[{"_id":"14844","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_identifier":{"issn":["0006-3495"],"eissn":["1542-0086"]},"ec_funded":1,"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","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)"},"citation":{"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, 2024. <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>, vol. 123, no. 3. Elsevier, pp. 307–316, 2024.","mla":"Azadbakht, Ali, et al. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” <i>Biophysical Journal</i>, vol. 123, no. 3, Elsevier, 2024, pp. 307–16, doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.12.020\">10.1016/j.bpj.2023.12.020</a>.","ista":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. 2024. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal. 123(3), 307–316.","short":"A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, D.J. Kraft, Biophysical Journal 123 (2024) 307–316.","ama":"Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. <i>Biophysical Journal</i>. 2024;123(3):307-316. 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. (2024). 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>"},"pmid":1,"has_accepted_license":"1","date_created":"2024-01-21T23:00:56Z","title":"Nonadditivity in interactions between three membrane-wrapped colloidal spheres","department":[{"_id":"AnSa"}],"quality_controlled":"1","month":"02","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).","ddc":["570"],"publication_status":"published","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","article_type":"original","scopus_import":"1","oa":1,"external_id":{"pmid":["38158654"],"isi":["001185235900001"]},"year":"2024","intvolume":"       123","date_updated":"2025-09-04T11:46:15Z","isi":1,"project":[{"call_identifier":"H2020","_id":"eba2549b-77a9-11ec-83b8-a81e493eae4e","name":"Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines","grant_number":"802960"}],"day":"06","author":[{"last_name":"Azadbakht","full_name":"Azadbakht, Ali","first_name":"Ali"},{"full_name":"Meadowcroft, Billie","last_name":"Meadowcroft","orcid":"0000-0003-3441-1337","first_name":"Billie","id":"a4725fd6-932b-11ed-81e2-c098c7f37ae1"},{"last_name":"Majek","full_name":"Majek, Juraj","id":"3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1","first_name":"Juraj"},{"full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"first_name":"Daniela J.","full_name":"Kraft, Daniela J.","last_name":"Kraft"}],"publisher":"Elsevier","type":"journal_article","oa_version":"Published Version","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."}],"status":"public","issue":"3","publication":"Biophysical Journal","file":[{"success":1,"date_created":"2024-07-16T12:09:55Z","checksum":"1c8fe1cf950394875b65b90da86428ff","relation":"main_file","creator":"dernst","file_size":3189926,"access_level":"open_access","date_updated":"2024-07-16T12:09:55Z","file_name":"2024_BiophysicalJournal_Azadbakht.pdf","file_id":"17266","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"date_published":"2024-02-06T00:00:00Z","file_date_updated":"2024-07-16T12:09:55Z","page":"307-316","doi":"10.1016/j.bpj.2023.12.020","article_processing_charge":"Yes (in subscription journal)","volume":123},{"year":"2024","external_id":{"pmid":["38462838"]},"intvolume":"       123","month":"06","scopus_import":"1","article_type":"original","publication_status":"published","pmid":1,"citation":{"chicago":"Kamatar, Advika, Jack Peter Kelly Bravo, Feng Yuan, Liping Wang, Eileen M. Lafer, David W. Taylor, Jeanne C. Stachowiak, and Sapun H. Parekh. “Lipid Droplets as Substrates for Protein Phase Separation.” <i>Biophysical Journal</i>. Elsevier, 2024. <a href=\"https://doi.org/10.1016/j.bpj.2024.03.015\">https://doi.org/10.1016/j.bpj.2024.03.015</a>.","ieee":"A. Kamatar <i>et al.</i>, “Lipid droplets as substrates for protein phase separation,” <i>Biophysical Journal</i>, vol. 123, no. 11. Elsevier, pp. 1494–1507, 2024.","mla":"Kamatar, Advika, et al. “Lipid Droplets as Substrates for Protein Phase Separation.” <i>Biophysical Journal</i>, vol. 123, no. 11, Elsevier, 2024, pp. 1494–507, doi:<a href=\"https://doi.org/10.1016/j.bpj.2024.03.015\">10.1016/j.bpj.2024.03.015</a>.","ista":"Kamatar A, Bravo JPK, Yuan F, Wang L, Lafer EM, Taylor DW, Stachowiak JC, Parekh SH. 2024. Lipid droplets as substrates for protein phase separation. Biophysical Journal. 123(11), 1494–1507.","short":"A. Kamatar, J.P.K. Bravo, F. Yuan, L. Wang, E.M. Lafer, D.W. Taylor, J.C. Stachowiak, S.H. Parekh, Biophysical Journal 123 (2024) 1494–1507.","apa":"Kamatar, A., Bravo, J. P. K., Yuan, F., Wang, L., Lafer, E. M., Taylor, D. W., … Parekh, S. H. (2024). Lipid droplets as substrates for protein phase separation. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2024.03.015\">https://doi.org/10.1016/j.bpj.2024.03.015</a>","ama":"Kamatar A, Bravo JPK, Yuan F, et al. Lipid droplets as substrates for protein phase separation. <i>Biophysical Journal</i>. 2024;123(11):1494-1507. doi:<a href=\"https://doi.org/10.1016/j.bpj.2024.03.015\">10.1016/j.bpj.2024.03.015</a>"},"quality_controlled":"1","title":"Lipid droplets as substrates for protein phase separation","extern":"1","date_created":"2024-06-04T06:41:03Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"17111","publication_identifier":{"issn":["0006-3495"]},"language":[{"iso":"eng"}],"date_published":"2024-06-04T00:00:00Z","volume":123,"article_processing_charge":"No","doi":"10.1016/j.bpj.2024.03.015","page":"1494-1507","oa_version":"None","publication":"Biophysical Journal","issue":"11","status":"public","abstract":[{"text":"Membrane-associated protein phase separation plays critical roles in cell biology, driving essential cellular phenomena from immune signaling to membrane traffic. Importantly, by reducing dimensionality from three to two dimensions, lipid bilayers can nucleate phase separation at far lower concentrations compared with those required for phase separation in solution. How might other intracellular lipid substrates, such as lipid droplets, contribute to nucleation of phase separation? Distinct from bilayer membranes, lipid droplets consist of a phospholipid monolayer surrounding a core of neutral lipids, and they are energy storage organelles that protect cells from lipotoxicity and oxidative stress. Here, we show that intrinsically disordered proteins can undergo phase separation on the surface of synthetic and cell-derived lipid droplets. Specifically, we find that the model disordered domains FUS LC and LAF-1 RGG separate into protein-rich and protein-depleted phases on the surfaces of lipid droplets. Owing to the hydrophobic nature of interactions between FUS LC proteins, increasing ionic strength drives an increase in its phase separation on droplet surfaces. The opposite is true for LAF-1 RGG, owing to the electrostatic nature of its interprotein interactions. In both cases, protein-rich phases on the surfaces of synthetic and cell-derived lipid droplets demonstrate molecular mobility indicative of a liquid-like state. Our results show that lipid droplets can nucleate protein condensates, suggesting that protein phase separation could be key in organizing biological processes involving lipid droplets.","lang":"eng"}],"publisher":"Elsevier","author":[{"first_name":"Advika","full_name":"Kamatar, Advika","last_name":"Kamatar"},{"first_name":"Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","orcid":"0000-0003-0456-0753","last_name":"Bravo","full_name":"Bravo, Jack Peter Kelly"},{"first_name":"Feng","full_name":"Yuan, Feng","last_name":"Yuan"},{"full_name":"Wang, Liping","last_name":"Wang","first_name":"Liping"},{"first_name":"Eileen M.","last_name":"Lafer","full_name":"Lafer, Eileen M."},{"full_name":"Taylor, David W.","last_name":"Taylor","first_name":"David W."},{"full_name":"Stachowiak, Jeanne C.","last_name":"Stachowiak","first_name":"Jeanne C."},{"first_name":"Sapun H.","full_name":"Parekh, Sapun H.","last_name":"Parekh"}],"type":"journal_article","date_updated":"2025-01-13T11:03:41Z","day":"04"},{"citation":{"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>.","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.","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>","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>","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.","short":"L. Baldauf, F.F. Frey, M. Arribas Perez, T. Idema, G.H. Koenderink, Biophysical Journal 122 (2023) 2311–2324."},"pmid":1,"has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","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)"},"title":"Branched actin cortices reconstituted in vesicles sense membrane curvature","quality_controlled":"1","department":[{"_id":"AnSa"}],"date_created":"2024-01-10T09:45:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14782","publication_identifier":{"issn":["0006-3495"]},"external_id":{"isi":["001016792600001"],"pmid":["36806830"]},"year":"2023","related_material":{"link":[{"url":"https://github.com/BioSoftMatterGroup/actin-curvature-sensing","relation":"software"}]},"keyword":["Biophysics"],"intvolume":"       122","month":"06","oa":1,"article_type":"original","publication_status":"published","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.","ddc":["570"],"publisher":"Elsevier","author":[{"first_name":"Lucia","full_name":"Baldauf, Lucia","last_name":"Baldauf"},{"id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","first_name":"Felix F","full_name":"Frey, Felix F","last_name":"Frey"},{"first_name":"Marcos","last_name":"Arribas Perez","full_name":"Arribas Perez, Marcos"},{"first_name":"Timon","full_name":"Idema, Timon","last_name":"Idema"},{"first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H.","last_name":"Koenderink"}],"type":"journal_article","date_updated":"2024-01-16T09:20:03Z","day":"06","isi":1,"language":[{"iso":"eng"}],"date_published":"2023-06-06T00:00:00Z","file_date_updated":"2024-01-16T09:09:29Z","volume":122,"page":"2311-2324","article_processing_charge":"Yes (in subscription journal)","doi":"10.1016/j.bpj.2023.02.018","oa_version":"Published Version","issue":"11","publication":"Biophysical Journal","file":[{"relation":"main_file","date_created":"2024-01-16T09:09:29Z","checksum":"70566e54cd95ea6df340909ad44c5cd5","success":1,"content_type":"application/pdf","date_updated":"2024-01-16T09:09:29Z","file_name":"2023_BiophysicalJournal_Baldauf.pdf","file_id":"14807","access_level":"open_access","file_size":3285810,"creator":"dernst"}],"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."}],"status":"public"},{"date_created":"2021-12-10T09:48:19Z","title":"Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"quality_controlled":"1","tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","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)"},"citation":{"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.","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>.","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.","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.","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>","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>"},"pmid":1,"has_accepted_license":"1","publication_identifier":{"issn":["0006-3495"]},"_id":"10530","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       121","keyword":["Biophysics"],"external_id":{"pmid":["34890578"],"isi":["000740815400007"]},"year":"2022","publication_status":"published","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.","ddc":["570"],"scopus_import":"1","oa":1,"article_type":"original","month":"01","type":"journal_article","publisher":"Elsevier","author":[{"full_name":"Zisis, Themistoklis","last_name":"Zisis","first_name":"Themistoklis"},{"full_name":"Brückner, David","last_name":"Brückner","orcid":"0000-0001-7205-2975","id":"e1e86031-6537-11eb-953a-f7ab92be508d","first_name":"David"},{"full_name":"Brandstätter, Tom","last_name":"Brandstätter","first_name":"Tom"},{"first_name":"Wei Xiong","last_name":"Siow","full_name":"Siow, Wei Xiong"},{"first_name":"Joseph","last_name":"d’Alessandro","full_name":"d’Alessandro, Joseph"},{"full_name":"Vollmar, Angelika M.","last_name":"Vollmar","first_name":"Angelika M."},{"first_name":"Chase P.","full_name":"Broedersz, Chase P.","last_name":"Broedersz"},{"full_name":"Zahler, Stefan","last_name":"Zahler","first_name":"Stefan"}],"isi":1,"project":[{"name":"NOMIS Fellowship Program","_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A"}],"day":"04","date_updated":"2025-06-11T13:59:29Z","page":"P44-60","article_processing_charge":"No","doi":"10.1016/j.bpj.2021.12.006","volume":121,"date_published":"2022-01-04T00:00:00Z","language":[{"iso":"eng"}],"file_date_updated":"2022-07-29T10:17:10Z","abstract":[{"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","lang":"eng"}],"status":"public","issue":"1","publication":"Biophysical Journal","file":[{"content_type":"application/pdf","file_name":"2022_BiophysicalJour_Zisis.pdf","file_id":"11697","date_updated":"2022-07-29T10:17:10Z","access_level":"open_access","creator":"dernst","file_size":4475504,"relation":"main_file","date_created":"2022-07-29T10:17:10Z","checksum":"1aa7c3478e0c8256b973b632efd1f6b4","success":1}],"oa_version":"Published Version"},{"day":"19","date_updated":"2022-04-01T10:34:38Z","type":"journal_article","author":[{"last_name":"Davis","full_name":"Davis, Luke K.","first_name":"Luke K."},{"full_name":"Šarić, Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela"},{"last_name":"Hoogenboom","full_name":"Hoogenboom, Bart W.","first_name":"Bart W."},{"last_name":"Zilman","full_name":"Zilman, Anton","first_name":"Anton"}],"publisher":"Elsevier","publication":"Biophysical Journal","issue":"9","status":"public","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."}],"oa_version":"Preprint","volume":120,"article_processing_charge":"No","doi":"10.1016/j.bpj.2021.01.039","page":"1565-1577","date_published":"2021-02-19T00:00:00Z","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0006-3495"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"10338","quality_controlled":"1","title":"Physical modeling of multivalent interactions in the nuclear pore complex","extern":"1","date_created":"2021-11-25T15:36:36Z","main_file_link":[{"url":"https://doi.org/10.1101/2020.10.01.322156","open_access":"1"}],"citation":{"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>.","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.","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>.","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>","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>","short":"L.K. Davis, A. Šarić, B.W. Hoogenboom, A. Zilman, Biophysical Journal 120 (2021) 1565–1577.","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."},"pmid":1,"oa":1,"article_type":"original","scopus_import":"1","publication_status":"published","month":"02","keyword":["biophysics"],"intvolume":"       120","year":"2021","external_id":{"pmid":["33617830"]}},{"author":[{"first_name":"Alexandru","full_name":"Paraschiv, Alexandru","last_name":"Paraschiv"},{"first_name":"Thibaut J.","last_name":"Lagny","full_name":"Lagny, Thibaut J."},{"last_name":"Campos","full_name":"Campos, Christian Vanhille","first_name":"Christian Vanhille"},{"first_name":"Evelyne","full_name":"Coudrier, Evelyne","last_name":"Coudrier"},{"first_name":"Patricia","last_name":"Bassereau","full_name":"Bassereau, Patricia"},{"last_name":"Šarić","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139"}],"publisher":"Cell Press","type":"journal_article","date_updated":"2024-10-14T11:13:03Z","day":"16","language":[{"iso":"eng"}],"date_published":"2021-01-16T00:00:00Z","article_processing_charge":"No","doi":"10.1016/j.bpj.2020.12.028","page":"598-606","volume":120,"oa_version":"Preprint","status":"public","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."}],"publication":"Biophysical Journal","issue":"4","pmid":1,"citation":{"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.","short":"A. Paraschiv, T.J. Lagny, C.V. Campos, E. Coudrier, P. Bassereau, A. Šarić, Biophysical Journal 120 (2021) 598–606.","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.","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>."},"extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.07.28.224741"}],"date_created":"2021-11-25T16:18:23Z","quality_controlled":"1","title":"Influence of membrane-cortex linkers on the extrusion of membrane tubes","_id":"10340","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0006-3495"]},"year":"2021","external_id":{"pmid":["33460596"]},"intvolume":"       120","keyword":["biophysics"],"month":"01","publication_status":"published","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.","scopus_import":"1","article_type":"original","oa":1},{"publication_identifier":{"eissn":["1542-0086"],"issn":["0006-3495"]},"_id":"9350","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://scholarlypublications.universiteitleiden.nl/access/item%3A3251048/view"}],"date_created":"2021-04-25T22:01:30Z","title":"Holding it together: when cadherin meets cadherin","department":[{"_id":"CaHe"}],"quality_controlled":"1","pmid":1,"citation":{"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>.","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.","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>.","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>","short":"F.N. Arslan, J. Eckert, T. Schmidt, C.-P.J. Heisenberg, Biophysical Journal 120 (2021) 4182–4192.","ista":"Arslan FN, Eckert J, Schmidt T, Heisenberg C-PJ. 2021. Holding it together: when cadherin meets cadherin. Biophysical Journal. 120, 4182–4192."},"publication_status":"published","ddc":["570"],"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).","oa":1,"scopus_import":"1","article_type":"original","month":"10","intvolume":"       120","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12368"}]},"external_id":{"pmid":["33794149"],"isi":["000704646900006"]},"year":"2021","isi":1,"day":"05","date_updated":"2026-06-18T19:47:51Z","type":"journal_article","publisher":"Biophysical Society","author":[{"last_name":"Arslan","full_name":"Arslan, Feyza N","first_name":"Feyza N","id":"49DA7910-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5809-9566"},{"first_name":"Julia","last_name":"Eckert","full_name":"Eckert, Julia"},{"last_name":"Schmidt","full_name":"Schmidt, Thomas","first_name":"Thomas"},{"full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"corr_author":"1","abstract":[{"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.","lang":"eng"}],"status":"public","publication":"Biophysical Journal","oa_version":"Published Version","page":"4182-4192","doi":"10.1016/j.bpj.2021.03.025","article_processing_charge":"No","volume":120,"language":[{"iso":"eng"}],"date_published":"2021-10-05T00:00:00Z"},{"title":"Modeling fibrillogenesis of collagen-mimetic molecules","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.06.08.140061v1"}],"date_created":"2021-11-26T07:27:24Z","extern":"1","citation":{"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>.","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.","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>.","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>","short":"A.E. Hafner, N.G. Gyori, C.A. Bench, L.K. Davis, A. Šarić, Biophysical Journal 119 (2020) 1791–1799.","ista":"Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. 2020. Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. 119(9), 1791–1799."},"pmid":1,"OA_place":"publisher","publication_identifier":{"issn":["0006-3495"]},"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","_id":"10346","keyword":["biophysics"],"intvolume":"       119","external_id":{"pmid":["33049216"]},"year":"2020","article_type":"original","scopus_import":"1","oa":1,"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).","publication_status":"published","month":"09","type":"journal_article","publisher":"Cell Press","author":[{"first_name":"Anne E.","last_name":"Hafner","full_name":"Hafner, Anne E."},{"first_name":"Noemi G.","last_name":"Gyori","full_name":"Gyori, Noemi G."},{"last_name":"Bench","full_name":"Bench, Ciaran A.","first_name":"Ciaran A."},{"full_name":"Davis, Luke K.","last_name":"Davis","first_name":"Luke K."},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela","last_name":"Šarić"}],"day":"23","date_updated":"2024-10-16T13:05:34Z","volume":119,"page":"1791-1799","doi":"10.1016/j.bpj.2020.09.013","article_processing_charge":"No","language":[{"iso":"eng"}],"date_published":"2020-09-23T00:00:00Z","OA_type":"hybrid","issue":"9","publication":"Biophysical Journal","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."}],"status":"public","oa_version":"Published Version"},{"month":"02","scopus_import":"1","article_type":"original","publication_status":"published","year":"2017","keyword":["Biophysics"],"intvolume":"       112","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14308","article_number":"25a","publication_identifier":{"issn":["0006-3495"]},"citation":{"ista":"Praetorius FM, Dietz H. 2017. Genetically encoded DNA-protein hybrid origami. Biophysical Journal. 112(3), 25a.","short":"F.M. Praetorius, H. Dietz, Biophysical Journal 112 (2017).","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>","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>","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.","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>."},"quality_controlled":"1","title":"Genetically encoded DNA-protein hybrid origami","extern":"1","date_created":"2023-09-06T13:19:10Z","oa_version":"None","publication":"Biophysical Journal","issue":"3","status":"public","abstract":[{"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.","lang":"eng"}],"language":[{"iso":"eng"}],"date_published":"2017-02-03T00:00:00Z","volume":112,"article_processing_charge":"No","doi":"10.1016/j.bpj.2016.11.171","date_updated":"2024-10-14T12:31:35Z","day":"03","author":[{"last_name":"Praetorius","full_name":"Praetorius, Florian M","first_name":"Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"last_name":"Dietz","full_name":"Dietz, Hendrik","first_name":"Hendrik"}],"publisher":"Elsevier","type":"journal_article"},{"date_updated":"2025-08-05T14:08:52Z","day":"07","publisher":"Biophysical Society","author":[{"full_name":"Fallesen, Todd","last_name":"Fallesen","first_name":"Todd"},{"last_name":"Roostalu","full_name":"Roostalu, Johanna","first_name":"Johanna"},{"last_name":"Düllberg","full_name":"Düllberg, Christian F","orcid":"0000-0001-6335-9748","first_name":"Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pruessner","full_name":"Pruessner, Gunnar","first_name":"Gunnar"},{"last_name":"Surrey","full_name":"Surrey, Thomas","first_name":"Thomas"}],"type":"journal_article","oa_version":"Published Version","abstract":[{"text":"Most kinesin motors move in only one direction along microtubules. Members of the kinesin-5 subfamily were initially described as unidirectional plus-end-directed motors and shown to produce piconewton forces. However, some fungal kinesin-5 motors are bidirectional. The force production of a bidirectional kinesin-5 has not yet been measured. Therefore, it remains unknown whether the mechanism of the unconventional minus-end-directed motility differs fundamentally from that of plus-end-directed stepping. Using force spectroscopy, we have measured here the forces that ensembles of purified budding yeast kinesin-5 Cin8 produce in microtubule gliding assays in both plus- and minus-end direction. Correlation analysis of pause forces demonstrated that individual Cin8 molecules produce additive forces in both directions of movement. In ensembles, Cin8 motors were able to produce single-motor forces up to a magnitude of ∼1.5 pN. Hence, these properties appear to be conserved within the kinesin-5 subfamily. Force production was largely independent of the directionality of movement, indicating similarities between the motility mechanisms for both directions. These results provide constraints for the development of models for the bidirectional motility mechanism of fission yeast kinesin-5 and provide insight into the function of this mitotic motor.","lang":"eng"}],"status":"public","issue":"9","file":[{"relation":"main_file","date_created":"2018-12-12T10:14:03Z","checksum":"99a2474088e20ac74b1882c4fbbb45b1","file_id":"5052","file_name":"IST-2018-965-v1+1_2017_Duellberg_Ensembles_of.pdf","date_updated":"2020-07-14T12:46:31Z","access_level":"open_access","file_size":977192,"creator":"system","content_type":"application/pdf"}],"publication":"Biophysical Journal","date_published":"2017-11-07T00:00:00Z","OA_type":"hybrid","language":[{"iso":"eng"}],"pubrep_id":"965","file_date_updated":"2020-07-14T12:46:31Z","page":"2055 - 2067","article_processing_charge":"No","doi":"10.1016/j.bpj.2017.09.006","volume":113,"_id":"453","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","OA_place":"publisher","publication_identifier":{"eissn":["1542-0086"],"issn":["0006-3495"]},"publist_id":"7369","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)"},"pmid":1,"citation":{"short":"T. Fallesen, J. Roostalu, C.F. Düllberg, G. Pruessner, T. Surrey, Biophysical Journal 113 (2017) 2055–2067.","ista":"Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. 2017. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. Biophysical Journal. 113(9), 2055–2067.","apa":"Fallesen, T., Roostalu, J., Düllberg, C. F., Pruessner, G., &#38; Surrey, T. (2017). Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2017.09.006\">https://doi.org/10.1016/j.bpj.2017.09.006</a>","ama":"Fallesen T, Roostalu J, Düllberg CF, Pruessner G, Surrey T. Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement. <i>Biophysical Journal</i>. 2017;113(9):2055-2067. doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.09.006\">10.1016/j.bpj.2017.09.006</a>","ieee":"T. Fallesen, J. Roostalu, C. F. Düllberg, G. Pruessner, and T. Surrey, “Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement,” <i>Biophysical Journal</i>, vol. 113, no. 9. Biophysical Society, pp. 2055–2067, 2017.","chicago":"Fallesen, Todd, Johanna Roostalu, Christian F Düllberg, Gunnar Pruessner, and Thomas Surrey. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” <i>Biophysical Journal</i>. Biophysical Society, 2017. <a href=\"https://doi.org/10.1016/j.bpj.2017.09.006\">https://doi.org/10.1016/j.bpj.2017.09.006</a>.","mla":"Fallesen, Todd, et al. “Ensembles of Bidirectional Kinesin Cin8 Produce Additive Forces in Both Directions of Movement.” <i>Biophysical Journal</i>, vol. 113, no. 9, Biophysical Society, 2017, pp. 2055–67, doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.09.006\">10.1016/j.bpj.2017.09.006</a>."},"has_accepted_license":"1","date_created":"2018-12-11T11:46:33Z","title":"Ensembles of bidirectional kinesin Cin8 produce additive forces in both directions of movement","quality_controlled":"1","department":[{"_id":"MaLo"}],"month":"11","ddc":["570"],"publication_status":"published","acknowledgement":"The plasmid for full-length kinesin-1 was a gift from G. Holzwarth and J. Macosko with permission from J. Howard. We thank I. Lueke and N. I. Cade for technical assistance. G.P. thanks the Francis Crick Institute, and in particular the Surrey and Salbreux groups, for their hospitality during his sabbatical stay, as well as Imperial College London for making it possible. This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001163), the United Kingdom Medical Research Council (FC001163), and the Wellcome Trust (FC001163), and by Imperial College London. J.R. was also supported by a Sir Henry Wellcome Postdoctoral Fellowship (100145/Z/12/Z) and T.S. by the European Research Council (Advanced Grant, project 323042). ","license":"https://creativecommons.org/licenses/by/4.0/","scopus_import":"1","article_type":"original","oa":1,"external_id":{"pmid":["29117528"]},"year":"2017","intvolume":"       113"},{"main_file_link":[{"open_access":"1","url":"https://www.cell.com/biophysj/fulltext/S0006-3495(16)33153-8"}],"date_created":"2021-10-12T07:47:55Z","extern":"1","title":"Curvature mediated interactions in highly curved membranes","quality_controlled":"1","citation":{"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>","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>","short":"A. Vahid Belarghou, A. Šarić, T. Idema, Biophysical Journal 112 (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>.","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.","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>."},"publication_identifier":{"issn":["0006-3495"]},"article_number":"391a","_id":"10126","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","intvolume":"       112","keyword":["biophysics"],"year":"2017","publication_status":"published","oa":1,"article_type":"letter_note","month":"02","type":"journal_article","author":[{"full_name":"Vahid Belarghou, Afshin","last_name":"Vahid Belarghou","first_name":"Afshin"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","last_name":"Šarić"},{"first_name":"Timon","full_name":"Idema, Timon","last_name":"Idema"}],"publisher":"Elsevier ","day":"03","date_updated":"2021-11-03T10:02:45Z","article_processing_charge":"No","doi":"10.1016/j.bpj.2016.11.2123","volume":112,"language":[{"iso":"eng"}],"date_published":"2017-02-03T00:00:00Z","status":"public","issue":"3","publication":"Biophysical Journal","oa_version":"Published Version"},{"publication_identifier":{"issn":["0006-3495"]},"day":"05","_id":"8444","date_updated":"2021-01-12T08:19:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","date_created":"2020-09-18T10:05:54Z","extern":"1","title":"Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity","quality_controlled":"1","citation":{"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>.","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.","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>.","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>","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>","short":"F. Dehez, P. Schanda, M.S. King, E.R.S. Kunji, C. Chipot, Biophysical Journal 113 (2017) 2311–2315.","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."},"publisher":"Elsevier","author":[{"full_name":"Dehez, François","last_name":"Dehez","first_name":"François"},{"orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul"},{"first_name":"Martin S.","full_name":"King, Martin S.","last_name":"King"},{"last_name":"Kunji","full_name":"Kunji, Edmund R.S.","first_name":"Edmund R.S."},{"first_name":"Christophe","full_name":"Chipot, Christophe","last_name":"Chipot"}],"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."}],"status":"public","publication_status":"published","issue":"11","article_type":"original","publication":"Biophysical Journal","month":"12","oa_version":"None","intvolume":"       113","page":"2311-2315","article_processing_charge":"No","doi":"10.1016/j.bpj.2017.09.019","volume":113,"keyword":["Biophysics"],"year":"2017","language":[{"iso":"eng"}],"date_published":"2017-12-05T00:00:00Z"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"2231","publist_id":"4730","publication_identifier":{"issn":["0006-3495"]},"pmid":1,"citation":{"mla":"Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” <i>Biophysical Journal</i>, vol. 106, no. 5, Biophysical Society, 2014, pp. 1194–204, doi:<a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">10.1016/j.bpj.2014.01.014</a>.","ieee":"G. Rieckh and G. Tkačik, “Noise and information transmission in promoters with multiple internal states,” <i>Biophysical Journal</i>, vol. 106, no. 5. Biophysical Society, pp. 1194–1204, 2014.","chicago":"Rieckh, Georg, and Gašper Tkačik. “Noise and Information Transmission in Promoters with Multiple Internal States.” <i>Biophysical Journal</i>. Biophysical Society, 2014. <a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">https://doi.org/10.1016/j.bpj.2014.01.014</a>.","apa":"Rieckh, G., &#38; Tkačik, G. (2014). Noise and information transmission in promoters with multiple internal states. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">https://doi.org/10.1016/j.bpj.2014.01.014</a>","ama":"Rieckh G, Tkačik G. Noise and information transmission in promoters with multiple internal states. <i>Biophysical Journal</i>. 2014;106(5):1194-1204. doi:<a href=\"https://doi.org/10.1016/j.bpj.2014.01.014\">10.1016/j.bpj.2014.01.014</a>","short":"G. Rieckh, G. Tkačik, Biophysical Journal 106 (2014) 1194–1204.","ista":"Rieckh G, Tkačik G. 2014. Noise and information transmission in promoters with multiple internal states. Biophysical Journal. 106(5), 1194–1204."},"title":"Noise and information transmission in promoters with multiple internal states","department":[{"_id":"GaTk"}],"quality_controlled":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4026790/","open_access":"1"}],"date_created":"2018-12-11T11:56:28Z","month":"03","scopus_import":"1","oa":1,"publication_status":"published","external_id":{"pmid":["24606943"],"isi":["000332501300022"]},"year":"2014","intvolume":"       106","date_updated":"2025-09-29T11:23:30Z","day":"04","isi":1,"author":[{"first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87","full_name":"Rieckh, Georg","last_name":"Rieckh"},{"last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"publisher":"Biophysical Society","type":"journal_article","oa_version":"Submitted Version","issue":"5","publication":"Biophysical Journal","abstract":[{"text":"Based on the measurements of noise in gene expression performed during the past decade, it has become customary to think of gene regulation in terms of a two-state model, where the promoter of a gene can stochastically switch between an ON and an OFF state. As experiments are becoming increasingly precise and the deviations from the two-state model start to be observable, we ask about the experimental signatures of complex multistate promoters, as well as the functional consequences of this additional complexity. In detail, we i), extend the calculations for noise in gene expression to promoters described by state transition diagrams with multiple states, ii), systematically compute the experimentally accessible noise characteristics for these complex promoters, and iii), use information theory to evaluate the channel capacities of complex promoter architectures and compare them with the baseline provided by the two-state model. We find that adding internal states to the promoter generically decreases channel capacity, except in certain cases, three of which (cooperativity, dual-role regulation, promoter cycling) we analyze in detail.","lang":"eng"}],"corr_author":"1","status":"public","date_published":"2014-03-04T00:00:00Z","language":[{"iso":"eng"}],"volume":106,"page":"1194 - 1204","doi":"10.1016/j.bpj.2014.01.014","article_processing_charge":"No"},{"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","_id":"11088","publication_identifier":{"issn":["0006-3495"]},"citation":{"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.","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>.","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.","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.","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>","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>"},"pmid":1,"quality_controlled":"1","title":"Anomalous diffusion of single particles in cytoplasm","extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.bpj.2013.01.049"}],"date_created":"2022-04-07T07:51:26Z","month":"04","oa":1,"scopus_import":"1","article_type":"original","publication_status":"published","year":"2013","external_id":{"pmid":["23601312"]},"keyword":["Biophysics"],"intvolume":"       104","date_updated":"2022-07-18T08:51:01Z","day":"16","author":[{"last_name":"Regner","full_name":"Regner, Benjamin M.","first_name":"Benjamin M."},{"last_name":"Vučinić","full_name":"Vučinić, Dejan","first_name":"Dejan"},{"last_name":"Domnisoru","full_name":"Domnisoru, Cristina","first_name":"Cristina"},{"first_name":"Thomas M.","full_name":"Bartol, Thomas M.","last_name":"Bartol"},{"orcid":"0000-0002-2111-992X","first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","full_name":"HETZER, Martin W"},{"full_name":"Tartakovsky, Daniel M.","last_name":"Tartakovsky","first_name":"Daniel M."},{"first_name":"Terrence J.","last_name":"Sejnowski","full_name":"Sejnowski, Terrence J."}],"publisher":"Elsevier","type":"journal_article","oa_version":"Published Version","publication":"Biophysical Journal","issue":"8","status":"public","abstract":[{"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.","lang":"eng"}],"date_published":"2013-04-16T00:00:00Z","language":[{"iso":"eng"}],"volume":104,"doi":"10.1016/j.bpj.2013.01.049","article_processing_charge":"No","page":"1652-1660"},{"language":[{"iso":"eng"}],"date_published":"2011-11-16T00:00:00Z","page":"2336-2340","article_processing_charge":"No","doi":"10.1016/j.bpj.2011.09.040","volume":101,"oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"status":"public","issue":"10","publication":"Biophysical Journal","publisher":"Elsevier","author":[{"last_name":"Park","full_name":"Park, Heungwon","first_name":"Heungwon"},{"first_name":"Panos","full_name":"Oikonomou, Panos","last_name":"Oikonomou"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C"},{"first_name":"Philippe","full_name":"Cluzel, Philippe","last_name":"Cluzel"}],"type":"journal_article","date_updated":"2026-06-18T19:06:05Z","isi":1,"day":"16","external_id":{"pmid":["22098731"],"isi":["000297143500008"]},"year":"2011","intvolume":"       101","month":"11","publication_status":"published","ddc":["570"],"oa":1,"scopus_import":"1","citation":{"ista":"Park H, Oikonomou P, Guet CC, Cluzel P. 2011. Noise underlies switching behavior of the bacterial flagellum. Biophysical Journal. 101(10), 2336–2340.","short":"H. Park, P. Oikonomou, C.C. Guet, P. Cluzel, Biophysical Journal 101 (2011) 2336–2340.","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.","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>."},"pmid":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218319/"}],"date_created":"2019-05-28T11:54:29Z","title":"Noise underlies switching behavior of the bacterial flagellum","department":[{"_id":"CaGu"}],"quality_controlled":"1","_id":"6496","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0006-3495"]}},{"day":"01","date_updated":"2026-08-27T10:00:40Z","type":"journal_article","publisher":"Biophysical Society","author":[{"full_name":"Le, Thuc","last_name":"Le","first_name":"Thuc"},{"first_name":"Thierry","full_name":"Emonet, Thierry","last_name":"Emonet"},{"full_name":"Harlepp, Sébastien","last_name":"Harlepp","first_name":"Sébastien"},{"full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"first_name":"Philippe","last_name":"Cluzel","full_name":"Cluzel, Philippe"}],"status":"public","abstract":[{"text":"A primitive example of adaptation in gene expression is the balance between the rate of synthesis and degradation of cellular RNA, which allows rapid responses to environmental signals. Here, we investigate how multidrug efflux pump systems mediate the dynamics of a simple drug-inducible system in response to a steady level of inducer. Using fluorescence correlation spectroscopy, we measured in real time within a single bacterium the transcription activity at the RNA level of the acrAB-TolC multidrug efflux pump system. When cells are exposed to constant level of anhydrotetracycline inducer and are adsorbed onto a poly-L-lysine-coated surface, we found that the acrAB-TolC promoter is steadily active. We also monitored the activity of the tet promoter to characterize the effect of this efflux system on the dynamics of drug-inducible transcription. We found that the transcriptional response of the tet promoter to a steady level of aTc rises and then falls back to its preinduction level. The rate of RNA degradation was constant throughout the transcriptional pulse, indicating that the modulation of intracellular inducer concentration alone can produce this pulsating response. Single-cell experiments together with numerical simulations suggest that such pulsating response in drug-inducible genetic systems is a property emerging from the dependence of drug-inducible transcription on multidrug efflux systems.","lang":"eng"}],"publication":"Biophysical Journal","issue":"9","oa_version":"None","doi":"10.1529/biophysj.105.073353","article_processing_charge":"No","page":"3315 - 3321","volume":90,"date_published":"2006-01-01T00:00:00Z","language":[{"iso":"eng"}],"OA_type":"closed access","publication_identifier":{"issn":["0006-3495"],"eissn":["1542-0086"]},"publist_id":"2472","_id":"3755","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","extern":"1","date_created":"2018-12-11T12:04:59Z","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1432126/","open_access":"1"}],"title":"Dynamical determinants of drug-inducible gene expression in a single bacterium","citation":{"chicago":"Le, Thuc, Thierry Emonet, Sébastien Harlepp, Calin C Guet, and Philippe Cluzel. “Dynamical Determinants of Drug-Inducible Gene Expression in a Single Bacterium.” <i>Biophysical Journal</i>. Biophysical Society, 2006. <a href=\"https://doi.org/10.1529/biophysj.105.073353\">https://doi.org/10.1529/biophysj.105.073353</a>.","ieee":"T. Le, T. Emonet, S. Harlepp, C. C. Guet, and P. Cluzel, “Dynamical determinants of drug-inducible gene expression in a single bacterium,” <i>Biophysical Journal</i>, vol. 90, no. 9. Biophysical Society, pp. 3315–3321, 2006.","mla":"Le, Thuc, et al. “Dynamical Determinants of Drug-Inducible Gene Expression in a Single Bacterium.” <i>Biophysical Journal</i>, vol. 90, no. 9, Biophysical Society, 2006, pp. 3315–21, doi:<a href=\"https://doi.org/10.1529/biophysj.105.073353\">10.1529/biophysj.105.073353</a>.","ista":"Le T, Emonet T, Harlepp S, Guet CC, Cluzel P. 2006. Dynamical determinants of drug-inducible gene expression in a single bacterium. Biophysical Journal. 90(9), 3315–3321.","short":"T. Le, T. Emonet, S. Harlepp, C.C. Guet, P. Cluzel, Biophysical Journal 90 (2006) 3315–3321.","ama":"Le T, Emonet T, Harlepp S, Guet CC, Cluzel P. Dynamical determinants of drug-inducible gene expression in a single bacterium. <i>Biophysical Journal</i>. 2006;90(9):3315-3321. doi:<a href=\"https://doi.org/10.1529/biophysj.105.073353\">10.1529/biophysj.105.073353</a>","apa":"Le, T., Emonet, T., Harlepp, S., Guet, C. C., &#38; Cluzel, P. (2006). Dynamical determinants of drug-inducible gene expression in a single bacterium. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1529/biophysj.105.073353\">https://doi.org/10.1529/biophysj.105.073353</a>"},"pmid":1,"publication_status":"published","oa":1,"article_type":"original","month":"01","intvolume":"        90","year":"2006","external_id":{"pmid":["16461398"]}},{"das_tickbox":"1","intvolume":"        88","year":"2005","external_id":{"pmid":["15792967"]},"article_type":"original","oa":1,"publication_status":"published","month":"05","title":"Complex stability of single proteins explored by forced unfolding experiments","extern":"1","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305525/","open_access":"1"}],"date_created":"2018-12-11T12:03:13Z","citation":{"ista":"Janovjak HL, Sapra T, Mueller D. 2005. Complex stability of single proteins explored by forced unfolding experiments. Biophysical Journal. 88(5), 37–39.","short":"H.L. Janovjak, T. Sapra, D. Mueller, Biophysical Journal 88 (2005) 37–39.","apa":"Janovjak, H. L., Sapra, T., &#38; Mueller, D. (2005). Complex stability of single proteins explored by forced unfolding experiments. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1529/biophysj.105.059774\">https://doi.org/10.1529/biophysj.105.059774</a>","ama":"Janovjak HL, Sapra T, Mueller D. Complex stability of single proteins explored by forced unfolding experiments. <i>Biophysical Journal</i>. 2005;88(5):37-39. doi:<a href=\"https://doi.org/10.1529/biophysj.105.059774\">10.1529/biophysj.105.059774</a>","chicago":"Janovjak, Harald L, Tanuj Sapra, and Daniel Mueller. “Complex Stability of Single Proteins Explored by Forced Unfolding Experiments.” <i>Biophysical Journal</i>. Biophysical Society, 2005. <a href=\"https://doi.org/10.1529/biophysj.105.059774\">https://doi.org/10.1529/biophysj.105.059774</a>.","ieee":"H. L. Janovjak, T. Sapra, and D. Mueller, “Complex stability of single proteins explored by forced unfolding experiments,” <i>Biophysical Journal</i>, vol. 88, no. 5. Biophysical Society, pp. 37–39, 2005.","mla":"Janovjak, Harald L., et al. “Complex Stability of Single Proteins Explored by Forced Unfolding Experiments.” <i>Biophysical Journal</i>, vol. 88, no. 5, Biophysical Society, 2005, pp. 37–39, doi:<a href=\"https://doi.org/10.1529/biophysj.105.059774\">10.1529/biophysj.105.059774</a>."},"pmid":1,"publist_id":"2985","OA_place":"repository","publication_identifier":{"eissn":["1542-0086"],"issn":["0006-3495"]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","_id":"3416","volume":88,"doi":"10.1529/biophysj.105.059774","article_processing_charge":"No","page":"37 - 39","OA_type":"green","language":[{"iso":"eng"}],"date_published":"2005-05-01T00:00:00Z","publication":"Biophysical Journal","issue":"5","status":"public","abstract":[{"lang":"eng","text":"In the last decade atomic force microscopy has been used to measure the mechanical stability of single proteins. These force spectroscopy experiments have shown that many water-soluble and membrane proteins unfold via one or more intermediates. Recently, Li and co-workers found a linear correlation between the unfolding force of the native state and the intermediate in fibronectin, which they suggested indicated the presence of a molecular memory or multiple unfolding pathways (1). Here, we apply two independent methods in combination with Monte Carlo simulations to analyze the unfolding of α-helices E and D of bacteriorhodopsin (BR). We show that correlation analysis of unfolding forces is very sensitive to errors in force calibration of the instrument. In contrast, a comparison of relative forces provides a robust measure for the stability of unfolding intermediates. The proposed approach detects three energetically different states of α-helices E and D in trimeric BR. These states are not observed for monomeric BR and indicate that substantial information is hidden in forced unfolding experiments of single proteins."}],"oa_version":"None","type":"journal_article","publisher":"Biophysical Society","author":[{"full_name":"Janovjak, Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sapra","full_name":"Sapra, Tanuj","first_name":"Tanuj"},{"first_name":"Daniel","full_name":"Mueller, Daniel","last_name":"Mueller"}],"day":"01","date_updated":"2026-07-02T07:29:18Z"},{"publication":"Biophysical Journal","issue":"5","status":"public","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."}],"oa_version":"Published Version","volume":81,"doi":"10.1016/S0006-3495(01)75909-7 ","article_processing_charge":"No","page":"2660 - 2670","date_published":"2001-11-01T00:00:00Z","language":[{"iso":"eng"}],"day":"01","date_updated":"2023-05-15T13:50:21Z","type":"journal_article","author":[{"first_name":"M.V","last_name":"Jones","full_name":"Jones, M.V"},{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas"},{"last_name":"Sahara","full_name":"Sahara, Y.","first_name":"Y."},{"last_name":"Westbrook","full_name":"Westbrook, G.","first_name":"G."}],"publisher":"Biophysical Society","oa":1,"article_type":"original","publication_status":"published","month":"11","intvolume":"        81","year":"2001","external_id":{"pmid":["11606279"]},"publist_id":"2894","publication_identifier":{"issn":["0006-3495"]},"user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","_id":"3493","quality_controlled":"1","title":"Microscopic kinetics and energetics distinguish GABAA receptor agonists from antagonists","extern":"1","date_created":"2018-12-11T12:03:37Z","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1301733/","open_access":"1"}],"pmid":1,"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>","short":"M.. Jones, P.M. Jonas, Y. Sahara, G. Westbrook, Biophysical Journal 81 (2001) 2660–2670.","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>.","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.","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>."}}]