[{"corr_author":"1","publication_status":"draft","oa_version":"Preprint","ec_funded":1,"date_published":"2023-10-10T00:00:00Z","status":"public","main_file_link":[{"url":"https://doi.org/10.1101/2023.10.09.561523","open_access":"1"}],"publication":"bioRxiv","abstract":[{"text":"Clathrin-mediated endocytosis (CME) is vital for the regulation of plant growth and development by controlling plasma membrane protein composition and cargo uptake. CME relies on the precise recruitment of regulators for vesicle maturation and release. Homologues of components of mammalian vesicle scission are strong candidates to be part of the scissin machinery in plants, but the precise roles of these proteins in this process is not fully understood. Here, we characterised the roles of Plant Dynamin-Related Proteins 2 (DRP2s) and SH3-domain containing protein 2 (SH3P2), the plant homologue to Dynamins’ recruiters, like Endophilin and Amphiphysin, in the CME by combining high-resolution imaging of endocytic events in vivo and characterisation of the purified proteins in vitro. Although DRP2s and SH3P2 arrive similarly late during CME and physically interact, genetic analysis of the Dsh3p1,2,3 triple-mutant and complementation assays with non-SH3P2-interacting DRP2 variants suggests that SH3P2 does not directly recruit DRP2s to the site of endocytosis. These observations imply that despite the presence of many well-conserved endocytic components, plants have acquired a distinct mechanism for CME. One Sentence Summary In contrast to predictions based on mammalian systems, plant Dynamin-related proteins 2 are recruited to the site of Clathrin-mediated endocytosis independently of BAR-SH3 proteins.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-11-22T10:17:49Z","oa":1,"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"type":"preprint","related_material":{"record":[{"status":"public","relation":"later_version","id":"15330"},{"relation":"dissertation_contains","status":"public","id":"14510"}]},"article_processing_charge":"No","month":"10","date_updated":"2026-04-30T22:30:31Z","title":"Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants","_id":"14591","year":"2023","doi":"10.1101/2023.10.09.561523","author":[{"id":"390C1120-F248-11E8-B48F-1D18A9856A87","full_name":"Gnyliukh, Nataliia","last_name":"Gnyliukh","first_name":"Nataliia","orcid":"0000-0002-2198-0509"},{"last_name":"Johnson","first_name":"Alexander J","orcid":"0000-0002-2739-8843","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","full_name":"Johnson, Alexander J"},{"last_name":"Nagel","first_name":"Marie-Kristin","full_name":"Nagel, Marie-Kristin"},{"first_name":"Aline","last_name":"Monzer","id":"2DB5D88C-D7B3-11E9-B8FD-7907E6697425","full_name":"Monzer, Aline"},{"id":"36062FEC-F248-11E8-B48F-1D18A9856A87","full_name":"Hlavata, Annamaria","first_name":"Annamaria","last_name":"Hlavata"},{"full_name":"Isono, Erika","last_name":"Isono","first_name":"Erika"},{"orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"}],"project":[{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"}],"department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"CaBe"}],"day":"10","citation":{"apa":"Gnyliukh, N., Johnson, A. J., Nagel, M.-K., Monzer, A., Hlavata, A., Isono, E., … Friml, J. (n.d.). Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. <i>bioRxiv</i>. <a href=\"https://doi.org/10.1101/2023.10.09.561523\">https://doi.org/10.1101/2023.10.09.561523</a>","mla":"Gnyliukh, Nataliia, et al. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” <i>BioRxiv</i>, doi:<a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>.","ama":"Gnyliukh N, Johnson AJ, Nagel M-K, et al. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. <i>bioRxiv</i>. doi:<a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>","short":"N. Gnyliukh, A.J. Johnson, M.-K. Nagel, A. Monzer, A. Hlavata, E. Isono, M. Loose, J. Friml, BioRxiv (n.d.).","ista":"Gnyliukh N, Johnson AJ, Nagel M-K, Monzer A, Hlavata A, Isono E, Loose M, Friml J. Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants. bioRxiv, <a href=\"https://doi.org/10.1101/2023.10.09.561523\">10.1101/2023.10.09.561523</a>.","chicago":"Gnyliukh, Nataliia, Alexander J Johnson, Marie-Kristin Nagel, Aline Monzer, Annamaria Hlavata, Erika Isono, Martin Loose, and Jiří Friml. “Role of Dynamin-Related Proteins 2 and SH3P2 in Clathrin-Mediated Endocytosis in Plants.” <i>BioRxiv</i>, n.d. <a href=\"https://doi.org/10.1101/2023.10.09.561523\">https://doi.org/10.1101/2023.10.09.561523</a>.","ieee":"N. Gnyliukh <i>et al.</i>, “Role of dynamin-related proteins 2 and SH3P2 in clathrin-mediated endocytosis in plants,” <i>bioRxiv</i>. ."},"language":[{"iso":"eng"}],"OA_place":"repository"},{"article_processing_charge":"No","date_updated":"2024-06-04T09:51:20Z","_id":"17057","issue":"2","language":[{"iso":"eng"}],"external_id":{"isi":["000762665200015"]},"department":[{"_id":"MaLo"}],"publication_identifier":{"issn":["0021-9533"],"eissn":["1477-9137"]},"citation":{"short":"M. Loose, Cell Scientist to Watch – Martin Loose, The Company of Biologists, 2022.","ista":"Loose M. 2022. Cell scientist to watch – Martin Loose, The Company of Biologists,p.","ama":"Loose M. <i>Cell Scientist to Watch – Martin Loose</i>. Vol 135. The Company of Biologists; 2022. doi:<a href=\"https://doi.org/10.1242/jcs.259715\">10.1242/jcs.259715</a>","mla":"Loose, Martin. “Cell Scientist to Watch – Martin Loose.” <i>Journal of Cell Science</i>, vol. 135, no. 2, jcs259715, The Company of Biologists, 2022, doi:<a href=\"https://doi.org/10.1242/jcs.259715\">10.1242/jcs.259715</a>.","apa":"Loose, M. (2022). <i>Cell scientist to watch – Martin Loose</i>. <i>Journal of Cell Science</i> (Vol. 135). The Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.259715\">https://doi.org/10.1242/jcs.259715</a>","ieee":"M. Loose, <i>Cell scientist to watch – Martin Loose</i>, vol. 135, no. 2. The Company of Biologists, 2022.","chicago":"Loose, Martin. <i>Cell Scientist to Watch – Martin Loose</i>. <i>Journal of Cell Science</i>. Vol. 135. The Company of Biologists, 2022. <a href=\"https://doi.org/10.1242/jcs.259715\">https://doi.org/10.1242/jcs.259715</a>."},"oa_version":"Published Version","date_published":"2022-01-19T00:00:00Z","volume":135,"publisher":"The Company of Biologists","publication_status":"published","isi":1,"publication":"Journal of Cell Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       135","month":"01","title":"Cell scientist to watch – Martin Loose","article_number":"jcs259715","doi":"10.1242/jcs.259715","year":"2022","author":[{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724"}],"day":"19","quality_controlled":"1","status":"public","oa":1,"type":"other_academic_publication","main_file_link":[{"url":"https://doi.org/10.1242/jcs.259715","open_access":"1"}],"abstract":[{"text":"Martin Loose studied chemistry at the University of Heidelberg, Germany. He then joined Petra Schwille's group at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden, where he obtained his PhD degree in 2010 for work on self-organization and pattern formation in the bacterial Min protein system. He then moved to Tim Mitchison's lab at Harvard Medical School, Boston, USA for his postdoc, funded by Human Frontier Science Program (HSFP) and European Molecular Biology Organization (EMBO) long-term fellowships; there, he discovered that the bacterial cell division proteins FtsA and FtsZ self-organize into dynamic cytoskeletal patterns. Martin established his independent research group at the Institute of Science and Technology (IST) Austria in 2015, supported by an European Research Council (ERC) starting grant and HFSP Young Investigator Grant. His lab studies the self-organization of bacterial cell division and small GTPase networks.","lang":"eng"}],"date_created":"2024-05-28T13:28:30Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file_date_updated":"2022-04-22T10:15:19Z","tmp":{"short":"CC BY (4.0)","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"},"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) as well as S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","publisher":"Institute of Science and Technology Austria","date_published":"2022-04-05T00:00:00Z","oa_version":"Submitted Version","ec_funded":1,"department":[{"_id":"GradSch"},{"_id":"MaLo"}],"citation":{"chicago":"Radler, Philipp. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/AT:ISTA:10934\">https://doi.org/10.15479/AT:ISTA:10934</a>.","ieee":"P. Radler, “In vitro reconstitution of Escherichia coli divisome activation.” Institute of Science and Technology Austria, 2022.","apa":"Radler, P. (2022). In vitro reconstitution of Escherichia coli divisome activation. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:10934\">https://doi.org/10.15479/AT:ISTA:10934</a>","mla":"Radler, Philipp. <i>In Vitro Reconstitution of Escherichia Coli Divisome Activation</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10934\">10.15479/AT:ISTA:10934</a>.","ama":"Radler P. In vitro reconstitution of Escherichia coli divisome activation. 2022. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:10934\">10.15479/AT:ISTA:10934</a>","short":"P. Radler, (2022).","ista":"Radler P. 2022. In vitro reconstitution of Escherichia coli divisome activation, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:10934\">10.15479/AT:ISTA:10934</a>."},"has_accepted_license":"1","_id":"10934","article_processing_charge":"No","date_updated":"2026-04-30T22:30:27Z","date_created":"2022-03-31T11:32:32Z","abstract":[{"text":"FtsA is crucial for assembly of the E. coli divisome, as it dynamically links cytoplasmic FtsZ filaments with transmembrane cell division proteins. FtsA allegedly initiates cell division by switching from an inactive polymeric to an active monomeric confirmation, which recruits downstream proteins and stabilizes FtsZ filaments. Here, we use biochemical reconstitution experiments combined with quantitative fluorescence microscopy to study divisome activation in vitro. We compare wildtype-FtsA with FtsA-R286W, a constantly active gain-of-function mutant and find that R286W outperforms the wildtype protein in replicating FtsZ treadmilling dynamics, stabilizing FtsZ filaments and recruiting FtsN. We attribute these differences to a faster membrane exchange of FtsA-R286W and its higher packing density below FtsZ filaments.  Using FRET microscopy, we find that FtsN binding does not compete with, but promotes FtsA self-interaction. Our findings suggest a model where FtsA always forms dynamic polymers on the membrane, which re-organize during assembly and activation of the divisome. 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Written by Christoph Sommer.","relation":"software"}],"record":[{"status":"public","relation":"used_in_publication","id":"11373"},{"id":"14280","relation":"used_in_publication","status":"public"}]},"ddc":["572"],"title":"In vitro reconstitution of Escherichia coli divisome activation","month":"04"},{"quality_controlled":"1","status":"public","corr_author":"1","keyword":["General Physics and Astronomy","General Biochemistry","Genetics and Molecular Biology","General Chemistry"],"oa":1,"file":[{"relation":"main_file","date_updated":"2022-05-13T09:10:51Z","access_level":"open_access","creator":"dernst","file_size":6945191,"checksum":"5af863ee1b95a0710f6ee864d68dc7a6","file_id":"11374","content_type":"application/pdf","date_created":"2022-05-13T09:10:51Z","file_name":"2022_NatureCommunications_Radler.pdf","success":1}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"type":"journal_article","abstract":[{"lang":"eng","text":"The actin-homologue FtsA is essential for E. coli cell division, as it links FtsZ filaments in the Z-ring to transmembrane proteins. FtsA is thought to initiate cell constriction by switching from an inactive polymeric to an active monomeric conformation, which recruits downstream proteins and stabilizes the Z-ring. However, direct biochemical evidence for this mechanism is missing. Here, we use reconstitution experiments and quantitative fluorescence microscopy to study divisome activation in vitro. By comparing wild-type FtsA with FtsA R286W, we find that this hyperactive mutant outperforms FtsA WT in replicating FtsZ treadmilling dynamics, FtsZ filament stabilization and recruitment of FtsN. We could attribute these differences to a faster exchange and denser packing of FtsA R286W below FtsZ filaments. Using FRET microscopy, we also find that FtsN binding promotes FtsA self-interaction. We propose that in the active divisome FtsA and FtsN exist as a dynamic copolymer that follows treadmilling filaments of FtsZ."}],"date_created":"2022-05-13T09:06:28Z","month":"05","title":"In vitro reconstitution of Escherichia coli divisome activation","ddc":["570"],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-34485-1"}],"record":[{"id":"10934","status":"public","relation":"research_data"},{"id":"14280","status":"public","relation":"dissertation_contains"}]},"article_number":"2635","article_type":"original","project":[{"_id":"2595697A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"679239","name":"Self-Organization of the Bacterial Cell"},{"name":"In vitro reconstitution of bacterial cell division","_id":"fc38323b-9c52-11eb-aca3-ff8afb4a011d","grant_number":"P34607"}],"author":[{"full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9198-2182 ","last_name":"Radler","first_name":"Philipp"},{"id":"38661662-F248-11E8-B48F-1D18A9856A87","full_name":"Baranova, Natalia S.","first_name":"Natalia S.","last_name":"Baranova","orcid":"0000-0002-3086-9124"},{"first_name":"Paulo R","last_name":"Dos Santos Caldas","orcid":"0000-0001-6730-4461","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","full_name":"Dos Santos Caldas, Paulo R"},{"orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M","full_name":"Sommer, Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lopez Pelegrin, Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","first_name":"Maria D","last_name":"Lopez Pelegrin"},{"full_name":"Michalik, David","id":"B9577E20-AA38-11E9-AC9A-0930E6697425","last_name":"Michalik","first_name":"David"},{"last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"}],"year":"2022","doi":"10.1038/s41467-022-30301-y","day":"12","scopus_import":"1","ec_funded":1,"oa_version":"Published Version","volume":13,"date_published":"2022-05-12T00:00:00Z","publication_status":"published","publisher":"Springer Nature","acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular L. Lindorfer for his assistance with cloning and purifications. We thank J. Löwe and T. Nierhaus (MRC-LMB Cambridge, UK) for sharing unpublished work and helpful discussions, as well as D. Vavylonis and D. Rutkowski (Lehigh University, Bethlehem, PA, USA) and S. Martin (University of Lausanne, Switzerland) for sharing their code for FRAP analysis. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L. and HFSP LT 000824/2016-L4 to N.B. For the purpose of open access, we have applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","isi":1,"tmp":{"short":"CC BY (4.0)","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"},"publication":"Nature Communications","intvolume":"        13","file_date_updated":"2022-05-13T09:10:51Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2026-04-30T22:30:27Z","article_processing_charge":"No","_id":"11373","language":[{"iso":"eng"}],"has_accepted_license":"1","external_id":{"isi":["000795171100037"]},"publication_identifier":{"issn":["2041-1723"]},"citation":{"chicago":"Radler, Philipp, Natalia S. Baranova, Paulo R Dos Santos Caldas, Christoph M Sommer, Maria D Lopez Pelegrin, David Michalik, and Martin Loose. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>.","ieee":"P. Radler <i>et al.</i>, “In vitro reconstitution of Escherichia coli divisome activation,” <i>Nature Communications</i>, vol. 13. Springer Nature, 2022.","ama":"Radler P, Baranova NS, Dos Santos Caldas PR, et al. In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. 2022;13. doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>","mla":"Radler, Philipp, et al. “In Vitro Reconstitution of Escherichia Coli Divisome Activation.” <i>Nature Communications</i>, vol. 13, 2635, Springer Nature, 2022, doi:<a href=\"https://doi.org/10.1038/s41467-022-30301-y\">10.1038/s41467-022-30301-y</a>.","short":"P. Radler, N.S. Baranova, P.R. Dos Santos Caldas, C.M. Sommer, M.D. Lopez Pelegrin, D. Michalik, M. Loose, Nature Communications 13 (2022).","ista":"Radler P, Baranova NS, Dos Santos Caldas PR, Sommer CM, Lopez Pelegrin MD, Michalik D, Loose M. 2022. In vitro reconstitution of Escherichia coli divisome activation. Nature Communications. 13, 2635.","apa":"Radler, P., Baranova, N. S., Dos Santos Caldas, P. R., Sommer, C. M., Lopez Pelegrin, M. D., Michalik, D., &#38; Loose, M. (2022). In vitro reconstitution of Escherichia coli divisome activation. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-022-30301-y\">https://doi.org/10.1038/s41467-022-30301-y</a>"},"department":[{"_id":"MaLo"}]},{"month":"01","title":"In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1","article_number":"e2010054118","article_type":"original","project":[{"name":"Reconstitution of cell polarity and axis determination in a cell-free system","grant_number":"RGY0083/2016","_id":"2599F062-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Düllberg","first_name":"Christian F","orcid":"0000-0001-6335-9748","full_name":"Düllberg, Christian F","id":"459064DC-F248-11E8-B48F-1D18A9856A87"},{"id":"3018E8C2-F248-11E8-B48F-1D18A9856A87","full_name":"Auer, Albert","orcid":"0000-0002-3580-2906","last_name":"Auer","first_name":"Albert"},{"full_name":"Canigova, Nikola","id":"3795523E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8518-5926","first_name":"Nikola","last_name":"Canigova"},{"id":"3760F32C-F248-11E8-B48F-1D18A9856A87","full_name":"Loibl, Katrin","orcid":"0000-0002-2429-7668","first_name":"Katrin","last_name":"Loibl"},{"last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"}],"year":"2021","doi":"10.1073/pnas.2010054118","day":"05","scopus_import":"1","quality_controlled":"1","status":"public","corr_author":"1","oa":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"type":"journal_article","abstract":[{"text":"The differentiation of cells depends on a precise control of their internal organization, which is the result of a complex dynamic interplay between the cytoskeleton, molecular motors, signaling molecules, and membranes. For example, in the developing neuron, the protein ADAP1 (ADP-ribosylation factor GTPase-activating protein [ArfGAP] with dual pleckstrin homology [PH] domains 1) has been suggested to control dendrite branching by regulating the small GTPase ARF6. Together with the motor protein KIF13B, ADAP1 is also thought to mediate delivery of the second messenger phosphatidylinositol (3,4,5)-trisphosphate (PIP3) to the axon tip, thus contributing to PIP3 polarity. However, what defines the function of ADAP1 and how its different roles are coordinated are still not clear. Here, we studied ADAP1’s functions using in vitro reconstitutions. We found that KIF13B transports ADAP1 along microtubules, but that PIP3 as well as PI(3,4)P2 act as stop signals for this transport instead of being transported. We also demonstrate that these phosphoinositides activate ADAP1’s enzymatic activity to catalyze GTP hydrolysis by ARF6. Together, our results support a model for the cellular function of ADAP1, where KIF13B transports ADAP1 until it encounters high PIP3/PI(3,4)P2 concentrations in the plasma membrane. Here, ADAP1 disassociates from the motor to inactivate ARF6, promoting dendrite branching.","lang":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1073/pnas.2010054118","open_access":"1"}],"date_created":"2021-01-03T23:01:23Z","date_updated":"2025-05-14T10:59:29Z","article_processing_charge":"No","_id":"8988","issue":"1","language":[{"iso":"eng"}],"external_id":{"isi":["000607270100018"],"pmid":["33443153"]},"citation":{"chicago":"Düllberg, Christian F, Albert Auer, Nikola Canigova, Katrin Loibl, and Martin Loose. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>.","ieee":"C. F. Düllberg, A. Auer, N. Canigova, K. Loibl, and M. Loose, “In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 1. National Academy of Sciences, 2021.","apa":"Düllberg, C. F., Auer, A., Canigova, N., Loibl, K., &#38; Loose, M. (2021). In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2010054118\">https://doi.org/10.1073/pnas.2010054118</a>","mla":"Düllberg, Christian F., et al. “In Vitro Reconstitution Reveals Phosphoinositides as Cargo-Release Factors and Activators of the ARF6 GAP ADAP1.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 1, e2010054118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2010054118\">10.1073/pnas.2010054118</a>.","ama":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(1). doi:<a href=\"https://doi.org/10.1073/pnas.2010054118\">10.1073/pnas.2010054118</a>","short":"C.F. Düllberg, A. Auer, N. Canigova, K. Loibl, M. Loose, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","ista":"Düllberg CF, Auer A, Canigova N, Loibl K, Loose M. 2021. In vitro reconstitution reveals phosphoinositides as cargo-release factors and activators of the ARF6 GAP ADAP1. Proceedings of the National Academy of Sciences of the United States of America. 118(1), e2010054118."},"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"department":[{"_id":"MaLo"},{"_id":"MiSi"}],"pmid":1,"oa_version":"Published Version","date_published":"2021-01-05T00:00:00Z","volume":118,"publication_status":"published","publisher":"National Academy of Sciences","acknowledgement":"We thank Urban Bezeljak, Natalia Baranova, Mar Lopez-Pelegrin, Catarina Alcarva, and Victoria Faas for sharing reagents and helpful discussions. We thank Veronika Szentirmai for help with protein purifications. We thank Carrie Bernecky, Sascha Martens, and the M.L. lab for comments on the manuscript. We thank the bioimaging facility, the life science facility, and Armel Nicolas from the mass spec facility at the Institute of Science and Technology (IST) Austria for technical support. C.D. acknowledges funding from the IST fellowship program; this work was supported by Human Frontier Science Program Young Investigator Grant\r\nRGY0083/2016. ","isi":1,"publication":"Proceedings of the National Academy of Sciences of the United States of America","intvolume":"       118","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publisher":"eLife Sciences Publications","publication_status":"published","date_published":"2021-02-24T00:00:00Z","volume":10,"oa_version":"Published Version","ec_funded":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2021-03-22T07:36:08Z","intvolume":"        10","publication":"eLife","tmp":{"short":"CC BY (4.0)","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"},"isi":1,"acknowledgement":"We thank Alexander Egan (Newcastle University) for purified proteins LpoB(sol) and LpoPPa(sol), Federico Corona (Newcastle University) for purified MepM, and Oliver Birkholz and Jacob Piehler (Department of Biology and Center of Cellular Nanoanalytics, University of Osnabru¨ ck) for their help with PBP1B reconstitution into polymer-SLBs and initial guidance on single particle tracking. We also acknowledge Christian P Richter and Changjiang You (Department of Biology and Center of Cellular Nanoanalytics, University of Osnabru¨ ck) for providing SLIMfast software and tris-DODA-NTA reagent, respectively. This work was funded by the BBSRC grant BB/R017409/1 (to WV), the European Research Council through grant ERC-2015-StG-679239 (to ML), and long-term fellowships HFSP LT 000824/2016-L4 and EMBO ALTF 1163–2015 (to NB). ","_id":"9243","article_processing_charge":"No","date_updated":"2024-10-22T10:04:21Z","department":[{"_id":"MaLo"}],"publication_identifier":{"eissn":["2050-084X"]},"citation":{"chicago":"Hernández-Rocamora, Víctor M., Natalia S. Baranova, Katharina Peters, Eefjan Breukink, Martin Loose, and Waldemar Vollmer. “Real Time Monitoring of Peptidoglycan Synthesis by Membrane-Reconstituted Penicillin Binding Proteins.” <i>ELife</i>. eLife Sciences Publications, 2021. <a href=\"https://doi.org/10.7554/eLife.61525\">https://doi.org/10.7554/eLife.61525</a>.","ieee":"V. M. Hernández-Rocamora, N. S. Baranova, K. Peters, E. Breukink, M. Loose, and W. Vollmer, “Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins,” <i>eLife</i>, vol. 10. eLife Sciences Publications, 2021.","apa":"Hernández-Rocamora, V. M., Baranova, N. S., Peters, K., Breukink, E., Loose, M., &#38; Vollmer, W. (2021). Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.61525\">https://doi.org/10.7554/eLife.61525</a>","ama":"Hernández-Rocamora VM, Baranova NS, Peters K, Breukink E, Loose M, Vollmer W. Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins. <i>eLife</i>. 2021;10. doi:<a href=\"https://doi.org/10.7554/eLife.61525\">10.7554/eLife.61525</a>","mla":"Hernández-Rocamora, Víctor M., et al. “Real Time Monitoring of Peptidoglycan Synthesis by Membrane-Reconstituted Penicillin Binding Proteins.” <i>ELife</i>, vol. 10, 1–32, eLife Sciences Publications, 2021, doi:<a href=\"https://doi.org/10.7554/eLife.61525\">10.7554/eLife.61525</a>.","short":"V.M. Hernández-Rocamora, N.S. Baranova, K. Peters, E. Breukink, M. Loose, W. Vollmer, ELife 10 (2021).","ista":"Hernández-Rocamora VM, Baranova NS, Peters K, Breukink E, Loose M, Vollmer W. 2021. Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins. eLife. 10, 1–32."},"external_id":{"isi":["000627596400001"]},"has_accepted_license":"1","language":[{"iso":"eng"}],"status":"public","quality_controlled":"1","date_created":"2021-03-14T23:01:33Z","abstract":[{"text":"Peptidoglycan is an essential component of the bacterial cell envelope that surrounds the cytoplasmic membrane to protect the cell from osmotic lysis. Important antibiotics such as β-lactams and glycopeptides target peptidoglycan biosynthesis. Class A penicillin-binding proteins (PBPs) are bifunctional membrane-bound peptidoglycan synthases that polymerize glycan chains and connect adjacent stem peptides by transpeptidation. How these enzymes work in their physiological membrane environment is poorly understood. Here, we developed a novel Förster resonance energy transfer-based assay to follow in real time both reactions of class A PBPs reconstituted in liposomes or supported lipid bilayers and applied this assay with PBP1B homologues from Escherichia coli, Pseudomonas aeruginosa, and Acinetobacter baumannii in the presence or absence of their cognate lipoprotein activator. Our assay will allow unravelling the mechanisms of peptidoglycan synthesis in a lipid-bilayer environment and can be further developed to be used for high-throughput screening for new antimicrobials.","lang":"eng"}],"type":"journal_article","file":[{"date_updated":"2021-03-22T07:36:08Z","access_level":"open_access","creator":"dernst","relation":"main_file","file_id":"9268","file_size":2314698,"checksum":"79897a09bfecd9914d39c4aea2841855","success":1,"content_type":"application/pdf","date_created":"2021-03-22T07:36:08Z","file_name":"2021_eLife_HernandezRocamora.pdf"}],"oa":1,"ddc":["570"],"title":"Real time monitoring of peptidoglycan synthesis by membrane-reconstituted penicillin binding proteins","month":"02","scopus_import":"1","day":"24","doi":"10.7554/eLife.61525","year":"2021","project":[{"grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell"},{"grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425","name":"Synthesis of bacterial cell wall"},{"grant_number":"LT000824/2016","_id":"259B655A-B435-11E9-9278-68D0E5697425","name":"Reconstitution of bacterial cell wall synthesis"}],"author":[{"full_name":"Hernández-Rocamora, Víctor M.","last_name":"Hernández-Rocamora","first_name":"Víctor M."},{"full_name":"Baranova, Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","last_name":"Baranova","first_name":"Natalia S."},{"last_name":"Peters","first_name":"Katharina","full_name":"Peters, Katharina"},{"first_name":"Eefjan","last_name":"Breukink","full_name":"Breukink, Eefjan"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin"},{"first_name":"Waldemar","last_name":"Vollmer","full_name":"Vollmer, Waldemar"}],"article_type":"original","article_number":"1-32"},{"abstract":[{"text":"Microtubule plus-end depolymerization rate is a potentially important target of physiological regulation, but it has been challenging to measure, so its role in spatial organization is poorly understood. Here we apply a method for tracking plus ends based on time difference imaging to measure depolymerization rates in large interphase asters growing in Xenopus egg extract. We observed strong spatial regulation of depolymerization rates, which were higher in the aster interior compared with the periphery, and much less regulation of polymerization or catastrophe rates. We interpret these data in terms of a limiting component model, where aster growth results in lower levels of soluble tubulin and microtubule-associated proteins (MAPs) in the interior cytosol compared with that at the periphery. The steady-state polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the aster interior. We propose that the limiting component for microtubule assembly is a MAP that inhibits depolymerization, and that egg asters are tuned to low microtubule density.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://www.molbiolcell.org/doi/10.1091/mbc.E20-11-0723"}],"date_created":"2021-05-23T22:01:45Z","oa":1,"type":"journal_article","quality_controlled":"1","status":"public","project":[{"call_identifier":"H2020","grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell"},{"name":"Reconstitution of Bacterial Cell Division Using Purified Components","_id":"260D98C8-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Ishihara, Keisuke","last_name":"Ishihara","first_name":"Keisuke"},{"first_name":"Franziska","last_name":"Decker","full_name":"Decker, Franziska"},{"orcid":"0000-0001-6730-4461","last_name":"Dos Santos Caldas","first_name":"Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","full_name":"Dos Santos Caldas, Paulo R"},{"first_name":"James F.","last_name":"Pelletier","full_name":"Pelletier, James F."},{"first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"},{"full_name":"Brugués, Jan","first_name":"Jan","last_name":"Brugués"},{"last_name":"Mitchison","first_name":"Timothy J.","full_name":"Mitchison, Timothy J."}],"doi":"10.1091/MBC.E20-11-0723","year":"2021","day":"19","scopus_import":"1","page":"869-879","article_type":"original","month":"04","title":"Spatial variation of microtubule depolymerization in large asters","publication":"Molecular Biology of the Cell","license":"https://creativecommons.org/licenses/by-nc-sa/3.0/","intvolume":"        32","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"The authors thank the members of Mitchison, Brugués, and Jay Gatlin groups (University of Wyoming) for discussions. We thank Heino Andreas (MPI-CBG) for frog maintenance. We thank Nikon for microscopy support at Marine Biological Laboratory (MBL). K.I. was supported by fellowships from the Honjo International Scholarship Foundation and Center of Systems Biology Dresden. F.D. was supported by the DIGGS-BB fellowship provided by the German Research Foundation (DFG). P.C. is supported by a Boehringer Ingelheim Fonds PhD fellowship. J.F.P. was supported by a fellowship from the Fannie and John Hertz Foundation. M.L.’s research is supported by European Research Council (ERC) Grant no. ERC-2015-StG-679239. J.B.’s research is supported by the Human Frontiers Science Program (CDA00074/2014). T.J.M.’s research is supported by National Institutes of Health Grant no. R35GM131753.","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/3.0/legalcode","short":"CC BY-NC-SA (3.0)","name":"Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0)","image":"/images/cc_by_nc_sa.png"},"publication_status":"published","publisher":"American Society for Cell Biology","ec_funded":1,"oa_version":"Published Version","date_published":"2021-04-19T00:00:00Z","volume":32,"external_id":{"isi":["000641574700005"],"pmid":["33439671"]},"citation":{"ieee":"K. Ishihara <i>et al.</i>, “Spatial variation of microtubule depolymerization in large asters,” <i>Molecular Biology of the Cell</i>, vol. 32, no. 9. American Society for Cell Biology, pp. 869–879, 2021.","chicago":"Ishihara, Keisuke, Franziska Decker, Paulo R Dos Santos Caldas, James F. Pelletier, Martin Loose, Jan Brugués, and Timothy J. Mitchison. “Spatial Variation of Microtubule Depolymerization in Large Asters.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2021. <a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">https://doi.org/10.1091/MBC.E20-11-0723</a>.","apa":"Ishihara, K., Decker, F., Dos Santos Caldas, P. R., Pelletier, J. F., Loose, M., Brugués, J., &#38; Mitchison, T. J. (2021). Spatial variation of microtubule depolymerization in large asters. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">https://doi.org/10.1091/MBC.E20-11-0723</a>","short":"K. Ishihara, F. Decker, P.R. Dos Santos Caldas, J.F. Pelletier, M. Loose, J. Brugués, T.J. Mitchison, Molecular Biology of the Cell 32 (2021) 869–879.","ista":"Ishihara K, Decker F, Dos Santos Caldas PR, Pelletier JF, Loose M, Brugués J, Mitchison TJ. 2021. Spatial variation of microtubule depolymerization in large asters. Molecular Biology of the Cell. 32(9), 869–879.","mla":"Ishihara, Keisuke, et al. “Spatial Variation of Microtubule Depolymerization in Large Asters.” <i>Molecular Biology of the Cell</i>, vol. 32, no. 9, American Society for Cell Biology, 2021, pp. 869–79, doi:<a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">10.1091/MBC.E20-11-0723</a>.","ama":"Ishihara K, Decker F, Dos Santos Caldas PR, et al. Spatial variation of microtubule depolymerization in large asters. <i>Molecular Biology of the Cell</i>. 2021;32(9):869-879. doi:<a href=\"https://doi.org/10.1091/MBC.E20-11-0723\">10.1091/MBC.E20-11-0723</a>"},"publication_identifier":{"issn":["1059-1524"],"eissn":["1939-4586"]},"department":[{"_id":"MaLo"}],"pmid":1,"language":[{"iso":"eng"}],"issue":"9","date_updated":"2025-04-14T07:21:30Z","article_processing_charge":"No","_id":"9414"},{"tmp":{"short":"CC BY (4.0)","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"},"isi":1,"acknowledgement":"We thank Daniela Krajˇcíkova, Katarína Muchová, Zuzana Chromíkova and other members of Barák’s laboratory for useful discussions, suggestions and help. Special thanks also to Emília Chovancová for technical support. We are grateful to Juraj Labaj for drawing the model and for help with graphics. Many thanks to all members of Loose’s laboratory: Maria del Mar\r\nLópez, Paulo Caldas, Philipp Radler, and other members of the Loose’s laboratory for sharing their knowledge of SLB preparation and TIRF experiment chambers, for sharing coverslips and for help with the TIRF microscope and data analysis. We also thank the members of the Dept. of Biochemistry of Biomembranes at the Institute of Animal Biochemistry and Genetics, CBs SAS for their help with preparing the lipid mixtures. We thank J. Bauer for critically reading the manuscript.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        22","file_date_updated":"2021-08-16T09:35:56Z","publication":"International Journal of Molecular Sciences","date_published":"2021-08-01T00:00:00Z","volume":22,"oa_version":"Published Version","ec_funded":1,"publisher":"MDPI","publication_status":"published","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"MaLo"}],"pmid":1,"citation":{"ama":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. <i>International Journal of Molecular Sciences</i>. 2021;22(15). doi:<a href=\"https://doi.org/10.3390/ijms22158350\">10.3390/ijms22158350</a>","mla":"Labajová, Naďa, et al. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 15, 8350, MDPI, 2021, doi:<a href=\"https://doi.org/10.3390/ijms22158350\">10.3390/ijms22158350</a>.","short":"N. Labajová, N.S. Baranova, M. Jurásek, R. Vácha, M. Loose, I. Barák, International Journal of Molecular Sciences 22 (2021).","ista":"Labajová N, Baranova NS, Jurásek M, Vácha R, Loose M, Barák I. 2021. Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. International Journal of Molecular Sciences. 22(15), 8350.","apa":"Labajová, N., Baranova, N. S., Jurásek, M., Vácha, R., Loose, M., &#38; Barák, I. (2021). Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva. <i>International Journal of Molecular Sciences</i>. MDPI. <a href=\"https://doi.org/10.3390/ijms22158350\">https://doi.org/10.3390/ijms22158350</a>","chicago":"Labajová, Naďa, Natalia S. Baranova, Miroslav Jurásek, Robert Vácha, Martin Loose, and Imrich Barák. “Cardiolipin-Containing Lipid Membranes Attract the Bacterial Cell Division Protein Diviva.” <i>International Journal of Molecular Sciences</i>. MDPI, 2021. <a href=\"https://doi.org/10.3390/ijms22158350\">https://doi.org/10.3390/ijms22158350</a>.","ieee":"N. Labajová, N. S. Baranova, M. Jurásek, R. Vácha, M. Loose, and I. Barák, “Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva,” <i>International Journal of Molecular Sciences</i>, vol. 22, no. 15. MDPI, 2021."},"publication_identifier":{"issn":["1661-6596"],"eissn":["1422-0067"]},"external_id":{"pmid":["34361115"],"isi":["000681815400001"]},"_id":"9907","article_processing_charge":"Yes","date_updated":"2025-07-10T12:02:05Z","issue":"15","type":"journal_article","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa":1,"file":[{"relation":"main_file","date_updated":"2021-08-16T09:35:56Z","creator":"asandaue","access_level":"open_access","file_size":6132410,"checksum":"a4bc06e9a2c803ceff5a91f10b174054","file_id":"9923","content_type":"application/pdf","date_created":"2021-08-16T09:35:56Z","file_name":"2021_InternationalJournalOfMolecularSciences_Labajová .pdf","success":1}],"date_created":"2021-08-15T22:01:27Z","abstract":[{"text":"DivIVA is a protein initially identified as a spatial regulator of cell division in the model organism Bacillus subtilis, but its homologues are present in many other Gram-positive bacteria, including Clostridia species. Besides its role as topological regulator of the Min system during bacterial cell division, DivIVA is involved in chromosome segregation during sporulation, genetic competence, and cell wall synthesis. DivIVA localizes to regions of high membrane curvature, such as the cell poles and cell division site, where it recruits distinct binding partners. Previously, it was suggested that negative curvature sensing is the main mechanism by which DivIVA binds to these specific regions. Here, we show that Clostridioides difficile DivIVA binds preferably to membranes containing negatively charged phospholipids, especially cardiolipin. Strikingly, we observed that upon binding, DivIVA modifies the lipid distribution and induces changes to lipid bilayers containing cardiolipin. Our observations indicate that DivIVA might play a more complex and so far unknown active role during the formation of the cell division septal membrane. ","lang":"eng"}],"status":"public","quality_controlled":"1","article_type":"original","article_number":"8350","scopus_import":"1","day":"01","doi":"10.3390/ijms22158350","year":"2021","project":[{"grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell"}],"author":[{"last_name":"Labajová","first_name":"Naďa","full_name":"Labajová, Naďa"},{"orcid":"0000-0002-3086-9124","last_name":"Baranova","first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","full_name":"Baranova, Natalia S."},{"full_name":"Jurásek, Miroslav","first_name":"Miroslav","last_name":"Jurásek"},{"full_name":"Vácha, Robert","first_name":"Robert","last_name":"Vácha"},{"first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"},{"first_name":"Imrich","last_name":"Barák","full_name":"Barák, Imrich"}],"title":"Cardiolipin-containing lipid membranes attract the bacterial cell division protein diviva","month":"08","ddc":["570"]},{"type":"journal_article","acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"file":[{"relation":"main_file","date_updated":"2021-12-15T08:59:40Z","access_level":"open_access","creator":"cchlebak","file_size":2757340,"checksum":"8d01e72e22c4fb1584e72d8601947069","file_id":"10546","date_created":"2021-12-15T08:59:40Z","content_type":"application/pdf","file_name":"2021_PNAS_Johnson.pdf","success":1}],"oa":1,"date_created":"2021-08-11T14:11:43Z","abstract":[{"text":"Clathrin-mediated endocytosis is the major route of entry of cargos into cells and thus underpins many physiological processes. During endocytosis, an area of flat membrane is remodeled by proteins to create a spherical vesicle against intracellular forces. The protein machinery which mediates this membrane bending in plants is unknown. However, it is known that plant endocytosis is actin independent, thus indicating that plants utilize a unique mechanism to mediate membrane bending against high-turgor pressure compared to other model systems. Here, we investigate the TPLATE complex, a plant-specific endocytosis protein complex. It has been thought to function as a classical adaptor functioning underneath the clathrin coat. However, by using biochemical and advanced live microscopy approaches, we found that TPLATE is peripherally associated with clathrin-coated vesicles and localizes at the rim of endocytosis events. As this localization is more fitting to the protein machinery involved in membrane bending during endocytosis, we examined cells in which the TPLATE complex was disrupted and found that the clathrin structures present as flat patches. This suggests a requirement of the TPLATE complex for membrane bending during plant clathrin–mediated endocytosis. Next, we used in vitro biophysical assays to confirm that the TPLATE complex possesses protein domains with intrinsic membrane remodeling activity. These results redefine the role of the TPLATE complex and implicate it as a key component of the evolutionarily distinct plant endocytosis mechanism, which mediates endocytic membrane bending against the high-turgor pressure in plant cells.","lang":"eng"}],"status":"public","quality_controlled":"1","corr_author":"1","article_type":"original","article_number":"e2113046118","scopus_import":"1","day":"14","doi":"10.1073/pnas.2113046118","year":"2021","project":[{"call_identifier":"FWF","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants"}],"author":[{"orcid":"0000-0002-2739-8843","first_name":"Alexander J","last_name":"Johnson","full_name":"Johnson, Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Dahhan, Dana A","last_name":"Dahhan","first_name":"Dana A"},{"orcid":"0000-0002-2198-0509","last_name":"Gnyliukh","first_name":"Nataliia","id":"390C1120-F248-11E8-B48F-1D18A9856A87","full_name":"Gnyliukh, Nataliia"},{"orcid":"0000-0001-9735-5315","last_name":"Kaufmann","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","full_name":"Kaufmann, Walter"},{"id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa","orcid":"0000-0002-9438-4783","first_name":"Vanessa","last_name":"Zheden"},{"full_name":"Costanzo, Tommaso","id":"D93824F4-D9BA-11E9-BB12-F207E6697425","last_name":"Costanzo","first_name":"Tommaso","orcid":"0000-0001-9732-3815"},{"last_name":"Mahou","first_name":"Pierre","full_name":"Mahou, Pierre"},{"last_name":"Hrtyan","first_name":"Mónika","id":"45A71A74-F248-11E8-B48F-1D18A9856A87","full_name":"Hrtyan, Mónika"},{"full_name":"Wang, Jie","last_name":"Wang","first_name":"Jie"},{"orcid":"0000-0002-2862-8372","first_name":"Juan L","last_name":"Aguilera Servin","full_name":"Aguilera Servin, Juan L","id":"2A67C376-F248-11E8-B48F-1D18A9856A87"},{"last_name":"van Damme","first_name":"Daniël","full_name":"van Damme, Daniël"},{"first_name":"Emmanuel","last_name":"Beaurepaire","full_name":"Beaurepaire, Emmanuel"},{"orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"},{"last_name":"Bednarek","first_name":"Sebastian Y","full_name":"Bednarek, Sebastian Y"},{"last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis","month":"12","related_material":{"record":[{"id":"14988","status":"public","relation":"research_data"},{"id":"14510","status":"public","relation":"dissertation_contains"}],"link":[{"url":"https://doi.org/10.1101/2021.04.26.441441","relation":"earlier_version"}]},"ddc":["580"],"tmp":{"short":"CC BY (4.0)","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"},"isi":1,"acknowledgement":"We gratefully thank Julie Neveu and Dr. Amanda Barranco of the Grégory Vert laboratory for help preparing plants in France, Dr. Zuzana Gelova for help and advice with protoplast generation, Dr. Stéphane Vassilopoulos and Dr. Florian Schur for advice regarding EM tomography, Alejandro Marquiegui Alvaro for help with material generation, and Dr. Lukasz Kowalski for generously gifting us the mWasabi protein. This research was supported by the Scientific Service Units of Institute of Science and Technology Austria (IST Austria) through resources provided by the Electron Microscopy Facility, Lab Support Facility (particularly Dorota Jaworska), and the Bioimaging Facility. We acknowledge the Advanced Microscopy Facility of the Vienna BioCenter Core Facilities for use of the 3D SIM. For the mass spectrometry analysis of proteins, we acknowledge the University of Natural Resources and Life Sciences (BOKU) Core Facility Mass Spectrometry. This work was supported by the following funds: A.J. is supported by funding from the Austrian Science Fund I3630B25 to J.F. P.M. and E.B. are supported by Agence Nationale de la Recherche ANR-11-EQPX-0029 Morphoscope2 and ANR-10-INBS-04 France BioImaging. S.Y.B. is supported by the NSF No. 1121998 and 1614915. J.W. and D.V.D. are supported by the European Research Council Grant 682436 (to D.V.D.), a China Scholarship Council Grant 201508440249 (to J.W.), and by a Ghent University Special Research Co-funding Grant ST01511051 (to J.W.).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       118","file_date_updated":"2021-12-15T08:59:40Z","publication":"Proceedings of the National Academy of Sciences of the United States of America","volume":118,"date_published":"2021-12-14T00:00:00Z","oa_version":"Published Version","publisher":"National Academy of Sciences","publication_status":"published","has_accepted_license":"1","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"},{"_id":"MaLo"},{"_id":"EvBe"},{"_id":"EM-Fac"},{"_id":"NanoFab"}],"pmid":1,"citation":{"chicago":"Johnson, Alexander J, Dana A Dahhan, Nataliia Gnyliukh, Walter Kaufmann, Vanessa Zheden, Tommaso Costanzo, Pierre Mahou, et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2021. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>.","ieee":"A. J. Johnson <i>et al.</i>, “The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 51. National Academy of Sciences, 2021.","ama":"Johnson AJ, Dahhan DA, Gnyliukh N, et al. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2021;118(51). doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>","mla":"Johnson, Alexander J., et al. “The TPLATE Complex Mediates Membrane Bending during Plant Clathrin-Mediated Endocytosis.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 118, no. 51, e2113046118, National Academy of Sciences, 2021, doi:<a href=\"https://doi.org/10.1073/pnas.2113046118\">10.1073/pnas.2113046118</a>.","short":"A.J. Johnson, D.A. Dahhan, N. Gnyliukh, W. Kaufmann, V. Zheden, T. Costanzo, P. Mahou, M. Hrtyan, J. Wang, J.L. Aguilera Servin, D. van Damme, E. Beaurepaire, M. Loose, S.Y. Bednarek, J. Friml, Proceedings of the National Academy of Sciences of the United States of America 118 (2021).","ista":"Johnson AJ, Dahhan DA, Gnyliukh N, Kaufmann W, Zheden V, Costanzo T, Mahou P, Hrtyan M, Wang J, Aguilera Servin JL, van Damme D, Beaurepaire E, Loose M, Bednarek SY, Friml J. 2021. The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. Proceedings of the National Academy of Sciences of the United States of America. 118(51), e2113046118.","apa":"Johnson, A. J., Dahhan, D. A., Gnyliukh, N., Kaufmann, W., Zheden, V., Costanzo, T., … Friml, J. (2021). The TPLATE complex mediates membrane bending during plant clathrin-mediated endocytosis. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2113046118\">https://doi.org/10.1073/pnas.2113046118</a>"},"publication_identifier":{"eissn":["1091-6490"]},"external_id":{"isi":["000736417600043"],"pmid":["34907016"]},"_id":"9887","article_processing_charge":"No","date_updated":"2026-04-30T22:30:31Z","issue":"51"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       432","publication":"Journal of Molecular Biology","publisher":"Elsevier","publication_status":"published","volume":432,"date_published":"2020-10-02T00:00:00Z","oa_version":"Published Version","pmid":1,"department":[{"_id":"MaLo"}],"citation":{"short":"H.V.D. Rosa, D.A. Leonardo, G. Brognara, J. Brandão-Neto, H. D’Muniz Pereira, A.P.U. Araújo, R.C. Garratt, Journal of Molecular Biology 432 (2020) 5784–5801.","ista":"Rosa HVD, Leonardo DA, Brognara G, Brandão-Neto J, D’Muniz Pereira H, Araújo APU, Garratt RC. 2020. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 432(21), 5784–5801.","ama":"Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin interfaces: The switches hold the key. <i>Journal of Molecular Biology</i>. 2020;432(21):5784-5801. doi:<a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">10.1016/j.jmb.2020.09.001</a>","mla":"Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” <i>Journal of Molecular Biology</i>, vol. 432, no. 21, Elsevier, 2020, pp. 5784–801, doi:<a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">10.1016/j.jmb.2020.09.001</a>.","apa":"Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira, H., Araújo, A. P. U., &#38; Garratt, R. C. (2020). Molecular recognition at septin interfaces: The switches hold the key. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">https://doi.org/10.1016/j.jmb.2020.09.001</a>","ieee":"H. V. D. Rosa <i>et al.</i>, “Molecular recognition at septin interfaces: The switches hold the key,” <i>Journal of Molecular Biology</i>, vol. 432, no. 21. Elsevier, pp. 5784–5801, 2020.","chicago":"Rosa, Higor Vinícius Dias, Diego Antonio Leonardo, Gabriel Brognara, José Brandão-Neto, Humberto D’Muniz Pereira, Ana Paula Ulian Araújo, and Richard Charles Garratt. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” <i>Journal of Molecular Biology</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">https://doi.org/10.1016/j.jmb.2020.09.001</a>."},"publication_identifier":{"issn":["0022-2836"]},"external_id":{"pmid":["32910969"]},"language":[{"iso":"eng"}],"issue":"21","_id":"15036","article_processing_charge":"No","date_updated":"2024-02-28T12:37:54Z","date_created":"2024-02-28T08:50:34Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jmb.2020.09.001"}],"abstract":[{"text":"The assembly of a septin filament requires that homologous monomers must distinguish between one another in establishing appropriate interfaces with their neighbors. To understand this phenomenon at the molecular level, we present the first four crystal structures of heterodimeric septin complexes. We describe in detail the two distinct types of G-interface present within the octameric particles, which must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and between SEPT7 and SEPT3, and their description permits an understanding of the structural basis for the selectivity necessary for correct filament assembly. By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's postulate, which predicts the exchangeability of septins from within a subgroup. Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent conformational change, have been repurposed in septins to play a fundamental role in molecular recognition. Specifically, it is switch I which holds the key to discriminating between the two different G-interfaces. Moreover, residues which are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing that the correct interfaces are formed.","lang":"eng"}],"type":"journal_article","oa":1,"keyword":["Molecular Biology","Structural Biology"],"status":"public","quality_controlled":"1","page":"5784-5801","day":"02","doi":"10.1016/j.jmb.2020.09.001","year":"2020","author":[{"full_name":"Rosa, Higor Vinícius Dias","last_name":"Rosa","first_name":"Higor Vinícius Dias"},{"full_name":"Leonardo, Diego Antonio","first_name":"Diego Antonio","last_name":"Leonardo"},{"last_name":"Brognara","first_name":"Gabriel","full_name":"Brognara, Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425"},{"full_name":"Brandão-Neto, José","first_name":"José","last_name":"Brandão-Neto"},{"last_name":"D'Muniz Pereira","first_name":"Humberto","full_name":"D'Muniz Pereira, Humberto"},{"full_name":"Araújo, Ana Paula Ulian","last_name":"Araújo","first_name":"Ana Paula Ulian"},{"first_name":"Richard Charles","last_name":"Garratt","full_name":"Garratt, Richard Charles"}],"article_type":"original","title":"Molecular recognition at septin interfaces: The switches hold the key","month":"10"},{"citation":{"apa":"Felhofer, M., Bock, P., Singh, A., Prats Mateu, B., Zirbs, R., &#38; Gierlinger, N. (2020). Wood deformation leads to rearrangement of molecules at the nanoscale. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.0c00205\">https://doi.org/10.1021/acs.nanolett.0c00205</a>","ama":"Felhofer M, Bock P, Singh A, Prats Mateu B, Zirbs R, Gierlinger N. Wood deformation leads to rearrangement of molecules at the nanoscale. <i>Nano Letters</i>. 2020;20(4):2647-2653. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c00205\">10.1021/acs.nanolett.0c00205</a>","mla":"Felhofer, Martin, et al. “Wood Deformation Leads to Rearrangement of Molecules at the Nanoscale.” <i>Nano Letters</i>, vol. 20, no. 4, American Chemical Society, 2020, pp. 2647–53, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.0c00205\">10.1021/acs.nanolett.0c00205</a>.","ista":"Felhofer M, Bock P, Singh A, Prats Mateu B, Zirbs R, Gierlinger N. 2020. Wood deformation leads to rearrangement of molecules at the nanoscale. Nano Letters. 20(4), 2647–2653.","short":"M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, N. Gierlinger, Nano Letters 20 (2020) 2647–2653.","chicago":"Felhofer, Martin, Peter Bock, Adya Singh, Batirtze Prats Mateu, Ronald Zirbs, and Notburga Gierlinger. “Wood Deformation Leads to Rearrangement of Molecules at the Nanoscale.” <i>Nano Letters</i>. American Chemical Society, 2020. <a href=\"https://doi.org/10.1021/acs.nanolett.0c00205\">https://doi.org/10.1021/acs.nanolett.0c00205</a>.","ieee":"M. Felhofer, P. Bock, A. Singh, B. Prats Mateu, R. Zirbs, and N. Gierlinger, “Wood deformation leads to rearrangement of molecules at the nanoscale,” <i>Nano Letters</i>, vol. 20, no. 4. American Chemical Society, pp. 2647–2653, 2020."},"publication_identifier":{"eissn":["1530-6992"]},"department":[{"_id":"MaLo"}],"pmid":1,"external_id":{"isi":["000526413400055"],"pmid":["32196350"]},"language":[{"iso":"eng"}],"has_accepted_license":"1","issue":"4","_id":"7663","date_updated":"2026-04-02T14:26:44Z","article_processing_charge":"No","intvolume":"        20","file_date_updated":"2020-07-14T12:48:01Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","publication":"Nano Letters","tmp":{"short":"CC BY (4.0)","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"},"isi":1,"publication_status":"published","publisher":"American Chemical Society","date_published":"2020-04-08T00:00:00Z","volume":20,"oa_version":"Published Version","day":"08","scopus_import":"1","page":"2647-2653","author":[{"full_name":"Felhofer, Martin","first_name":"Martin","last_name":"Felhofer"},{"full_name":"Bock, Peter","first_name":"Peter","last_name":"Bock"},{"last_name":"Singh","first_name":"Adya","full_name":"Singh, Adya"},{"id":"299FE892-F248-11E8-B48F-1D18A9856A87","full_name":"Prats Mateu, Batirtze","first_name":"Batirtze","last_name":"Prats Mateu"},{"full_name":"Zirbs, Ronald","last_name":"Zirbs","first_name":"Ronald"},{"last_name":"Gierlinger","first_name":"Notburga","full_name":"Gierlinger, Notburga"}],"year":"2020","doi":"10.1021/acs.nanolett.0c00205","article_type":"original","ddc":["530"],"title":"Wood deformation leads to rearrangement of molecules at the nanoscale","month":"04","date_created":"2020-04-19T22:00:54Z","abstract":[{"text":"Wood, as the most abundant carbon dioxide storing bioresource, is currently driven beyond its traditional use through creative innovations and nanotechnology. For many properties the micro- and nanostructure plays a crucial role and one key challenge is control and detection of chemical and physical processes in the confined microstructure and nanopores of the wooden cell wall. In this study, correlative Raman and atomic force microscopy show high potential for tracking in situ molecular rearrangement of wood polymers during compression. More water molecules (interpreted as wider cellulose microfibril distances) and disentangling of hemicellulose chains are detected in the opened cell wall regions, whereas an increase of lignin is revealed in the compressed areas. These results support a new more “loose” cell wall model based on flexible lignin nanodomains and advance our knowledge of the molecular reorganization during deformation of wood for optimized processing and utilization.","lang":"eng"}],"type":"journal_article","file":[{"content_type":"application/pdf","date_created":"2020-04-20T10:43:36Z","file_name":"2020_NanoLetters_Felhofer.pdf","file_id":"7667","file_size":7108014,"checksum":"fe46146a9c4c620592a1932a8599069e","date_updated":"2020-07-14T12:48:01Z","creator":"dernst","access_level":"open_access","relation":"main_file"}],"oa":1,"status":"public","quality_controlled":"1"},{"author":[{"first_name":"Urban","last_name":"Bezeljak","orcid":"0000-0003-1365-5631","full_name":"Bezeljak, Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:8341","year":"2020","day":"08","page":"215","month":"09","title":"In vitro reconstitution of a Rab activation switch","ddc":["570"],"degree_awarded":"PhD","related_material":{"record":[{"id":"7580","status":"public","relation":"part_of_dissertation"}]},"oa":1,"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"file":[{"date_created":"2020-09-08T09:00:29Z","content_type":"application/x-zip-compressed","file_name":"2020_Urban_Bezeljak_Thesis_TeX.zip","file_id":"8342","file_size":65246782,"checksum":"70871b335a595252a66c6bbf0824fb02","date_updated":"2021-09-16T12:49:12Z","creator":"dernst","access_level":"closed","relation":"source_file"},{"file_name":"2020_Urban_Bezeljak_Thesis.pdf","content_type":"application/pdf","date_created":"2020-09-08T09:00:27Z","access_level":"open_access","creator":"dernst","date_updated":"2021-09-16T12:49:12Z","relation":"main_file","file_id":"8343","checksum":"59a62275088b00b7241e6ff4136434c7","file_size":31259058}],"type":"dissertation","abstract":[{"text":"One of the most striking hallmarks of the eukaryotic cell is the presence of intracellular vesicles and organelles. Each of these membrane-enclosed compartments has a distinct composition of lipids and proteins, which is essential for accurate membrane traffic and homeostasis. Interestingly, their biochemical identities are achieved with the help\r\nof small GTPases of the Rab family, which cycle between GDP- and GTP-bound forms on the selected membrane surface. While this activity switch is well understood for an individual protein, how Rab GTPases collectively transition between states to generate decisive signal propagation in space and time is unclear. In my PhD thesis, I present\r\nin vitro reconstitution experiments with theoretical modeling to systematically study a minimal Rab5 activation network from bottom-up. We find that positive feedback based on known molecular interactions gives rise to bistable GTPase activity switching on system’s scale. Furthermore, we determine that collective transition near the critical\r\npoint is intrinsically stochastic and provide evidence that the inactive Rab5 abundance on the membrane can shape the network response. Finally, we demonstrate that collective switching can spread on the lipid bilayer as a traveling activation wave, representing a possible emergent activity pattern in endosomal maturation. Together, our\r\nfindings reveal new insights into the self-organization properties of signaling networks away from chemical equilibrium. Our work highlights the importance of systematic characterization of biochemical systems in well-defined physiological conditions. This way, we were able to answer long-standing open questions in the field and close the gap between regulatory processes on a molecular scale and emergent responses on system’s level.","lang":"eng"}],"date_created":"2020-09-08T08:53:53Z","status":"public","corr_author":"1","OA_place":"publisher","language":[{"iso":"eng"}],"has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"citation":{"chicago":"Bezeljak, Urban. “In Vitro Reconstitution of a Rab Activation Switch.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8341\">https://doi.org/10.15479/AT:ISTA:8341</a>.","ieee":"U. Bezeljak, “In vitro reconstitution of a Rab activation switch,” Institute of Science and Technology Austria, 2020.","ama":"Bezeljak U. In vitro reconstitution of a Rab activation switch. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8341\">10.15479/AT:ISTA:8341</a>","mla":"Bezeljak, Urban. <i>In Vitro Reconstitution of a Rab Activation Switch</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8341\">10.15479/AT:ISTA:8341</a>.","short":"U. Bezeljak, In Vitro Reconstitution of a Rab Activation Switch, Institute of Science and Technology Austria, 2020.","ista":"Bezeljak U. 2020. In vitro reconstitution of a Rab activation switch. Institute of Science and Technology Austria.","apa":"Bezeljak, U. (2020). <i>In vitro reconstitution of a Rab activation switch</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8341\">https://doi.org/10.15479/AT:ISTA:8341</a>"},"department":[{"_id":"MaLo"}],"date_updated":"2026-04-08T07:24:56Z","article_processing_charge":"No","_id":"8341","alternative_title":["ISTA Thesis"],"acknowledgement":"My thanks goes to the Loose lab members, BioImaging, Life Science and Nanofabrication Facilities and the wonderful international community at IST for sharing this experience with me.","supervisor":[{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode"},"file_date_updated":"2021-09-16T12:49:12Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","oa_version":"Published Version","date_published":"2020-09-08T00:00:00Z","publication_status":"published","publisher":"Institute of Science and Technology Austria"},{"issue":"12","_id":"7580","date_updated":"2026-04-08T07:24:55Z","article_processing_charge":"No","citation":{"ama":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. Stochastic activation and bistability in a Rab GTPase regulatory network. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(12):6504-6549. doi:<a href=\"https://doi.org/10.1073/pnas.1921027117\">10.1073/pnas.1921027117</a>","mla":"Bezeljak, Urban, et al. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 12, National Academy of Sciences, 2020, pp. 6504–49, doi:<a href=\"https://doi.org/10.1073/pnas.1921027117\">10.1073/pnas.1921027117</a>.","ista":"Bezeljak U, Loya H, Kaczmarek BM, Saunders TE, Loose M. 2020. Stochastic activation and bistability in a Rab GTPase regulatory network. Proceedings of the National Academy of Sciences of the United States of America. 117(12), 6504–6549.","short":"U. Bezeljak, H. Loya, B.M. Kaczmarek, T.E. Saunders, M. Loose, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 6504–6549.","apa":"Bezeljak, U., Loya, H., Kaczmarek, B. M., Saunders, T. E., &#38; Loose, M. (2020). Stochastic activation and bistability in a Rab GTPase regulatory network. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1921027117\">https://doi.org/10.1073/pnas.1921027117</a>","chicago":"Bezeljak, Urban, Hrushikesh Loya, Beata M Kaczmarek, Timothy E. Saunders, and Martin Loose. “Stochastic Activation and Bistability in a Rab GTPase Regulatory Network.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1921027117\">https://doi.org/10.1073/pnas.1921027117</a>.","ieee":"U. Bezeljak, H. Loya, B. M. Kaczmarek, T. E. Saunders, and M. Loose, “Stochastic activation and bistability in a Rab GTPase regulatory network,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 12. National Academy of Sciences, pp. 6504–6549, 2020."},"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"department":[{"_id":"MaLo"},{"_id":"CaBe"}],"pmid":1,"external_id":{"isi":["000521821800040"],"pmid":["32161136"]},"language":[{"iso":"eng"}],"publication_status":"published","publisher":"National Academy of Sciences","date_published":"2020-03-24T00:00:00Z","volume":117,"oa_version":"Preprint","intvolume":"       117","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"Proceedings of the National Academy of Sciences of the United States of America","isi":1,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/proteins-as-molecular-switches/","relation":"press_release"}],"record":[{"id":"8341","relation":"dissertation_contains","status":"public"}]},"title":"Stochastic activation and bistability in a Rab GTPase regulatory network","month":"03","day":"24","page":"6504-6549","scopus_import":"1","project":[{"grant_number":"RGY0083/2016","_id":"2599F062-B435-11E9-9278-68D0E5697425","name":"Reconstitution of cell polarity and axis determination in a cell-free system"}],"author":[{"orcid":"0000-0003-1365-5631","first_name":"Urban","last_name":"Bezeljak","full_name":"Bezeljak, Urban","id":"2A58201A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Loya, Hrushikesh","first_name":"Hrushikesh","last_name":"Loya"},{"full_name":"Kaczmarek, Beata M","id":"36FA4AFA-F248-11E8-B48F-1D18A9856A87","first_name":"Beata M","last_name":"Kaczmarek"},{"full_name":"Saunders, Timothy E.","first_name":"Timothy E.","last_name":"Saunders"},{"id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin","orcid":"0000-0001-7309-9724","last_name":"Loose","first_name":"Martin"}],"year":"2020","doi":"10.1073/pnas.1921027117","article_type":"original","status":"public","quality_controlled":"1","date_created":"2020-03-12T05:32:26Z","abstract":[{"lang":"eng","text":"The eukaryotic endomembrane system is controlled by small GTPases of the Rab family, which are activated at defined times and locations in a switch-like manner. While this switch is well understood for an individual protein, how regulatory networks produce intracellular activity patterns is currently not known. Here, we combine in vitro reconstitution experiments with computational modeling to study a minimal Rab5 activation network. We find that the molecular interactions in this system give rise to a positive feedback and bistable collective switching of Rab5. Furthermore, we find that switching near the critical point is intrinsically stochastic and provide evidence that controlling the inactive population of Rab5 on the membrane can shape the network response. Notably, we demonstrate that collective switching can spread on the membrane surface as a traveling wave of Rab5 activation. Together, our findings reveal how biochemical signaling networks control vesicle trafficking pathways and how their nonequilibrium properties define the spatiotemporal organization of the cell."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/776567"}],"type":"journal_article","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"oa":1},{"year":"2020","doi":"10.15479/AT:ISTA:8358","author":[{"id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","full_name":"Dos Santos Caldas, Paulo R","orcid":"0000-0001-6730-4461","first_name":"Paulo R","last_name":"Dos Santos Caldas"}],"page":"135","day":"10","month":"09","title":"Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers","ddc":["572"],"related_material":{"record":[{"id":"7197","relation":"part_of_dissertation","status":"public"},{"id":"7572","relation":"dissertation_contains","status":"public"}]},"degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"}],"oa":1,"file":[{"file_id":"8364","file_size":141602462,"checksum":"882f93fe9c351962120e2669b84bf088","date_updated":"2020-09-10T12:11:29Z","creator":"pcaldas","access_level":"open_access","relation":"main_file","success":1,"content_type":"application/pdf","date_created":"2020-09-10T12:11:29Z","file_name":"phd_thesis_pcaldas.pdf"},{"file_name":"phd_thesis_latex_pcaldas.zip","content_type":"application/x-zip-compressed","date_created":"2020-09-10T12:18:17Z","checksum":"70cc9e399c4e41e6e6ac445ae55e8558","file_size":450437458,"file_id":"8365","relation":"source_file","creator":"pcaldas","access_level":"closed","date_updated":"2020-09-11T07:48:10Z"}],"type":"dissertation","abstract":[{"text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This so-called Z-ring acts as a scaffold recruiting several division-related proteins to mid-cell and plays a key role in distributing proteins at the division site, a feature driven by the treadmilling motion of FtsZ filaments around the septum. What regulates the architecture, dynamics and stability of the Z-ring is still poorly understood, but FtsZ-associated proteins (Zaps) are known to play an important role. \r\nAdvances in fluorescence microscopy and in vitro reconstitution experiments have helped to shed light into some of the dynamic properties of these complex systems, but methods that allow to collect and analyze large quantitative data sets of the underlying polymer dynamics are still missing.\r\nHere, using an in vitro reconstitution approach, we studied how different Zaps affect FtsZ filament dynamics and organization into large-scale patterns, giving special emphasis to the role of the well-conserved protein ZapA. For this purpose, we use high-resolution fluorescence microscopy combined with novel image analysis workfows to study pattern organization and polymerization dynamics of active filaments. We quantified the influence of Zaps on FtsZ on three diferent spatial scales: the large-scale organization of the membrane-bound filament network, the underlying\r\npolymerization dynamics and the behavior of single molecules.\r\nWe found that ZapA cooperatively increases the spatial order of the filament network, binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a\r\nswitch-like manner, without compromising filament dynamics. Furthermore, we believe that our automated quantitative methods can be used to analyze a large variety of dynamic cytoskeletal systems, using standard time-lapse\r\nmovies of homogeneously labeled proteins obtained from experiments in vitro or even inside the living cell.\r\n","lang":"eng"}],"date_created":"2020-09-10T09:26:49Z","status":"public","corr_author":"1","has_accepted_license":"1","language":[{"iso":"eng"}],"OA_place":"publisher","department":[{"_id":"MaLo"}],"citation":{"ieee":"P. R. Dos Santos Caldas, “Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers,” Institute of Science and Technology Austria, 2020.","chicago":"Dos Santos Caldas, Paulo R. “Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8358\">https://doi.org/10.15479/AT:ISTA:8358</a>.","short":"P.R. Dos Santos Caldas, Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers, Institute of Science and Technology Austria, 2020.","ista":"Dos Santos Caldas PR. 2020. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. Institute of Science and Technology Austria.","mla":"Dos Santos Caldas, Paulo R. <i>Organization and Dynamics of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinkers</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8358\">10.15479/AT:ISTA:8358</a>.","ama":"Dos Santos Caldas PR. Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8358\">10.15479/AT:ISTA:8358</a>","apa":"Dos Santos Caldas, P. R. (2020). <i>Organization and dynamics of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinkers</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8358\">https://doi.org/10.15479/AT:ISTA:8358</a>"},"publication_identifier":{"isbn":["978-3-99078-009-1"],"issn":["2663-337X"]},"article_processing_charge":"No","date_updated":"2026-04-08T07:26:30Z","_id":"8358","supervisor":[{"orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"}],"alternative_title":["ISTA Thesis"],"acknowledgement":"I should also express my gratitude to the bioimaging facility at IST Austria, for their assistance with the TIRF setup over the years, and especially to Christoph Sommer, who gave me a lot of input when I was starting to dive into programming.","tmp":{"short":"CC BY (4.0)","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"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2020-09-11T07:48:10Z","oa_version":"Published Version","date_published":"2020-09-10T00:00:00Z","publisher":"Institute of Science and Technology Austria","publication_status":"published"},{"quality_controlled":"1","status":"public","abstract":[{"lang":"eng","text":"The polymerization–depolymerization dynamics of cytoskeletal proteins play essential roles in the self-organization of cytoskeletal structures, in eukaryotic as well as prokaryotic cells. While advances in fluorescence microscopy and in vitro reconstitution experiments have helped to study the dynamic properties of these complex systems, methods that allow to collect and analyze large quantitative datasets of the underlying polymer dynamics are still missing. Here, we present a novel image analysis workflow to study polymerization dynamics of active filaments in a nonbiased, highly automated manner. Using treadmilling filaments of the bacterial tubulin FtsZ as an example, we demonstrate that our method is able to specifically detect, track and analyze growth and shrinkage of polymers, even in dense networks of filaments. We believe that this automated method can facilitate the analysis of a large variety of dynamic cytoskeletal systems, using standard time-lapse movies obtained from experiments in vitro as well as in the living cell. Moreover, we provide scripts implementing this method as supplementary material."}],"editor":[{"last_name":"Tran","first_name":"Phong ","full_name":"Tran, Phong "}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/839571"}],"date_created":"2020-03-08T23:00:47Z","oa":1,"type":"book_chapter","related_material":{"record":[{"id":"8358","relation":"part_of_dissertation","status":"public"}]},"month":"02","title":"Computational analysis of filament polymerization dynamics in cytoskeletal networks","author":[{"full_name":"Dos Santos Caldas, Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6730-4461","last_name":"Dos Santos Caldas","first_name":"Paulo R"},{"orcid":"0000-0001-9198-2182 ","first_name":"Philipp","last_name":"Radler","full_name":"Radler, Philipp","id":"40136C2A-F248-11E8-B48F-1D18A9856A87"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","last_name":"Sommer","first_name":"Christoph M","orcid":"0000-0003-1216-9105"},{"last_name":"Loose","first_name":"Martin","orcid":"0000-0001-7309-9724","id":"462D4284-F248-11E8-B48F-1D18A9856A87","full_name":"Loose, Martin"}],"project":[{"grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425","name":"Self-Organization of the Bacterial Cell"},{"_id":"260D98C8-B435-11E9-9278-68D0E5697425","name":"Reconstitution of Bacterial Cell Division Using Purified Components"}],"year":"2020","doi":"10.1016/bs.mcb.2020.01.006","day":"27","scopus_import":"1","page":"145-161","publication_status":"published","publisher":"Elsevier","ec_funded":1,"oa_version":"Preprint","volume":158,"date_published":"2020-02-27T00:00:00Z","publication":"Methods in Cell Biology","intvolume":"       158","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["Methods in Cell Biology"],"isi":1,"date_updated":"2026-04-08T07:26:30Z","article_processing_charge":"No","_id":"7572","external_id":{"isi":["000611826500008"]},"publication_identifier":{"issn":["0091-679X"]},"citation":{"apa":"Dos Santos Caldas, P. R., Radler, P., Sommer, C. M., &#38; Loose, M. (2020). Computational analysis of filament polymerization dynamics in cytoskeletal networks. In P. Tran (Ed.), <i>Methods in Cell Biology</i> (Vol. 158, pp. 145–161). Elsevier. <a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">https://doi.org/10.1016/bs.mcb.2020.01.006</a>","ama":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Tran P, ed. <i>Methods in Cell Biology</i>. Vol 158. Elsevier; 2020:145-161. doi:<a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">10.1016/bs.mcb.2020.01.006</a>","mla":"Dos Santos Caldas, Paulo R., et al. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” <i>Methods in Cell Biology</i>, edited by Phong  Tran, vol. 158, Elsevier, 2020, pp. 145–61, doi:<a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">10.1016/bs.mcb.2020.01.006</a>.","short":"P.R. Dos Santos Caldas, P. Radler, C.M. Sommer, M. Loose, in:, P. Tran (Ed.), Methods in Cell Biology, Elsevier, 2020, pp. 145–161.","ista":"Dos Santos Caldas PR, Radler P, Sommer CM, Loose M. 2020.Computational analysis of filament polymerization dynamics in cytoskeletal networks. In: Methods in Cell Biology. Methods in Cell Biology, vol. 158, 145–161.","chicago":"Dos Santos Caldas, Paulo R, Philipp Radler, Christoph M Sommer, and Martin Loose. “Computational Analysis of Filament Polymerization Dynamics in Cytoskeletal Networks.” In <i>Methods in Cell Biology</i>, edited by Phong  Tran, 158:145–61. Elsevier, 2020. <a href=\"https://doi.org/10.1016/bs.mcb.2020.01.006\">https://doi.org/10.1016/bs.mcb.2020.01.006</a>.","ieee":"P. R. Dos Santos Caldas, P. Radler, C. M. Sommer, and M. Loose, “Computational analysis of filament polymerization dynamics in cytoskeletal networks,” in <i>Methods in Cell Biology</i>, vol. 158, P. Tran, Ed. Elsevier, 2020, pp. 145–161."},"department":[{"_id":"MaLo"}],"language":[{"iso":"eng"}]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"         5","publication":"Nature Microbiology","isi":1,"acknowledgement":"We acknowledge members of the Loose laboratory at IST Austria for helpful discussions—in particular, P. Caldas for help with the treadmilling analysis, M. Jimenez, A. Raso and N. Ropero for providing Alexa Fluor 488- and Alexa Fluor 647-labelled FtsA for the MST and analytical ultracentrifugation experiments. We thank C. You for providing the DODA-tris-NTA phospholipids, as well as J. Piehler and C. Richter (Department of Biology, University of Osnabruck, Germany) for the SLIMfast single-molecule tracking software and help with the confinement analysis. We thank J. Errington and H. Murray (both at Newcastle University, UK) for critical reading of the manuscript, and J. Brugués (MPI-CBG and MPI-PKS, Dresden, Germany) for help with the MATLAB programming and reading of the manuscript. This work was supported by the European Research Council through grant ERC-2015-StG-679239 to M.L. and grants HFSP LT 000824/2016-L4 and EMBO ALTF 1163-2015 to N.B., a grant from the Ministry of Economy and Competitiveness of the Spanish Government (BFU2016-75471-C2-1-P) to C.A. and G.R., and a Wellcome Trust Senior Investigator award (101824/Z/13/Z) and a grant from the BBSRC (BB/R017409/1) to W.V.","publisher":"Springer Nature","publication_status":"published","date_published":"2020-01-20T00:00:00Z","volume":5,"oa_version":"Submitted Version","ec_funded":1,"pmid":1,"department":[{"_id":"MaLo"}],"publication_identifier":{"issn":["2058-5276"]},"citation":{"ieee":"N. S. Baranova <i>et al.</i>, “Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins,” <i>Nature Microbiology</i>, vol. 5. Springer Nature, pp. 407–417, 2020.","chicago":"Baranova, Natalia S., Philipp Radler, Víctor M. Hernández-Rocamora, Carlos Alfonso, Maria D Lopez Pelegrin, Germán Rivas, Waldemar Vollmer, and Martin Loose. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” <i>Nature Microbiology</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41564-019-0657-5\">https://doi.org/10.1038/s41564-019-0657-5</a>.","short":"N.S. Baranova, P. Radler, V.M. Hernández-Rocamora, C. Alfonso, M.D. Lopez Pelegrin, G. Rivas, W. Vollmer, M. Loose, Nature Microbiology 5 (2020) 407–417.","ista":"Baranova NS, Radler P, Hernández-Rocamora VM, Alfonso C, Lopez Pelegrin MD, Rivas G, Vollmer W, Loose M. 2020. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. Nature Microbiology. 5, 407–417.","ama":"Baranova NS, Radler P, Hernández-Rocamora VM, et al. Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. <i>Nature Microbiology</i>. 2020;5:407-417. doi:<a href=\"https://doi.org/10.1038/s41564-019-0657-5\">10.1038/s41564-019-0657-5</a>","mla":"Baranova, Natalia S., et al. “Diffusion and Capture Permits Dynamic Coupling between Treadmilling FtsZ Filaments and Cell Division Proteins.” <i>Nature Microbiology</i>, vol. 5, Springer Nature, 2020, pp. 407–17, doi:<a href=\"https://doi.org/10.1038/s41564-019-0657-5\">10.1038/s41564-019-0657-5</a>.","apa":"Baranova, N. S., Radler, P., Hernández-Rocamora, V. M., Alfonso, C., Lopez Pelegrin, M. D., Rivas, G., … Loose, M. (2020). Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins. <i>Nature Microbiology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41564-019-0657-5\">https://doi.org/10.1038/s41564-019-0657-5</a>"},"external_id":{"pmid":["31959972"],"isi":["000508584700007"]},"language":[{"iso":"eng"}],"_id":"7387","article_processing_charge":"No","date_updated":"2026-04-30T22:30:27Z","date_created":"2020-01-28T16:14:41Z","main_file_link":[{"url":"http://europepmc.org/article/PMC/7048620","open_access":"1"}],"abstract":[{"lang":"eng","text":"Most bacteria accomplish cell division with the help of a dynamic protein complex called the divisome, which spans the cell envelope in the plane of division. Assembly and activation of this machinery are coordinated by the tubulin-related GTPase FtsZ, which was found to form treadmilling filaments on supported bilayers in vitro1, as well as in live cells, in which filaments circle around the cell division site2,3. Treadmilling of FtsZ is thought to actively move proteins around the division septum, thereby distributing peptidoglycan synthesis and coordinating the inward growth of the septum to form the new poles of the daughter cells4. However, the molecular mechanisms underlying this function are largely unknown. Here, to study how FtsZ polymerization dynamics are coupled to downstream proteins, we reconstituted part of the bacterial cell division machinery using its purified components FtsZ, FtsA and truncated transmembrane proteins essential for cell division. We found that the membrane-bound cytosolic peptides of FtsN and FtsQ co-migrated with treadmilling FtsZ–FtsA filaments, but despite their directed collective behaviour, individual peptides showed random motion and transient confinement. Our work suggests that divisome proteins follow treadmilling FtsZ filaments by a diffusion-and-capture mechanism, which can give rise to a moving zone of signalling activity at the division site."}],"type":"journal_article","oa":1,"corr_author":"1","status":"public","quality_controlled":"1","scopus_import":"1","page":"407-417","day":"20","year":"2020","doi":"10.1038/s41564-019-0657-5","project":[{"name":"Self-Organization of the Bacterial Cell","grant_number":"679239","call_identifier":"H2020","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"_id":"259B655A-B435-11E9-9278-68D0E5697425","grant_number":"LT000824/2016","name":"Reconstitution of bacterial cell wall synthesis"},{"name":"Synthesis of bacterial cell wall","grant_number":"ALTF 2015-1163","_id":"2596EAB6-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Baranova","first_name":"Natalia S.","orcid":"0000-0002-3086-9124","full_name":"Baranova, Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87"},{"id":"40136C2A-F248-11E8-B48F-1D18A9856A87","full_name":"Radler, Philipp","orcid":"0000-0001-9198-2182 ","first_name":"Philipp","last_name":"Radler"},{"first_name":"Víctor M.","last_name":"Hernández-Rocamora","full_name":"Hernández-Rocamora, Víctor M."},{"last_name":"Alfonso","first_name":"Carlos","full_name":"Alfonso, Carlos"},{"first_name":"Maria D","last_name":"Lopez Pelegrin","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","full_name":"Lopez Pelegrin, Maria D"},{"full_name":"Rivas, Germán","first_name":"Germán","last_name":"Rivas"},{"full_name":"Vollmer, Waldemar","last_name":"Vollmer","first_name":"Waldemar"},{"orcid":"0000-0001-7309-9724","first_name":"Martin","last_name":"Loose","full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87"}],"article_type":"letter_note","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/little-cell-big-cover-story/"}],"record":[{"status":"public","relation":"dissertation_contains","id":"14280"}]},"title":"Diffusion and capture permits dynamic coupling between treadmilling FtsZ filaments and cell division proteins","month":"01"},{"publisher":"Elsevier","publication_status":"published","oa_version":"Submitted Version","volume":"78-79","date_published":"2019-05-01T00:00:00Z","publication":"Matrix Biology","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file_date_updated":"2020-07-14T12:47:27Z","isi":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"},"article_processing_charge":"No","date_updated":"2023-08-25T10:11:28Z","_id":"6297","external_id":{"isi":["000468707600005"]},"department":[{"_id":"MaLo"}],"publication_identifier":{"issn":["0945-053X"]},"citation":{"ieee":"H. S. Davies <i>et al.</i>, “An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments,” <i>Matrix Biology</i>, vol. 78–79. Elsevier, pp. 47–59, 2019.","chicago":"Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” <i>Matrix Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">https://doi.org/10.1016/j.matbio.2018.12.002</a>.","apa":"Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. <i>Matrix Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">https://doi.org/10.1016/j.matbio.2018.12.002</a>","ista":"Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. Matrix Biology. 78–79, 47–59.","short":"H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, Matrix Biology 78–79 (2019) 47–59.","ama":"Davies HS, Baranova NS, El Amri N, et al. An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments. <i>Matrix Biology</i>. 2019;78-79:47-59. doi:<a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">10.1016/j.matbio.2018.12.002</a>","mla":"Davies, Heather S., et al. “An Integrated Assay to Probe Endothelial Glycocalyx-Blood Cell Interactions under Flow in Mechanically and Biochemically Well-Defined Environments.” <i>Matrix Biology</i>, vol. 78–79, Elsevier, 2019, pp. 47–59, doi:<a href=\"https://doi.org/10.1016/j.matbio.2018.12.002\">10.1016/j.matbio.2018.12.002</a>."},"has_accepted_license":"1","language":[{"iso":"eng"}],"quality_controlled":"1","status":"public","abstract":[{"text":"Cell-cell and cell-glycocalyx interactions under flow are important for the behaviour of circulating cells in blood and lymphatic vessels. However, such interactions are not well understood due in part to a lack of tools to study them in defined environments. Here, we develop a versatile in vitro platform for the study of cell-glycocalyx interactions in well-defined physical and chemical settings under flow. Our approach is demonstrated with the interaction between hyaluronan (HA, a key component of the endothelial glycocalyx) and its cell receptor CD44. We generate HA brushes in situ within a microfluidic device, and demonstrate the tuning of their physical (thickness and softness) and chemical (density of CD44 binding sites) properties using characterisation with reflection interference contrast microscopy (RICM) and application of polymer theory. We highlight the interactions of HA brushes with CD44-displaying beads and cells under flow. Observations of CD44+ beads on a HA brush with RICM enabled the 3-dimensional trajectories to be generated, and revealed interactions in the form of stop and go phases with reduced rolling velocity and reduced distance between the bead and the HA brush, compared to uncoated beads. Combined RICM and bright-field microscopy of CD44+ AKR1 T-lymphocytes revealed complementary information about the dynamics of cell rolling and cell morphology, and highlighted the formation of tethers and slings, as they interacted with a HA brush under flow. This platform can readily incorporate more complex models of the glycocalyx, and should permit the study of how mechanical and biochemical factors are orchestrated to enable highly selective blood cell-vessel wall interactions under flow.","lang":"eng"}],"date_created":"2019-04-11T20:55:01Z","oa":1,"file":[{"content_type":"application/pdf","date_created":"2020-05-14T09:02:07Z","file_name":"2018_MatrixBiology_Davies.pdf","file_id":"7825","file_size":4444339,"checksum":"790878cd78bfc54a147ddcc7c8f286a0","date_updated":"2020-07-14T12:47:27Z","creator":"dernst","access_level":"open_access","relation":"main_file"}],"type":"journal_article","ddc":["570"],"month":"05","title":"An integrated assay to probe endothelial glycocalyx-blood cell interactions under flow in mechanically and biochemically well-defined environments","year":"2019","doi":"10.1016/j.matbio.2018.12.002","author":[{"first_name":"Heather S.","last_name":"Davies","full_name":"Davies, Heather S."},{"full_name":"Baranova, Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87","first_name":"Natalia S.","last_name":"Baranova","orcid":"0000-0002-3086-9124"},{"full_name":"El Amri, Nouha","first_name":"Nouha","last_name":"El Amri"},{"last_name":"Coche-Guérente","first_name":"Liliane","full_name":"Coche-Guérente, Liliane"},{"full_name":"Verdier, Claude","last_name":"Verdier","first_name":"Claude"},{"full_name":"Bureau, Lionel","last_name":"Bureau","first_name":"Lionel"},{"first_name":"Ralf P.","last_name":"Richter","full_name":"Richter, Ralf P."},{"first_name":"Delphine","last_name":"Débarre","full_name":"Débarre, Delphine"}],"page":"47-59","day":"01","article_type":"original"},{"oa_version":"Published Version","volume":11076,"date_published":"2019-07-22T00:00:00Z","publication_status":"published","publisher":"SPIE","isi":1,"conference":{"start_date":"2019-06-26","location":"Munich, Germany","name":"European Conferences on Biomedical Optics","end_date":"2019-06-27"},"publication":"Advances in Microscopic Imaging II","intvolume":"     11076","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-29T06:54:38Z","article_processing_charge":"No","_id":"7010","language":[{"iso":"eng"}],"external_id":{"isi":["000535353000023"]},"publication_identifier":{"isbn":["9781510628458"],"issn":["1605-7422"]},"citation":{"ama":"Davies HS, Baranova NS, El Amri N, et al. Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. In: <i>Advances in Microscopic Imaging II</i>. Vol 11076. SPIE; 2019. doi:<a href=\"https://doi.org/10.1117/12.2527058\">10.1117/12.2527058</a>","mla":"Davies, Heather S., et al. “Blood Cell-Vessel Wall Interactions Probed by Reflection Interference Contrast Microscopy.” <i>Advances in Microscopic Imaging II</i>, vol. 11076, 110760V, SPIE, 2019, doi:<a href=\"https://doi.org/10.1117/12.2527058\">10.1117/12.2527058</a>.","ista":"Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. Advances in Microscopic Imaging II. European Conferences on Biomedical Optics vol. 11076, 110760V.","short":"H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, in:, Advances in Microscopic Imaging II, SPIE, 2019.","apa":"Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. In <i>Advances in Microscopic Imaging II</i> (Vol. 11076). Munich, Germany: SPIE. <a href=\"https://doi.org/10.1117/12.2527058\">https://doi.org/10.1117/12.2527058</a>","chicago":"Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “Blood Cell-Vessel Wall Interactions Probed by Reflection Interference Contrast Microscopy.” In <i>Advances in Microscopic Imaging II</i>, Vol. 11076. SPIE, 2019. <a href=\"https://doi.org/10.1117/12.2527058\">https://doi.org/10.1117/12.2527058</a>.","ieee":"H. S. Davies <i>et al.</i>, “Blood cell-vessel wall interactions probed by reflection interference contrast microscopy,” in <i>Advances in Microscopic Imaging II</i>, Munich, Germany, 2019, vol. 11076."},"department":[{"_id":"MaLo"}],"quality_controlled":"1","status":"public","oa":1,"type":"conference","abstract":[{"text":"Numerous biophysical questions require the quantification of short-range interactions between (functionalized) surfaces and synthetic or biological objects such as cells. Here, we present an original, custom built setup for reflection interference contrast microscopy that can assess distances between a substrate and a flowing object at high speed with nanometric accuracy. We demonstrate its use to decipher the complex biochemical and mechanical interplay regulating blood cell homing at the vessel wall in the microcirculation using an in vitro approach. We show that in the absence of specific biochemical interactions, flowing cells are repelled from the soft layer lining the vessel wall, contributing to red blood cell repulsion in vivo. In contrast, this so-called glycocalyx stabilizes rolling of cells under flow in the presence of a specific receptor naturally present on activated leucocytes and a number of cancer cell lines.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-02368135/file/110760V.pdf"}],"date_created":"2019-11-12T15:10:18Z","month":"07","title":"Blood cell-vessel wall interactions probed by reflection interference contrast microscopy","article_number":"110760V","author":[{"full_name":"Davies, Heather S.","last_name":"Davies","first_name":"Heather S."},{"first_name":"Natalia S.","last_name":"Baranova","orcid":"0000-0002-3086-9124","id":"38661662-F248-11E8-B48F-1D18A9856A87","full_name":"Baranova, Natalia S."},{"first_name":"Nouha","last_name":"El Amri","full_name":"El Amri, Nouha"},{"full_name":"Coche-Guérente, Liliane","last_name":"Coche-Guérente","first_name":"Liliane"},{"full_name":"Verdier, Claude","last_name":"Verdier","first_name":"Claude"},{"first_name":"Lionel","last_name":"Bureau","full_name":"Bureau, Lionel"},{"last_name":"Richter","first_name":"Ralf P.","full_name":"Richter, Ralf P."},{"full_name":"Débarre, Delphine","first_name":"Delphine","last_name":"Débarre"}],"doi":"10.1117/12.2527058","year":"2019","day":"22","scopus_import":"1"},{"date_created":"2019-12-20T12:22:57Z","abstract":[{"lang":"eng","text":"During bacterial cell division, the tubulin-homolog FtsZ forms a ring-like structure at the center of the cell. This Z-ring not only organizes the division machinery, but treadmilling of FtsZ filaments was also found to play a key role in distributing proteins at the division site. What regulates the architecture, dynamics and stability of the Z-ring is currently unknown, but FtsZ-associated proteins are known to play an important role. Here, using an in vitro reconstitution approach, we studied how the well-conserved protein ZapA affects FtsZ treadmilling and filament organization into large-scale patterns. Using high-resolution fluorescence microscopy and quantitative image analysis, we found that ZapA cooperatively increases the spatial order of the filament network, but binds only transiently to FtsZ filaments and has no effect on filament length and treadmilling velocity. Together, our data provides a model for how FtsZ-associated proteins can increase the precision and stability of the bacterial cell division machinery in a switch-like manner."}],"type":"journal_article","file":[{"date_created":"2019-12-23T07:34:56Z","content_type":"application/pdf","file_name":"2019_NatureComm_Caldas.pdf","date_updated":"2020-07-14T12:47:53Z","access_level":"open_access","creator":"dernst","relation":"main_file","file_id":"7208","file_size":8488733,"checksum":"a1b44b427ba341383197790d0e8789fa"}],"oa":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"corr_author":"1","status":"public","quality_controlled":"1","scopus_import":"1","day":"17","year":"2019","doi":"10.1038/s41467-019-13702-4","project":[{"name":"Self-Organization of the Bacterial Cell","call_identifier":"H2020","grant_number":"679239","_id":"2595697A-B435-11E9-9278-68D0E5697425"},{"_id":"260D98C8-B435-11E9-9278-68D0E5697425","name":"Reconstitution of Bacterial Cell Division Using Purified Components"}],"author":[{"orcid":"0000-0001-6730-4461","first_name":"Paulo R","last_name":"Dos Santos Caldas","full_name":"Dos Santos Caldas, Paulo R","id":"38FCDB4C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lopez Pelegrin, Maria D","id":"319AA9CE-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Pelegrin","first_name":"Maria D"},{"last_name":"Pearce","first_name":"Daniel J. G.","full_name":"Pearce, Daniel J. G."},{"full_name":"Budanur, Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0423-5010","first_name":"Nazmi B","last_name":"Budanur"},{"full_name":"Brugués, Jan","last_name":"Brugués","first_name":"Jan"},{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Loose","orcid":"0000-0001-7309-9724"}],"article_type":"original","article_number":"5744","related_material":{"record":[{"id":"8358","relation":"dissertation_contains","status":"public"}]},"ddc":["570"],"title":"Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA","month":"12","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"        10","file_date_updated":"2020-07-14T12:47:53Z","publication":"Nature Communications","tmp":{"short":"CC BY (4.0)","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"},"isi":1,"publisher":"Springer Nature","publication_status":"published","volume":10,"date_published":"2019-12-17T00:00:00Z","oa_version":"Published Version","ec_funded":1,"department":[{"_id":"MaLo"},{"_id":"BjHo"}],"publication_identifier":{"issn":["2041-1723"]},"citation":{"ieee":"P. R. Dos Santos Caldas, M. D. Lopez Pelegrin, D. J. G. Pearce, N. B. Budanur, J. Brugués, and M. Loose, “Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA,” <i>Nature Communications</i>, vol. 10. Springer Nature, 2019.","chicago":"Dos Santos Caldas, Paulo R, Maria D Lopez Pelegrin, Daniel J. G. Pearce, Nazmi B Budanur, Jan Brugués, and Martin Loose. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-13702-4\">https://doi.org/10.1038/s41467-019-13702-4</a>.","short":"P.R. Dos Santos Caldas, M.D. Lopez Pelegrin, D.J.G. Pearce, N.B. Budanur, J. Brugués, M. Loose, Nature Communications 10 (2019).","ista":"Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J, Loose M. 2019. Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. Nature Communications. 10, 5744.","mla":"Dos Santos Caldas, Paulo R., et al. “Cooperative Ordering of Treadmilling Filaments in Cytoskeletal Networks of FtsZ and Its Crosslinker ZapA.” <i>Nature Communications</i>, vol. 10, 5744, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-13702-4\">10.1038/s41467-019-13702-4</a>.","ama":"Dos Santos Caldas PR, Lopez Pelegrin MD, Pearce DJG, Budanur NB, Brugués J, Loose M. Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. <i>Nature Communications</i>. 2019;10. doi:<a href=\"https://doi.org/10.1038/s41467-019-13702-4\">10.1038/s41467-019-13702-4</a>","apa":"Dos Santos Caldas, P. R., Lopez Pelegrin, M. D., Pearce, D. J. G., Budanur, N. B., Brugués, J., &#38; Loose, M. (2019). Cooperative ordering of treadmilling filaments in cytoskeletal networks of FtsZ and its crosslinker ZapA. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-13702-4\">https://doi.org/10.1038/s41467-019-13702-4</a>"},"external_id":{"isi":["000503009300001"]},"has_accepted_license":"1","language":[{"iso":"eng"}],"_id":"7197","article_processing_charge":"No","date_updated":"2026-04-08T07:26:30Z"},{"department":[{"_id":"MaLo"}],"citation":{"apa":"Richter, R., Baranova, N. S., Day, A., &#38; Kwok, J. (2018). Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? <i>Current Opinion in Structural Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">https://doi.org/10.1016/j.sbi.2017.12.002</a>","mla":"Richter, Ralf, et al. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” <i>Current Opinion in Structural Biology</i>, vol. 50, Elsevier, 2018, pp. 65–74, doi:<a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">10.1016/j.sbi.2017.12.002</a>.","ama":"Richter R, Baranova NS, Day A, Kwok J. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? <i>Current Opinion in Structural Biology</i>. 2018;50:65-74. doi:<a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">10.1016/j.sbi.2017.12.002</a>","short":"R. Richter, N.S. Baranova, A. Day, J. Kwok, Current Opinion in Structural Biology 50 (2018) 65–74.","ista":"Richter R, Baranova NS, Day A, Kwok J. 2018. Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets? Current Opinion in Structural Biology. 50, 65–74.","chicago":"Richter, Ralf, Natalia S. Baranova, Anthony Day, and Jessica Kwok. “Glycosaminoglycans in Extracellular Matrix Organisation: Are Concepts from Soft Matter Physics Key to Understanding the Formation of Perineuronal Nets?” <i>Current Opinion in Structural Biology</i>. Elsevier, 2018. <a href=\"https://doi.org/10.1016/j.sbi.2017.12.002\">https://doi.org/10.1016/j.sbi.2017.12.002</a>.","ieee":"R. Richter, N. S. Baranova, A. Day, and J. Kwok, “Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?,” <i>Current Opinion in Structural Biology</i>, vol. 50. Elsevier, pp. 65–74, 2018."},"external_id":{"isi":["000443661300011"]},"publist_id":"7259","language":[{"iso":"eng"}],"_id":"555","article_processing_charge":"No","date_updated":"2023-09-11T14:07:03Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"        50","publication":"Current Opinion in Structural Biology","isi":1,"acknowledgement":"This work was supported by the European Research Council [Starting Grant 306435 ‘JELLY’; to RPR], the Spanish Ministry of Competitiveness and Innovation [MAT2014-54867-R, to RPR], the EPSRC Centre for Doctoral Training in Tissue Engineering and Regenerative Medicine — Innovation in Medical and Biological Engineering [EP/L014823/1, to JCFK], the Royal Society [RG160410, to JCFK], Wings for Life [WFL-UK-008/15, to JCFK] and the European Union, the Operational Programme Research, Development and Education in the framework of the project ‘Centre of Reconstructive Neuroscience’ [CZ.02.1.01/0.0./0.0/15_003/0000419, to JCFK]. AJD would like to thank Arthritis Research UK [16539, 19489] and the MRC [76445, G0900538] for funding his work on GAG–protein interactions.\r\n","publisher":"Elsevier","publication_status":"published","date_published":"2018-06-01T00:00:00Z","volume":50,"oa_version":"Submitted Version","page":"65 - 74","scopus_import":"1","day":"01","doi":"10.1016/j.sbi.2017.12.002","year":"2018","author":[{"full_name":"Richter, Ralf","last_name":"Richter","first_name":"Ralf"},{"full_name":"Baranova, Natalia","id":"38661662-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3086-9124","last_name":"Baranova","first_name":"Natalia"},{"last_name":"Day","first_name":"Anthony","full_name":"Day, Anthony"},{"full_name":"Kwok, Jessica","first_name":"Jessica","last_name":"Kwok"}],"article_type":"original","title":"Glycosaminoglycans in extracellular matrix organisation: Are concepts from soft matter physics key to understanding the formation of perineuronal nets?","month":"06","date_created":"2018-12-11T11:47:09Z","main_file_link":[{"url":"http://eprints.whiterose.ac.uk/125524/","open_access":"1"}],"abstract":[{"lang":"eng","text":"Conventional wisdom has it that proteins fold and assemble into definite structures, and that this defines their function. Glycosaminoglycans (GAGs) are different. In most cases the structures they form have a low degree of order, even when interacting with proteins. Here, we discuss how physical features common to all GAGs — hydrophilicity, charge, linearity and semi-flexibility — underpin the overall properties of GAG-rich matrices. By integrating soft matter physics concepts (e.g. polymer brushes and phase separation) with our molecular understanding of GAG–protein interactions, we can better comprehend how GAG-rich matrices assemble, what their properties are, and how they function. Taking perineuronal nets (PNNs) — a GAG-rich matrix enveloping neurons — as a relevant example, we propose that microphase separation determines the holey PNN anatomy that is pivotal to PNN functions."}],"type":"journal_article","oa":1,"status":"public","quality_controlled":"1"}]