    of multivalent interactions in the nuclear pore complex,” <i>Biophysical Journal</i>,
    vol. 120, no. 9. Elsevier, pp. 1565–1577, 2021.
  ista: Davis LK, Šarić A, Hoogenboom BW, Zilman A. 2021. Physical modeling of multivalent
    interactions in the nuclear pore complex. Biophysical Journal. 120(9), 1565–1577.
  mla: Davis, Luke K., et al. “Physical Modeling of Multivalent Interactions in the
    Nuclear Pore Complex.” <i>Biophysical Journal</i>, vol. 120, no. 9, Elsevier,
    2021, pp. 1565–77, doi:<a href="https://doi.org/10.1016/j.bpj.2021.01.039">10.1016/j.bpj.2021.01.039</a>.
  short: L.K. Davis, A. Šarić, B.W. Hoogenboom, A. Zilman, Biophysical Journal 120
    (2021) 1565–1577.
date_created: 2021-11-25T15:36:36Z
date_published: 2021-02-19T00:00:00Z
date_updated: 2022-04-01T10:34:38Z
day: '19'
doi: 10.1016/j.bpj.2021.01.039
extern: '1'
external_id:
  pmid:
  - '33617830'
intvolume: '       120'
issue: '9'
keyword:
- biophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/2020.10.01.322156
month: '02'
oa: 1
oa_version: Preprint
page: 1565-1577
pmid: 1
publication: Biophysical Journal
publication_identifier:
  issn:
  - 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Physical modeling of multivalent interactions in the nuclear pore complex
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2021'
...
---
_id: '10340'
abstract:
- lang: eng
  text: 'The cell membrane is an inhomogeneous system composed of phospholipids, sterols,
    carbohydrates, and proteins that can be directly attached to underlying cytoskeleton.
    The protein linkers between the membrane and the cytoskeleton are believed to
    have a profound effect on the mechanical properties of the cell membrane and its
    ability to reshape. Here, we investigate the role of membrane-cortex linkers on
    the extrusion of membrane tubes using computer simulations and experiments. In
    simulations, we find that the force for tube extrusion has a nonlinear dependence
    on the density of membrane-cortex attachments: at a range of low and intermediate
    linker densities, the force is not significantly influenced by the presence of
    the membrane-cortex attachments and resembles that of the bare membrane. For large
    concentrations of linkers, however, the force substantially increases compared
    with the bare membrane. In both cases, the linkers provided membrane tubes with
    increased stability against coalescence. We then pulled tubes from HEK cells using
    optical tweezers for varying expression levels of the membrane-cortex attachment
    protein Ezrin. In line with simulations, we observed that overexpression of Ezrin
    led to an increased extrusion force, while Ezrin depletion had a negligible effect
    on the force. Our results shed light on the importance of local protein rearrangements
    for membrane reshaping at nanoscopic scales.'
acknowledgement: We thank Ewa Paluch, Alba Diz-Muñoz, Guillaume Salbreux, Guillaume
  Charras, and Shiladitya Banerjee for helpful discussions. We acknowledge support
  from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the
  UCL Institute for the Physics of Living Systems (A.P., C.V.C., and A.Š.), the Royal
  Society (C.V.C. and A.Š.), and the European Research Council (Starting grant EP/R011818/1
  to A.Š.; E.C. and P.B. are partners of the advanced grant, project 339847) and from
  Institut Curie (E.C. and P.B.) and Centre National de la Recherche Scientifique
  (CNRS) (E.C. and P.B.). The P.B. and E.C. groups belong to Labex CelTisPhyBio (ANR-11-LABX0038)
  and to Paris Sciences et Lettres (ANR-10-IDEX-0001-02). T.L. received a PhD grant
  from Paris Sciences et Lettres Research University and support from the Institut
  Curie.
article_processing_charge: No
article_type: original
author:
- first_name: Alexandru
  full_name: Paraschiv, Alexandru
  last_name: Paraschiv
- first_name: Thibaut J.
  full_name: Lagny, Thibaut J.
  last_name: Lagny
- first_name: Christian Vanhille
  full_name: Campos, Christian Vanhille
  last_name: Campos
- first_name: Evelyne
  full_name: Coudrier, Evelyne
  last_name: Coudrier
- first_name: Patricia
  full_name: Bassereau, Patricia
  last_name: Bassereau
- first_name: Anđela
  full_name: Šarić, Anđela
  id: bf63d406-f056-11eb-b41d-f263a6566d8b
  last_name: Šarić
  orcid: 0000-0002-7854-2139
citation:
  ama: Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. Influence
    of membrane-cortex linkers on the extrusion of membrane tubes. <i>Biophysical
    Journal</i>. 2021;120(4):598-606. doi:<a href="https://doi.org/10.1016/j.bpj.2020.12.028">10.1016/j.bpj.2020.12.028</a>
  apa: Paraschiv, A., Lagny, T. J., Campos, C. V., Coudrier, E., Bassereau, P., &#38;
    Šarić, A. (2021). Influence of membrane-cortex linkers on the extrusion of membrane
    tubes. <i>Biophysical Journal</i>. Cell Press. <a href="https://doi.org/10.1016/j.bpj.2020.12.028">https://doi.org/10.1016/j.bpj.2020.12.028</a>
  chicago: Paraschiv, Alexandru, Thibaut J. Lagny, Christian Vanhille Campos, Evelyne
    Coudrier, Patricia Bassereau, and Anđela Šarić. “Influence of Membrane-Cortex
    Linkers on the Extrusion of Membrane Tubes.” <i>Biophysical Journal</i>. Cell
    Press, 2021. <a href="https://doi.org/10.1016/j.bpj.2020.12.028">https://doi.org/10.1016/j.bpj.2020.12.028</a>.
  ieee: A. Paraschiv, T. J. Lagny, C. V. Campos, E. Coudrier, P. Bassereau, and A.
    Šarić, “Influence of membrane-cortex linkers on the extrusion of membrane tubes,”
    <i>Biophysical Journal</i>, vol. 120, no. 4. Cell Press, pp. 598–606, 2021.
  ista: Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. 2021.
    Influence of membrane-cortex linkers on the extrusion of membrane tubes. Biophysical
    Journal. 120(4), 598–606.
  mla: Paraschiv, Alexandru, et al. “Influence of Membrane-Cortex Linkers on the Extrusion
    of Membrane Tubes.” <i>Biophysical Journal</i>, vol. 120, no. 4, Cell Press, 2021,
    pp. 598–606, doi:<a href="https://doi.org/10.1016/j.bpj.2020.12.028">10.1016/j.bpj.2020.12.028</a>.
  short: A. Paraschiv, T.J. Lagny, C.V. Campos, E. Coudrier, P. Bassereau, A. Šarić,
    Biophysical Journal 120 (2021) 598–606.
date_created: 2021-11-25T16:18:23Z
date_published: 2021-01-16T00:00:00Z
date_updated: 2022-04-01T10:38:01Z
day: '16'
doi: 10.1016/j.bpj.2020.12.028
extern: '1'
external_id:
  pmid:
  - '33460596'
intvolume: '       120'
issue: '4'
keyword:
- biophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1101/2020.07.28.224741
month: '01'
oa: 1
oa_version: Preprint
page: 598-606
pmid: 1
publication: Biophysical Journal
publication_identifier:
  issn:
  - 0006-3495
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Influence of membrane-cortex linkers on the extrusion of membrane tubes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 120
year: '2021'
...
---
_id: '10346'
abstract:
- lang: eng
  text: One of the most robust examples of self-assembly in living organisms is the
    formation of collagen architectures. Collagen type I molecules are a crucial component
    of the extracellular matrix, where they self-assemble into fibrils of well-defined
    axial striped patterns. This striped fibrillar pattern is preserved across the
    animal kingdom and is important for the determination of cell phenotype, cell
    adhesion, and tissue regulation and signaling. The understanding of the physical
    processes that determine such a robust morphology of self-assembled collagen fibrils
    is currently almost completely missing. Here, we develop a minimal coarse-grained
    computational model to identify the physical principles of the assembly of collagen-mimetic
    molecules. We find that screened electrostatic interactions can drive the formation
    of collagen-like filaments of well-defined striped morphologies. The fibril axial
    pattern is determined solely by the distribution of charges on the molecule and
    is robust to the changes in protein concentration, monomer rigidity, and environmental
    conditions. We show that the striped fibrillar pattern cannot be easily predicted
    from the interactions between two monomers but is an emergent result of multibody
    interactions. Our results can help address collagen remodeling in diseases and
    aging and guide the design of collagen scaffolds for biotechnological applications.
acknowledgement: We thank Melinda Duer, Patrick Mesquida, Lucy Colwell, Lucie Liu,
  Daan Frenkel, and Ivan Palaia for helpful discussions. We acknowledge support from
  the Engineering and Physical Sciences Research Council (A.E.H., L.K.D., and A.Š.),
  Biotechnology and Biological Sciences Research Council LIDo programme (N.G.G. and
  C.A.B.), the Royal Society (A.Š.), and the UK Materials and Molecular Modelling
  Hub for computational resources, which is partially funded by EPSRC ( EP/P020194/1).
article_processing_charge: No
article_type: original
author:
- first_name: Anne E.
  full_name: Hafner, Anne E.
  last_name: Hafner
- first_name: Noemi G.
  full_name: Gyori, Noemi G.
  last_name: Gyori
- first_name: Ciaran A.
  full_name: Bench, Ciaran A.
  last_name: Bench
- first_name: Luke K.
  full_name: Davis, Luke K.
  last_name: Davis
- first_name: Anđela
  full_name: Šarić, Anđela
  id: bf63d406-f056-11eb-b41d-f263a6566d8b
  last_name: Šarić
  orcid: 0000-0002-7854-2139
citation:
  ama: Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. Modeling fibrillogenesis
    of collagen-mimetic molecules. <i>Biophysical Journal</i>. 2020;119(9):1791-1799.
    doi:<a href="https://doi.org/10.1016/j.bpj.2020.09.013">10.1016/j.bpj.2020.09.013</a>
  apa: Hafner, A. E., Gyori, N. G., Bench, C. A., Davis, L. K., &#38; Šarić, A. (2020).
    Modeling fibrillogenesis of collagen-mimetic molecules. <i>Biophysical Journal</i>.
    Cell Press. <a href="https://doi.org/10.1016/j.bpj.2020.09.013">https://doi.org/10.1016/j.bpj.2020.09.013</a>
  chicago: Hafner, Anne E., Noemi G. Gyori, Ciaran A. Bench, Luke K. Davis, and Anđela
    Šarić. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” <i>Biophysical
    Journal</i>. Cell Press, 2020. <a href="https://doi.org/10.1016/j.bpj.2020.09.013">https://doi.org/10.1016/j.bpj.2020.09.013</a>.
  ieee: A. E. Hafner, N. G. Gyori, C. A. Bench, L. K. Davis, and A. Šarić, “Modeling
    fibrillogenesis of collagen-mimetic molecules,” <i>Biophysical Journal</i>, vol.
    119, no. 9. Cell Press, pp. 1791–1799, 2020.
  ista: Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. 2020. Modeling fibrillogenesis
    of collagen-mimetic molecules. Biophysical Journal. 119(9), 1791–1799.
  mla: Hafner, Anne E., et al. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.”
    <i>Biophysical Journal</i>, vol. 119, no. 9, Cell Press, 2020, pp. 1791–99, doi:<a
    href="https://doi.org/10.1016/j.bpj.2020.09.013">10.1016/j.bpj.2020.09.013</a>.
  short: A.E. Hafner, N.G. Gyori, C.A. Bench, L.K. Davis, A. Šarić, Biophysical Journal
    119 (2020) 1791–1799.
date_created: 2021-11-26T07:27:24Z
date_published: 2020-09-23T00:00:00Z
date_updated: 2021-11-26T07:45:24Z
day: '23'
doi: 10.1016/j.bpj.2020.09.013
extern: '1'
external_id:
  pmid:
  - '33049216'
intvolume: '       119'
issue: '9'
keyword:
- biophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.biorxiv.org/content/10.1101/2020.06.08.140061v1
month: '09'
oa: 1
oa_version: Published Version
page: 1791-1799
pmid: 1
publication: Biophysical Journal
publication_identifier:
  issn:
  - 0006-3495
publication_status: published
publisher: Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Modeling fibrillogenesis of collagen-mimetic molecules
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 119
year: '2020'
...
---
_id: '8444'
abstract:
- lang: eng
  text: Biophysical investigation of membrane proteins generally requires their extraction
    from native sources using detergents, a step that can lead, possibly irreversibly,
    to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent
    widely utilized in NMR studies of membrane proteins, to distort their structure
    has been the subject of much controversy. It has been recently proposed that the
    binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward
    cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment
    in which to study membrane proteins. In this communication, we used all-atom molecular
    dynamics simulations to investigate the specific binding of cardiolipins to yAAC3.
    Our data demonstrate that the interaction interface observed in a native-like
    environment differs markedly from that inferred from an NMR investigation in DPC,
    implying that in this detergent, the protein structure is distorted. We further
    investigated yAAC3 solubilized in DPC and in the milder dodecylmaltoside with
    thermal-shift assays. The loss of thermal transition observed in DPC confirms
    that the protein is no longer properly folded in this environment.
article_processing_charge: No
article_type: original
author:
- first_name: François
  full_name: Dehez, François
  last_name: Dehez
- first_name: Paul
  full_name: Schanda, Paul
  id: 7B541462-FAF6-11E9-A490-E8DFE5697425
  last_name: Schanda
  orcid: 0000-0002-9350-7606
- first_name: Martin S.
  full_name: King, Martin S.
  last_name: King
- first_name: Edmund R.S.
  full_name: Kunji, Edmund R.S.
  last_name: Kunji
- first_name: Christophe
  full_name: Chipot, Christophe
  last_name: Chipot
citation:
  ama: Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. Mitochondrial ADP/ATP carrier
    in dodecylphosphocholine binds cardiolipins with non-native affinity. <i>Biophysical
    Journal</i>. 2017;113(11):2311-2315. doi:<a href="https://doi.org/10.1016/j.bpj.2017.09.019">10.1016/j.bpj.2017.09.019</a>
  apa: Dehez, F., Schanda, P., King, M. S., Kunji, E. R. S., &#38; Chipot, C. (2017).
    Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with
    non-native affinity. <i>Biophysical Journal</i>. Elsevier. <a href="https://doi.org/10.1016/j.bpj.2017.09.019">https://doi.org/10.1016/j.bpj.2017.09.019</a>
  chicago: Dehez, François, Paul Schanda, Martin S. King, Edmund R.S. Kunji, and Christophe
    Chipot. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins
    with Non-Native Affinity.” <i>Biophysical Journal</i>. Elsevier, 2017. <a href="https://doi.org/10.1016/j.bpj.2017.09.019">https://doi.org/10.1016/j.bpj.2017.09.019</a>.
  ieee: F. Dehez, P. Schanda, M. S. King, E. R. S. Kunji, and C. Chipot, “Mitochondrial
    ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity,”
    <i>Biophysical Journal</i>, vol. 113, no. 11. Elsevier, pp. 2311–2315, 2017.
  ista: Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. 2017. Mitochondrial ADP/ATP
    carrier in dodecylphosphocholine binds cardiolipins with non-native affinity.
    Biophysical Journal. 113(11), 2311–2315.
  mla: Dehez, François, et al. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine
    Binds Cardiolipins with Non-Native Affinity.” <i>Biophysical Journal</i>, vol.
    113, no. 11, Elsevier, 2017, pp. 2311–15, doi:<a href="https://doi.org/10.1016/j.bpj.2017.09.019">10.1016/j.bpj.2017.09.019</a>.
  short: F. Dehez, P. Schanda, M.S. King, E.R.S. Kunji, C. Chipot, Biophysical Journal
    113 (2017) 2311–2315.
date_created: 2020-09-18T10:05:54Z
date_published: 2017-12-05T00:00:00Z
date_updated: 2021-01-12T08:19:18Z
day: '05'
doi: 10.1016/j.bpj.2017.09.019
extern: '1'
intvolume: '       113'
issue: '11'
keyword:
- Biophysics
language:
- iso: eng
month: '12'
oa_version: None
page: 2311-2315
publication: Biophysical Journal
publication_identifier:
  issn:
  - 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with
  non-native affinity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2017'
...
---
_id: '14308'
abstract:
- lang: eng
  text: Here we describe an approach to bottom-up fabrication with nanometer-precision
    that allows integrating the functional diversity of proteins in designed three-dimensional
    structural frameworks. We reimagined the successful DNA origami design principle
    using a set of custom staple proteins to fold a double-stranded DNA template into
    a user-defined shape. Each staple protein recognizes two distinct double-helical
    DNA sequences and can carry additional functionalities. The staple proteins we
    present here are based on the transcription activator-like (TAL) effector proteins.
    Due to their repetitive structure these proteins offer a unique programmability
    that enables us to construct numerous staple proteins targeting any desired DNA
    sequence. Our approach is general, meaning that many different objects may be
    created using the same set of rules, and it is modular, because components can
    be modified or exchanged individually. We present rules for constructing megadalton-scale
    DNA-protein hybrid nanostructures; introduce important structural motifs, such
    as curvature, corners, and vertices; describe principles for creating multi-layer
    DNA-protein objects with enhanced rigidity; and demonstrate the possibility to
    combine our DNA-protein hybrid origami with conventional DNA nanotechnology. Since
    all components can be encoded genetically, our structures should be amenable to
    biotechnological mass-production. Moreover, since the target objects can self-assemble
    at room temperature in near-physiological buffer, our hybrid origami may also
    provide an attractive method to realize positioning and scaffolding tasks in vivo.
    We expect our method to find application both in scaffolding protein functionalities
    and in manipulating the spatial arrangement of genomic DNA.
article_number: 25a
article_processing_charge: No
article_type: original
author:
- first_name: Florian M
  full_name: Praetorius, Florian M
  id: dfec9381-4341-11ee-8fd8-faa02bba7d62
  last_name: Praetorius
- first_name: Hendrik
  full_name: Dietz, Hendrik
  last_name: Dietz
citation:
  ama: Praetorius FM, Dietz H. Genetically encoded DNA-protein hybrid origami. <i>Biophysical
    Journal</i>. 2017;112(3). doi:<a href="https://doi.org/10.1016/j.bpj.2016.11.171">10.1016/j.bpj.2016.11.171</a>
  apa: Praetorius, F. M., &#38; Dietz, H. (2017). Genetically encoded DNA-protein
    hybrid origami. <i>Biophysical Journal</i>. Elsevier. <a href="https://doi.org/10.1016/j.bpj.2016.11.171">https://doi.org/10.1016/j.bpj.2016.11.171</a>
  chicago: Praetorius, Florian M, and Hendrik Dietz. “Genetically Encoded DNA-Protein
    Hybrid Origami.” <i>Biophysical Journal</i>. Elsevier, 2017. <a href="https://doi.org/10.1016/j.bpj.2016.11.171">https://doi.org/10.1016/j.bpj.2016.11.171</a>.
  ieee: F. M. Praetorius and H. Dietz, “Genetically encoded DNA-protein hybrid origami,”
    <i>Biophysical Journal</i>, vol. 112, no. 3. Elsevier, 2017.
  ista: Praetorius FM, Dietz H. 2017. Genetically encoded DNA-protein hybrid origami.
    Biophysical Journal. 112(3), 25a.
  mla: Praetorius, Florian M., and Hendrik Dietz. “Genetically Encoded DNA-Protein
    Hybrid Origami.” <i>Biophysical Journal</i>, vol. 112, no. 3, 25a, Elsevier, 2017,
    doi:<a href="https://doi.org/10.1016/j.bpj.2016.11.171">10.1016/j.bpj.2016.11.171</a>.
  short: F.M. Praetorius, H. Dietz, Biophysical Journal 112 (2017).
date_created: 2023-09-06T13:19:10Z
date_published: 2017-02-03T00:00:00Z
date_updated: 2023-11-07T11:28:58Z
day: '03'
doi: 10.1016/j.bpj.2016.11.171
extern: '1'
intvolume: '       112'
issue: '3'
keyword:
- Biophysics
language:
- iso: eng
month: '02'
oa_version: None
publication: Biophysical Journal
publication_identifier:
  issn:
  - 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetically encoded DNA-protein hybrid origami
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 112
year: '2017'
...
---
_id: '10126'
article_number: 391a
article_processing_charge: No
article_type: letter_note
author:
- first_name: Afshin
  full_name: Vahid Belarghou, Afshin
  last_name: Vahid Belarghou
- first_name: Anđela
  full_name: Šarić, Anđela
  id: bf63d406-f056-11eb-b41d-f263a6566d8b
  last_name: Šarić
  orcid: 0000-0002-7854-2139
- first_name: Timon
  full_name: Idema, Timon
  last_name: Idema
citation:
  ama: Vahid Belarghou A, Šarić A, Idema T. Curvature mediated interactions in highly
    curved membranes. <i>Biophysical Journal</i>. 2017;112(3). doi:<a href="https://doi.org/10.1016/j.bpj.2016.11.2123">10.1016/j.bpj.2016.11.2123</a>
  apa: Vahid Belarghou, A., Šarić, A., &#38; Idema, T. (2017). Curvature mediated
    interactions in highly curved membranes. <i>Biophysical Journal</i>. Elsevier
    . <a href="https://doi.org/10.1016/j.bpj.2016.11.2123">https://doi.org/10.1016/j.bpj.2016.11.2123</a>
  chicago: Vahid Belarghou, Afshin, Anđela Šarić, and Timon Idema. “Curvature Mediated
    Interactions in Highly Curved Membranes.” <i>Biophysical Journal</i>. Elsevier
    , 2017. <a href="https://doi.org/10.1016/j.bpj.2016.11.2123">https://doi.org/10.1016/j.bpj.2016.11.2123</a>.
  ieee: A. Vahid Belarghou, A. Šarić, and T. Idema, “Curvature mediated interactions
    in highly curved membranes,” <i>Biophysical Journal</i>, vol. 112, no. 3. Elsevier
    , 2017.
  ista: Vahid Belarghou A, Šarić A, Idema T. 2017. Curvature mediated interactions
    in highly curved membranes. Biophysical Journal. 112(3), 391a.
  mla: Vahid Belarghou, Afshin, et al. “Curvature Mediated Interactions in Highly
    Curved Membranes.” <i>Biophysical Journal</i>, vol. 112, no. 3, 391a, Elsevier
    , 2017, doi:<a href="https://doi.org/10.1016/j.bpj.2016.11.2123">10.1016/j.bpj.2016.11.2123</a>.
  short: A. Vahid Belarghou, A. Šarić, T. Idema, Biophysical Journal 112 (2017).
date_created: 2021-10-12T07:47:55Z
date_published: 2017-02-03T00:00:00Z
date_updated: 2021-11-03T10:02:45Z
day: '03'
doi: 10.1016/j.bpj.2016.11.2123
extern: '1'
intvolume: '       112'
issue: '3'
keyword:
- biophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.cell.com/biophysj/fulltext/S0006-3495(16)33153-8
month: '02'
oa: 1
oa_version: Published Version
publication: Biophysical Journal
publication_identifier:
  issn:
  - 0006-3495
publication_status: published
publisher: 'Elsevier '
quality_controlled: '1'
status: public
title: Curvature mediated interactions in highly curved membranes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 112
year: '2017'
...
---
_id: '11088'
abstract:
- lang: eng
  text: 'The crowded intracellular environment poses a formidable challenge to experimental
    and theoretical analyses of intracellular transport mechanisms. Our measurements
    of single-particle trajectories in cytoplasm and their random-walk interpretations
    elucidate two of these mechanisms: molecular diffusion in crowded environments
    and cytoskeletal transport along microtubules. We employed acousto-optic deflector
    microscopy to map out the three-dimensional trajectories of microspheres migrating
    in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM),
    continuous time random walk, and fractional BM were alternatively used to represent
    these trajectories. The comparison of the experimental and numerical data demonstrates
    that cytoskeletal transport along microtubules and diffusion in the cytosolic
    fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct
    signatures. Among the three random-walk models used, continuous time random walk
    provides the best representation of diffusion, whereas microtubular transport
    is accurately modeled with fractional BM.'
article_processing_charge: No
article_type: original
author:
- first_name: Benjamin M.
  full_name: Regner, Benjamin M.
  last_name: Regner
- first_name: Dejan
  full_name: Vučinić, Dejan
  last_name: Vučinić
- first_name: Cristina
  full_name: Domnisoru, Cristina
  last_name: Domnisoru
- first_name: Thomas M.
  full_name: Bartol, Thomas M.
  last_name: Bartol
- first_name: Martin W
  full_name: HETZER, Martin W
  id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
  last_name: HETZER
  orcid: 0000-0002-2111-992X
- first_name: Daniel M.
  full_name: Tartakovsky, Daniel M.
  last_name: Tartakovsky
- first_name: Terrence J.
  full_name: Sejnowski, Terrence J.
  last_name: Sejnowski
citation:
  ama: Regner BM, Vučinić D, Domnisoru C, et al. Anomalous diffusion of single particles
    in cytoplasm. <i>Biophysical Journal</i>. 2013;104(8):1652-1660. doi:<a href="https://doi.org/10.1016/j.bpj.2013.01.049">10.1016/j.bpj.2013.01.049</a>
  apa: Regner, B. M., Vučinić, D., Domnisoru, C., Bartol, T. M., Hetzer, M., Tartakovsky,
    D. M., &#38; Sejnowski, T. J. (2013). Anomalous diffusion of single particles
    in cytoplasm. <i>Biophysical Journal</i>. Elsevier. <a href="https://doi.org/10.1016/j.bpj.2013.01.049">https://doi.org/10.1016/j.bpj.2013.01.049</a>
  chicago: Regner, Benjamin M., Dejan Vučinić, Cristina Domnisoru, Thomas M. Bartol,
    Martin Hetzer, Daniel M. Tartakovsky, and Terrence J. Sejnowski. “Anomalous Diffusion
    of Single Particles in Cytoplasm.” <i>Biophysical Journal</i>. Elsevier, 2013.
    <a href="https://doi.org/10.1016/j.bpj.2013.01.049">https://doi.org/10.1016/j.bpj.2013.01.049</a>.
  ieee: B. M. Regner <i>et al.</i>, “Anomalous diffusion of single particles in cytoplasm,”
    <i>Biophysical Journal</i>, vol. 104, no. 8. Elsevier, pp. 1652–1660, 2013.
  ista: Regner BM, Vučinić D, Domnisoru C, Bartol TM, Hetzer M, Tartakovsky DM, Sejnowski
    TJ. 2013. Anomalous diffusion of single particles in cytoplasm. Biophysical Journal.
    104(8), 1652–1660.
  mla: Regner, Benjamin M., et al. “Anomalous Diffusion of Single Particles in Cytoplasm.”
    <i>Biophysical Journal</i>, vol. 104, no. 8, Elsevier, 2013, pp. 1652–60, doi:<a
    href="https://doi.org/10.1016/j.bpj.2013.01.049">10.1016/j.bpj.2013.01.049</a>.
  short: B.M. Regner, D. Vučinić, C. Domnisoru, T.M. Bartol, M. Hetzer, D.M. Tartakovsky,
    T.J. Sejnowski, Biophysical Journal 104 (2013) 1652–1660.
date_created: 2022-04-07T07:51:26Z
date_published: 2013-04-16T00:00:00Z
date_updated: 2022-07-18T08:51:01Z
day: '16'
doi: 10.1016/j.bpj.2013.01.049
extern: '1'
external_id:
  pmid:
  - '23601312'
intvolume: '       104'
issue: '8'
keyword:
- Biophysics
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1016/j.bpj.2013.01.049
month: '04'
oa: 1
oa_version: Published Version
page: 1652-1660
pmid: 1
publication: Biophysical Journal
publication_identifier:
  issn:
  - 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Anomalous diffusion of single particles in cytoplasm
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 104
year: '2013'
...
---
_id: '6496'
abstract:
- lang: eng
  text: We report the switching behavior of the full bacterial flagellum system that
    includes the filament and the motor in wild-type Escherichia coli cells. In sorting
    the motor behavior by the clockwise bias, we find that the distributions of the
    clockwise (CW) and counterclockwise (CCW) intervals are either exponential or
    nonexponential with long tails. At low bias, CW intervals are exponentially distributed
    and CCW intervals exhibit long tails. At intermediate CW bias (0.5) both CW and
    CCW intervals are mainly exponentially distributed. A simple model suggests that
    these two distinct switching behaviors are governed by the presence of signaling
    noise within the chemotaxis network. Low noise yields exponentially distributed
    intervals, whereas large noise yields nonexponential behavior with long tails.
    These drastically different motor statistics may play a role in optimizing bacterial
    behavior for a wide range of environmental conditions.
article_processing_charge: No
author:
- first_name: Heungwon
  full_name: Park, Heungwon
  last_name: Park
- first_name: Panos
  full_name: Oikonomou, Panos
  last_name: Oikonomou
- first_name: Calin C
  full_name: Guet, Calin C
  id: 47F8433E-F248-11E8-B48F-1D18A9856A87
  last_name: Guet
  orcid: 0000-0001-6220-2052
- first_name: Philippe
  full_name: Cluzel, Philippe
  last_name: Cluzel
citation:
  ama: Park H, Oikonomou P, Guet CC, Cluzel P. Noise underlies switching behavior
    of the bacterial flagellum. <i>Biophysical Journal</i>. 2011;101(10):2336-2340.
    doi:<a href="https://doi.org/10.1016/j.bpj.2011.09.040">10.1016/j.bpj.2011.09.040</a>
  apa: Park, H., Oikonomou, P., Guet, C. C., &#38; Cluzel, P. (2011). Noise underlies
    switching behavior of the bacterial flagellum. <i>Biophysical Journal</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.bpj.2011.09.040">https://doi.org/10.1016/j.bpj.2011.09.040</a>
  chicago: Park, Heungwon, Panos Oikonomou, Calin C Guet, and Philippe Cluzel. “Noise
    Underlies Switching Behavior of the Bacterial Flagellum.” <i>Biophysical Journal</i>.
    Elsevier, 2011. <a href="https://doi.org/10.1016/j.bpj.2011.09.040">https://doi.org/10.1016/j.bpj.2011.09.040</a>.
  ieee: H. Park, P. Oikonomou, C. C. Guet, and P. Cluzel, “Noise underlies switching
    behavior of the bacterial flagellum,” <i>Biophysical Journal</i>, vol. 101, no.
    10. Elsevier, pp. 2336–2340, 2011.
  ista: Park H, Oikonomou P, Guet CC, Cluzel P. 2011. Noise underlies switching behavior
    of the bacterial flagellum. Biophysical Journal. 101(10), 2336–2340.
  mla: Park, Heungwon, et al. “Noise Underlies Switching Behavior of the Bacterial
    Flagellum.” <i>Biophysical Journal</i>, vol. 101, no. 10, Elsevier, 2011, pp.
    2336–40, doi:<a href="https://doi.org/10.1016/j.bpj.2011.09.040">10.1016/j.bpj.2011.09.040</a>.
  short: H. Park, P. Oikonomou, C.C. Guet, P. Cluzel, Biophysical Journal 101 (2011)
    2336–2340.
date_created: 2019-05-28T11:54:29Z
date_published: 2011-11-16T00:00:00Z
date_updated: 2021-04-16T11:54:49Z
day: '16'
department:
- _id: CaGu
doi: 10.1016/j.bpj.2011.09.040
external_id:
  pmid:
  - '22098731'
intvolume: '       101'
issue: '10'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218319/
month: '11'
oa: 1
oa_version: Published Version
page: 2336-2340
pmid: 1
publication: Biophysical Journal
publication_identifier:
  issn:
  - 0006-3495
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Noise underlies switching behavior of the bacterial flagellum
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 101
year: '2011'
...
---
_id: '3493'
abstract:
- lang: eng
  text: Although agonists and competitive antagonists presumably occupy overlapping
    binding sites on ligand-gated channels, these interactions cannot be identical
    because agonists cause channel opening whereas antagonists do not. One explanation
    is that only agonist binding performs enough work on the receptor to cause the
    conformational changes that lead to gating. This idea is supported by agonist
    binding rates at GABAA and nicotinic acetylcholine receptors that are slower than
    expected for a diffusion-limited process, suggesting that agonist binding involves
    an energy-requiring event. This hypothesis predicts that competitive antagonist
    binding should require less activation energy than agonist binding. To test this
    idea, we developed a novel deconvolution-based method to compare binding and unbinding
    kinetics of GABAA receptor agonists and antagonists in outside-out patches from
    rat hippocampal neurons. Agonist and antagonist unbinding rates were steeply correlated
    with affinity. Unlike the agonists, three of the four antagonists tested had binding
    rates that were fast, independent of affinity, and could be accounted for by diffusion-
    and dehydration-limited processes. In contrast, agonist binding involved additional
    energy-requiring steps, consistent with the idea that channel gating is initiated
    by agonist-triggered movements within the ligand binding site. Antagonist binding
    does not appear to produce such movements, and may in fact prevent them.
article_processing_charge: No
article_type: original
author:
- first_name: M.V
  full_name: Jones, M.V
  last_name: Jones
- first_name: Peter M
  full_name: Jonas, Peter M
  id: 353C1B58-F248-11E8-B48F-1D18A9856A87
  last_name: Jonas
  orcid: 0000-0001-5001-4804
- first_name: Y.
  full_name: Sahara, Y.
  last_name: Sahara
- first_name: G.
  full_name: Westbrook, G.
  last_name: Westbrook
citation:
  ama: Jones M., Jonas PM, Sahara Y, Westbrook G. Microscopic kinetics and energetics
    distinguish GABAA receptor agonists from antagonists. <i>Biophysical Journal</i>.
    2001;81(5):2660-2670. doi:<a href="https://doi.org/10.1016/S0006-3495(01)75909-7
    ">10.1016/S0006-3495(01)75909-7 </a>
  apa: Jones, M. ., Jonas, P. M., Sahara, Y., &#38; Westbrook, G. (2001). Microscopic
    kinetics and energetics distinguish GABAA receptor agonists from antagonists.
    <i>Biophysical Journal</i>. Biophysical Society. <a href="https://doi.org/10.1016/S0006-3495(01)75909-7
    ">https://doi.org/10.1016/S0006-3495(01)75909-7 </a>
  chicago: Jones, M.V, Peter M Jonas, Y. Sahara, and G. Westbrook. “Microscopic Kinetics
    and Energetics Distinguish GABAA Receptor Agonists from Antagonists.” <i>Biophysical
    Journal</i>. Biophysical Society, 2001. <a href="https://doi.org/10.1016/S0006-3495(01)75909-7
    ">https://doi.org/10.1016/S0006-3495(01)75909-7 </a>.
  ieee: M. . Jones, P. M. Jonas, Y. Sahara, and G. Westbrook, “Microscopic kinetics
    and energetics distinguish GABAA receptor agonists from antagonists,” <i>Biophysical
    Journal</i>, vol. 81, no. 5. Biophysical Society, pp. 2660–2670, 2001.
  ista: Jones M., Jonas PM, Sahara Y, Westbrook G. 2001. Microscopic kinetics and
    energetics distinguish GABAA receptor agonists from antagonists. Biophysical Journal.
    81(5), 2660–2670.
  mla: Jones, M. .., et al. “Microscopic Kinetics and Energetics Distinguish GABAA
    Receptor Agonists from Antagonists.” <i>Biophysical Journal</i>, vol. 81, no.
    5, Biophysical Society, 2001, pp. 2660–70, doi:<a href="https://doi.org/10.1016/S0006-3495(01)75909-7
    ">10.1016/S0006-3495(01)75909-7 </a>.
  short: M.. Jones, P.M. Jonas, Y. Sahara, G. Westbrook, Biophysical Journal 81 (2001)
    2660–2670.
date_created: 2018-12-11T12:03:37Z
date_published: 2001-11-01T00:00:00Z
date_updated: 2023-05-15T13:50:21Z
day: '01'
doi: '10.1016/S0006-3495(01)75909-7 '
extern: '1'
external_id:
  pmid:
  - '11606279'
intvolume: '        81'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1301733/
month: '11'
oa: 1
oa_version: Published Version
page: 2660 - 2670
pmid: 1
publication: Biophysical Journal
publication_identifier:
  issn:
  - 0006-3495
publication_status: published
publisher: Biophysical Society
publist_id: '2894'
quality_controlled: '1'
status: public
title: Microscopic kinetics and energetics distinguish GABAA receptor agonists from
  antagonists
type: journal_article
user_id: ea97e931-d5af-11eb-85d4-e6957dddbf17
volume: 81
year: '2001'
...