[{"related_material":{"link":[{"relation":"software","url":"https://github.com/BioSoftMatterGroup/actin-curvature-sensing"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","file":[{"file_size":3285810,"checksum":"70566e54cd95ea6df340909ad44c5cd5","date_created":"2024-01-16T09:09:29Z","file_name":"2023_BiophysicalJournal_Baldauf.pdf","content_type":"application/pdf","date_updated":"2024-01-16T09:09:29Z","access_level":"open_access","success":1,"relation":"main_file","creator":"dernst","file_id":"14807"}],"oa":1,"publication_identifier":{"issn":["0006-3495"]},"type":"journal_article","date_published":"2023-06-06T00:00:00Z","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"},"keyword":["Biophysics"],"language":[{"iso":"eng"}],"month":"06","oa_version":"Published Version","has_accepted_license":"1","publication":"Biophysical Journal","ddc":["570"],"acknowledgement":"We thank Jeffrey den Haan for protein purification, Kristina Ganzinger (AMOLF) for providing the 10xHis VCA construct, David Kovar (University of Chicago) for the CP constructs, and Michael Way (Crick Institute) for providing purified human Arp2/3 proteins. We are grateful to Iris Lambert for early actin encapsulation experiments that formed the basis for establishing the eDICE method, to Federico Fanalista for acquiring images of dumbbell-shaped GUVs in samples produced by cDICE, and to Tom Aarts for images of dumbbell-shaped GUVs produced by gel-assisted swelling. Lennard van Buren is thanked for his help with image analysis to quantify actin concentrations in GUVs. We thank Kristina Ganzinger (AMOLF) for hosting us to perform pyrene assays in her lab, and Balász Antalicz (AMOLF) for technical assistance with the spectrophotometer. The authors also thank Matthieu Piel and Daniel Fletcher for insightful and inspiring discussions. We acknowledge financial support from The Netherlands Organization of Scientific Research (NWO/OCW) Gravitation program Building a Synthetic Cell (BaSyC) (024.003.019). F.F. gratefully acknowledges funding from the Kavli Synergy program of the Kavli Institute of Nanoscience Delft.","volume":122,"abstract":[{"lang":"eng","text":"The actin cortex is a complex cytoskeletal machinery that drives and responds to changes in cell shape. It must generate or adapt to plasma membrane curvature to facilitate diverse functions such as cell division, migration, and phagocytosis. Due to the complex molecular makeup of the actin cortex, it remains unclear whether actin networks are inherently able to sense and generate membrane curvature, or whether they rely on their diverse binding partners to accomplish this. Here, we show that curvature sensing is an inherent capability of branched actin networks nucleated by Arp2/3 and VCA. We develop a robust method to encapsulate actin inside giant unilamellar vesicles (GUVs) and assemble an actin cortex at the inner surface of the GUV membrane. We show that actin forms a uniform and thin cortical layer when present at high concentration and distinct patches associated with negative membrane curvature at low concentration. Serendipitously, we find that the GUV production method also produces dumbbell-shaped GUVs, which we explain using mathematical modeling in terms of membrane hemifusion of nested GUVs. We find that branched actin networks preferentially assemble at the neck of the dumbbells, which possess a micrometer-range convex curvature comparable with the curvature of the actin patches found in spherical GUVs. Minimal branched actin networks can thus sense membrane curvature, which may help mammalian cells to robustly recruit actin to curved membranes to facilitate diverse cellular functions such as cytokinesis and migration."}],"day":"06","doi":"10.1016/j.bpj.2023.02.018","external_id":{"isi":["001016792600001"],"pmid":["36806830"]},"isi":1,"citation":{"ista":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. 2023. Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. 122(11), 2311–2324.","mla":"Baldauf, Lucia, et al. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” <i>Biophysical Journal</i>, vol. 122, no. 11, Elsevier, 2023, pp. 2311–24, doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">10.1016/j.bpj.2023.02.018</a>.","short":"L. Baldauf, F.F. Frey, M. Arribas Perez, T. Idema, G.H. Koenderink, Biophysical Journal 122 (2023) 2311–2324.","ieee":"L. Baldauf, F. F. Frey, M. Arribas Perez, T. Idema, and G. H. Koenderink, “Branched actin cortices reconstituted in vesicles sense membrane curvature,” <i>Biophysical Journal</i>, vol. 122, no. 11. Elsevier, pp. 2311–2324, 2023.","chicago":"Baldauf, Lucia, Felix F Frey, Marcos Arribas Perez, Timon Idema, and Gijsje H. Koenderink. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” <i>Biophysical Journal</i>. Elsevier, 2023. <a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">https://doi.org/10.1016/j.bpj.2023.02.018</a>.","apa":"Baldauf, L., Frey, F. F., Arribas Perez, M., Idema, T., &#38; Koenderink, G. H. (2023). Branched actin cortices reconstituted in vesicles sense membrane curvature. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">https://doi.org/10.1016/j.bpj.2023.02.018</a>","ama":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. Branched actin cortices reconstituted in vesicles sense membrane curvature. <i>Biophysical Journal</i>. 2023;122(11):2311-2324. doi:<a href=\"https://doi.org/10.1016/j.bpj.2023.02.018\">10.1016/j.bpj.2023.02.018</a>"},"year":"2023","date_updated":"2024-01-16T09:20:03Z","article_type":"original","publisher":"Elsevier","file_date_updated":"2024-01-16T09:09:29Z","quality_controlled":"1","page":"2311-2324","intvolume":"       122","title":"Branched actin cortices reconstituted in vesicles sense membrane curvature","department":[{"_id":"AnSa"}],"article_processing_charge":"Yes (in subscription journal)","date_created":"2024-01-10T09:45:48Z","publication_status":"published","issue":"11","author":[{"first_name":"Lucia","last_name":"Baldauf","full_name":"Baldauf, Lucia"},{"id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","full_name":"Frey, Felix F","last_name":"Frey","first_name":"Felix F"},{"full_name":"Arribas Perez, Marcos","last_name":"Arribas Perez","first_name":"Marcos"},{"full_name":"Idema, Timon","first_name":"Timon","last_name":"Idema"},{"first_name":"Gijsje H.","last_name":"Koenderink","full_name":"Koenderink, Gijsje H."}],"_id":"14782","pmid":1},{"date_updated":"2023-08-16T08:32:29Z","citation":{"short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777.","mla":"Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.” <i>FEBS Letters</i>, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:<a href=\"https://doi.org/10.1002/1873-3468.14540\">10.1002/1873-3468.14540</a>.","ista":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. 2023. In vitro reconstitution of small GTPase regulation. FEBS Letters. 597(6), 762–777.","apa":"Loose, M., Auer, A., Brognara, G., Budiman, H. R., Kowalski, L. M., &#38; Matijevic, I. (2023). In vitro reconstitution of small GTPase regulation. <i>FEBS Letters</i>. Wiley. <a href=\"https://doi.org/10.1002/1873-3468.14540\">https://doi.org/10.1002/1873-3468.14540</a>","ama":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro reconstitution of small GTPase regulation. <i>FEBS Letters</i>. 2023;597(6):762-777. doi:<a href=\"https://doi.org/10.1002/1873-3468.14540\">10.1002/1873-3468.14540</a>","chicago":"Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.” <i>FEBS Letters</i>. Wiley, 2023. <a href=\"https://doi.org/10.1002/1873-3468.14540\">https://doi.org/10.1002/1873-3468.14540</a>.","ieee":"M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic, “In vitro reconstitution of small GTPase regulation,” <i>FEBS Letters</i>, vol. 597, no. 6. Wiley, pp. 762–777, 2023."},"year":"2023","isi":1,"external_id":{"isi":["000891573000001"],"pmid":["36448231"]},"doi":"10.1002/1873-3468.14540","day":"01","abstract":[{"text":"Small GTPases play essential roles in the organization of eukaryotic cells. In recent years, it has become clear that their intracellular functions result from intricate biochemical networks of the GTPase and their regulators that dynamically bind to a membrane surface. Due to the inherent complexities of their interactions, however, revealing the underlying mechanisms of action is often difficult to achieve from in vivo studies. This review summarizes in vitro reconstitution approaches developed to obtain a better mechanistic understanding of how small GTPase activities are regulated in space and time.","lang":"eng"}],"acknowledgement":"The authors acknowledge support from IST Austria and helpful comments from the anonymous reviewers that helped to improve this manuscript. We apologize to the authors of primary literature and outstanding research not cited here due to space restraints.","volume":597,"ddc":["570"],"pmid":1,"_id":"12163","scopus_import":"1","author":[{"orcid":"0000-0001-7309-9724","full_name":"Loose, Martin","first_name":"Martin","last_name":"Loose","id":"462D4284-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":"Brognara, Gabriel","last_name":"Brognara","first_name":"Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425"},{"id":"55380f95-15b2-11ec-abd3-aff8e230696b","full_name":"Budiman, Hanifatul R","first_name":"Hanifatul R","last_name":"Budiman"},{"id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2","full_name":"Kowalski, Lukasz M","last_name":"Kowalski","first_name":"Lukasz M"},{"id":"83c17ce3-15b2-11ec-abd3-f486545870bd","first_name":"Ivana","last_name":"Matijevic","full_name":"Matijevic, Ivana"}],"issue":"6","publication_status":"published","department":[{"_id":"MaLo"}],"date_created":"2023-01-12T12:09:58Z","article_processing_charge":"Yes (via OA deal)","title":"In vitro reconstitution of small GTPase regulation","intvolume":"       597","page":"762-777","quality_controlled":"1","file_date_updated":"2023-08-16T08:31:04Z","publisher":"Wiley","article_type":"review","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"},"date_published":"2023-03-01T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["0014-5793"],"eissn":["1873-3468"]},"oa":1,"file":[{"content_type":"application/pdf","file_name":"2023_FEBSLetters_Loose.pdf","date_updated":"2023-08-16T08:31:04Z","file_size":3148143,"checksum":"7492244d3f9c5faa1347ef03f6e5bc84","date_created":"2023-08-16T08:31:04Z","creator":"dernst","file_id":"14063","success":1,"access_level":"open_access","relation":"main_file"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication":"FEBS Letters","has_accepted_license":"1","oa_version":"Published Version","month":"03","language":[{"iso":"eng"}],"keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"]},{"year":"2022","citation":{"mla":"Zisis, Themistoklis, et al. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” <i>Biophysical Journal</i>, vol. 121, no. 1, Elsevier, 2022, pp. P44-60, doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">10.1016/j.bpj.2021.12.006</a>.","short":"T. Zisis, D. Brückner, T. Brandstätter, W.X. Siow, J. d’Alessandro, A.M. Vollmar, C.P. Broedersz, S. Zahler, Biophysical Journal 121 (2022) P44-60.","ista":"Zisis T, Brückner D, Brandstätter T, Siow WX, d’Alessandro J, Vollmar AM, Broedersz CP, Zahler S. 2022. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. Biophysical Journal. 121(1), P44-60.","ama":"Zisis T, Brückner D, Brandstätter T, et al. Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. <i>Biophysical Journal</i>. 2022;121(1):P44-60. doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">10.1016/j.bpj.2021.12.006</a>","apa":"Zisis, T., Brückner, D., Brandstätter, T., Siow, W. X., d’Alessandro, J., Vollmar, A. M., … Zahler, S. (2022). Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">https://doi.org/10.1016/j.bpj.2021.12.006</a>","chicago":"Zisis, Themistoklis, David Brückner, Tom Brandstätter, Wei Xiong Siow, Joseph d’Alessandro, Angelika M. Vollmar, Chase P. Broedersz, and Stefan Zahler. “Disentangling Cadherin-Mediated Cell-Cell Interactions in Collective Cancer Cell Migration.” <i>Biophysical Journal</i>. Elsevier, 2022. <a href=\"https://doi.org/10.1016/j.bpj.2021.12.006\">https://doi.org/10.1016/j.bpj.2021.12.006</a>.","ieee":"T. Zisis <i>et al.</i>, “Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration,” <i>Biophysical Journal</i>, vol. 121, no. 1. Elsevier, pp. P44-60, 2022."},"date_updated":"2023-08-02T13:34:25Z","external_id":{"isi":["000740815400007"]},"isi":1,"day":"04","doi":"10.1016/j.bpj.2021.12.006","abstract":[{"lang":"eng","text":"Cell dispersion from a confined area is fundamental in a number of biological processes,\r\nincluding cancer metastasis. To date, a quantitative understanding of the interplay of single\r\ncell motility, cell proliferation, and intercellular contacts remains elusive. In particular, the role\r\nof E- and N-Cadherin junctions, central components of intercellular contacts, is still\r\ncontroversial. Combining theoretical modeling with in vitro observations, we investigate the\r\ncollective spreading behavior of colonies of human cancer cells (T24). The spreading of these\r\ncolonies is driven by stochastic single-cell migration with frequent transient cell-cell contacts.\r\nWe find that inhibition of E- and N-Cadherin junctions decreases colony spreading and average\r\nspreading velocities, without affecting the strength of correlations in spreading velocities of\r\nneighboring cells. Based on a biophysical simulation model for cell migration, we show that the\r\nbehavioral changes upon disruption of these junctions can be explained by reduced repulsive\r\nexcluded volume interactions between cells. This suggests that in cancer cell migration,\r\ncadherin-based intercellular contacts sharpen cell boundaries leading to repulsive rather than\r\ncohesive interactions between cells, thereby promoting efficient cell spreading during collective\r\nmigration.\r\n"}],"acknowledgement":"Funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 201269156 - SFB 1032 (Projects B8 and B12). D.B.B. is supported in part by a DFG fellowship within the Graduate School of Quantitative Biosciences Munich (QBM) and by the Joachim Herz Stiftung.","volume":121,"ddc":["570"],"_id":"10530","issue":"1","author":[{"full_name":"Zisis, Themistoklis","last_name":"Zisis","first_name":"Themistoklis"},{"first_name":"David","last_name":"Brückner","orcid":"0000-0001-7205-2975","full_name":"Brückner, David","id":"e1e86031-6537-11eb-953a-f7ab92be508d"},{"last_name":"Brandstätter","first_name":"Tom","full_name":"Brandstätter, Tom"},{"first_name":"Wei Xiong","last_name":"Siow","full_name":"Siow, Wei Xiong"},{"full_name":"d’Alessandro, Joseph","first_name":"Joseph","last_name":"d’Alessandro"},{"first_name":"Angelika M.","last_name":"Vollmar","full_name":"Vollmar, Angelika M."},{"last_name":"Broedersz","first_name":"Chase P.","full_name":"Broedersz, Chase P."},{"first_name":"Stefan","last_name":"Zahler","full_name":"Zahler, Stefan"}],"article_processing_charge":"No","date_created":"2021-12-10T09:48:19Z","department":[{"_id":"EdHa"},{"_id":"GaTk"}],"publication_status":"published","intvolume":"       121","title":"Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration","quality_controlled":"1","page":"P44-60","file_date_updated":"2022-07-29T10:17:10Z","publisher":"Elsevier","article_type":"original","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"},"type":"journal_article","date_published":"2022-01-04T00:00:00Z","publication_identifier":{"issn":["0006-3495"]},"oa":1,"file":[{"content_type":"application/pdf","file_name":"2022_BiophysicalJour_Zisis.pdf","date_updated":"2022-07-29T10:17:10Z","checksum":"1aa7c3478e0c8256b973b632efd1f6b4","file_size":4475504,"date_created":"2022-07-29T10:17:10Z","creator":"dernst","file_id":"11697","access_level":"open_access","relation":"main_file","success":1}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","has_accepted_license":"1","publication":"Biophysical Journal","project":[{"_id":"9B861AAC-BA93-11EA-9121-9846C619BF3A","name":"NOMIS Fellowship Program"}],"oa_version":"Published Version","month":"01","keyword":["Biophysics"],"language":[{"iso":"eng"}]},{"external_id":{"pmid":["33617830"]},"date_updated":"2022-04-01T10:34:38Z","year":"2021","citation":{"ieee":"L. K. Davis, A. Šarić, B. W. Hoogenboom, and A. Zilman, “Physical modeling of multivalent interactions in the nuclear pore complex,” <i>Biophysical Journal</i>, vol. 120, no. 9. Elsevier, pp. 1565–1577, 2021.","chicago":"Davis, Luke K., Anđela Šarić, Bart W. Hoogenboom, and Anton Zilman. “Physical Modeling of Multivalent Interactions in the Nuclear Pore Complex.” <i>Biophysical Journal</i>. Elsevier, 2021. <a href=\"https://doi.org/10.1016/j.bpj.2021.01.039\">https://doi.org/10.1016/j.bpj.2021.01.039</a>.","ama":"Davis LK, Šarić A, Hoogenboom BW, Zilman A. Physical modeling of multivalent interactions in the nuclear pore complex. <i>Biophysical Journal</i>. 2021;120(9):1565-1577. doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.01.039\">10.1016/j.bpj.2021.01.039</a>","apa":"Davis, L. K., Šarić, A., Hoogenboom, B. W., &#38; Zilman, A. (2021). Physical modeling of multivalent interactions in the nuclear pore complex. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2021.01.039\">https://doi.org/10.1016/j.bpj.2021.01.039</a>","ista":"Davis LK, Šarić A, Hoogenboom BW, Zilman A. 2021. Physical modeling of multivalent interactions in the nuclear pore complex. Biophysical Journal. 120(9), 1565–1577.","short":"L.K. Davis, A. Šarić, B.W. Hoogenboom, A. Zilman, Biophysical Journal 120 (2021) 1565–1577.","mla":"Davis, Luke K., et al. “Physical Modeling of Multivalent Interactions in the Nuclear Pore Complex.” <i>Biophysical Journal</i>, vol. 120, no. 9, Elsevier, 2021, pp. 1565–77, doi:<a href=\"https://doi.org/10.1016/j.bpj.2021.01.039\">10.1016/j.bpj.2021.01.039</a>."},"abstract":[{"text":"In the nuclear pore complex, intrinsically disordered proteins (FG Nups), along with their interactions with more globular proteins called nuclear transport receptors (NTRs), are vital to the selectivity of transport into and out of the cell nucleus. Although such interactions can be modeled at different levels of coarse graining, in vitro experimental data have been quantitatively described by minimal models that describe FG Nups as cohesive homogeneous polymers and NTRs as uniformly cohesive spheres, in which the heterogeneous effects have been smeared out. By definition, these minimal models do not account for the explicit heterogeneities in FG Nup sequences, essentially a string of cohesive and noncohesive polymer units, and at the NTR surface. Here, we develop computational and analytical models that do take into account such heterogeneity in a minimal fashion and compare them with experimental data on single-molecule interactions between FG Nups and NTRs. Overall, we find that the heterogeneous nature of FG Nups and NTRs does play a role in determining equilibrium binding properties but is of much greater significance when it comes to unbinding and binding kinetics. Using our models, we predict how binding equilibria and kinetics depend on the distribution of cohesive blocks in the FG Nup sequences and of the binding pockets at the NTR surface, with multivalency playing a key role. Finally, we observe that single-molecule binding kinetics has a rather minor influence on the diffusion of NTRs in polymer melts consisting of FG-Nup-like sequences.","lang":"eng"}],"doi":"10.1016/j.bpj.2021.01.039","day":"19","extern":"1","volume":120,"author":[{"full_name":"Davis, Luke K.","first_name":"Luke K.","last_name":"Davis"},{"first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"},{"full_name":"Hoogenboom, Bart W.","first_name":"Bart W.","last_name":"Hoogenboom"},{"full_name":"Zilman, Anton","first_name":"Anton","last_name":"Zilman"}],"issue":"9","_id":"10338","pmid":1,"scopus_import":"1","title":"Physical modeling of multivalent interactions in the nuclear pore complex","intvolume":"       120","publication_status":"published","date_created":"2021-11-25T15:36:36Z","article_processing_charge":"No","page":"1565-1577","quality_controlled":"1","article_type":"original","publisher":"Elsevier","date_published":"2021-02-19T00:00:00Z","type":"journal_article","oa":1,"publication_identifier":{"issn":["0006-3495"]},"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"https://doi.org/10.1101/2020.10.01.322156","open_access":"1"}],"publication":"Biophysical Journal","month":"02","oa_version":"Preprint","language":[{"iso":"eng"}],"keyword":["biophysics"]},{"publication_identifier":{"issn":["0006-3495"]},"oa":1,"type":"journal_article","date_published":"2021-01-16T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.07.28.224741"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","oa_version":"Preprint","month":"01","publication":"Biophysical Journal","keyword":["biophysics"],"language":[{"iso":"eng"}],"day":"16","doi":"10.1016/j.bpj.2020.12.028","abstract":[{"text":"The cell membrane is an inhomogeneous system composed of phospholipids, sterols, carbohydrates, and proteins that can be directly attached to underlying cytoskeleton. The protein linkers between the membrane and the cytoskeleton are believed to have a profound effect on the mechanical properties of the cell membrane and its ability to reshape. Here, we investigate the role of membrane-cortex linkers on the extrusion of membrane tubes using computer simulations and experiments. In simulations, we find that the force for tube extrusion has a nonlinear dependence on the density of membrane-cortex attachments: at a range of low and intermediate linker densities, the force is not significantly influenced by the presence of the membrane-cortex attachments and resembles that of the bare membrane. For large concentrations of linkers, however, the force substantially increases compared with the bare membrane. In both cases, the linkers provided membrane tubes with increased stability against coalescence. We then pulled tubes from HEK cells using optical tweezers for varying expression levels of the membrane-cortex attachment protein Ezrin. In line with simulations, we observed that overexpression of Ezrin led to an increased extrusion force, while Ezrin depletion had a negligible effect on the force. Our results shed light on the importance of local protein rearrangements for membrane reshaping at nanoscopic scales.","lang":"eng"}],"citation":{"apa":"Paraschiv, A., Lagny, T. J., Campos, C. V., Coudrier, E., Bassereau, P., &#38; Šarić, A. (2021). Influence of membrane-cortex linkers on the extrusion of membrane tubes. <i>Biophysical Journal</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">https://doi.org/10.1016/j.bpj.2020.12.028</a>","ama":"Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. Influence of membrane-cortex linkers on the extrusion of membrane tubes. <i>Biophysical Journal</i>. 2021;120(4):598-606. doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">10.1016/j.bpj.2020.12.028</a>","chicago":"Paraschiv, Alexandru, Thibaut J. Lagny, Christian Vanhille Campos, Evelyne Coudrier, Patricia Bassereau, and Anđela Šarić. “Influence of Membrane-Cortex Linkers on the Extrusion of Membrane Tubes.” <i>Biophysical Journal</i>. Cell Press, 2021. <a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">https://doi.org/10.1016/j.bpj.2020.12.028</a>.","ieee":"A. Paraschiv, T. J. Lagny, C. V. Campos, E. Coudrier, P. Bassereau, and A. Šarić, “Influence of membrane-cortex linkers on the extrusion of membrane tubes,” <i>Biophysical Journal</i>, vol. 120, no. 4. Cell Press, pp. 598–606, 2021.","mla":"Paraschiv, Alexandru, et al. “Influence of Membrane-Cortex Linkers on the Extrusion of Membrane Tubes.” <i>Biophysical Journal</i>, vol. 120, no. 4, Cell Press, 2021, pp. 598–606, doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.12.028\">10.1016/j.bpj.2020.12.028</a>.","short":"A. Paraschiv, T.J. Lagny, C.V. Campos, E. Coudrier, P. Bassereau, A. Šarić, Biophysical Journal 120 (2021) 598–606.","ista":"Paraschiv A, Lagny TJ, Campos CV, Coudrier E, Bassereau P, Šarić A. 2021. Influence of membrane-cortex linkers on the extrusion of membrane tubes. Biophysical Journal. 120(4), 598–606."},"year":"2021","date_updated":"2022-04-01T10:38:01Z","external_id":{"pmid":["33460596"]},"volume":120,"acknowledgement":"We thank Ewa Paluch, Alba Diz-Muñoz, Guillaume Salbreux, Guillaume Charras, and Shiladitya Banerjee for helpful discussions. We acknowledge support from the Engineering and Physical Sciences Research Council (A.P. and A.Š.), the UCL Institute for the Physics of Living Systems (A.P., C.V.C., and A.Š.), the Royal Society (C.V.C. and A.Š.), and the European Research Council (Starting grant EP/R011818/1 to A.Š.; E.C. and P.B. are partners of the advanced grant, project 339847) and from Institut Curie (E.C. and P.B.) and Centre National de la Recherche Scientifique (CNRS) (E.C. and P.B.). The P.B. and E.C. groups belong to Labex CelTisPhyBio (ANR-11-LABX0038) and to Paris Sciences et Lettres (ANR-10-IDEX-0001-02). T.L. received a PhD grant from Paris Sciences et Lettres Research University and support from the Institut Curie.","extern":"1","article_processing_charge":"No","date_created":"2021-11-25T16:18:23Z","publication_status":"published","intvolume":"       120","title":"Influence of membrane-cortex linkers on the extrusion of membrane tubes","scopus_import":"1","pmid":1,"_id":"10340","issue":"4","author":[{"first_name":"Alexandru","last_name":"Paraschiv","full_name":"Paraschiv, Alexandru"},{"full_name":"Lagny, Thibaut J.","first_name":"Thibaut J.","last_name":"Lagny"},{"full_name":"Campos, Christian Vanhille","last_name":"Campos","first_name":"Christian Vanhille"},{"last_name":"Coudrier","first_name":"Evelyne","full_name":"Coudrier, Evelyne"},{"last_name":"Bassereau","first_name":"Patricia","full_name":"Bassereau, Patricia"},{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"publisher":"Cell Press","article_type":"original","quality_controlled":"1","page":"598-606"},{"volume":55,"acknowledgement":"The authors would like to thank Feyza Nur Arslan, Suyash Naik, Diana Pinheiro, Alexandra Schauer, and Shayan Shamipour for their comments on the draft. N.M. is supported by an ISTplus postdoctoral fellowship (H2020 Marie-Sklodowska-Curie COFUND Action).","doi":"10.1146/annurev-genet-071819-103748","day":"30","abstract":[{"lang":"eng","text":"Multicellular organisms develop complex shapes from much simpler, single-celled zygotes through a process commonly called morphogenesis. Morphogenesis involves an interplay between several factors, ranging from the gene regulatory networks determining cell fate and differentiation to the mechanical processes underlying cell and tissue shape changes. Thus, the study of morphogenesis has historically been based on multidisciplinary approaches at the interface of biology with physics and mathematics. Recent technological advances have further improved our ability to study morphogenesis by bridging the gap between the genetic and biophysical factors through the development of new tools for visualizing, analyzing, and perturbing these factors and their biochemical intermediaries. Here, we review how a combination of genetic, microscopic, biophysical, and biochemical approaches has aided our attempts to understand morphogenesis and discuss potential approaches that may be beneficial to such an inquiry in the future."}],"date_updated":"2023-08-14T13:05:13Z","year":"2021","citation":{"ista":"Mishra N, Heisenberg C-PJ. 2021. Dissecting organismal morphogenesis by bridging genetics and biophysics. Annual Review of Genetics. 55, 209–233.","mla":"Mishra, Nikhil, and Carl-Philipp J. Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” <i>Annual Review of Genetics</i>, vol. 55, Annual Reviews, 2021, pp. 209–33, doi:<a href=\"https://doi.org/10.1146/annurev-genet-071819-103748\">10.1146/annurev-genet-071819-103748</a>.","short":"N. Mishra, C.-P.J. Heisenberg, Annual Review of Genetics 55 (2021) 209–233.","chicago":"Mishra, Nikhil, and Carl-Philipp J Heisenberg. “Dissecting Organismal Morphogenesis by Bridging Genetics and Biophysics.” <i>Annual Review of Genetics</i>. Annual Reviews, 2021. <a href=\"https://doi.org/10.1146/annurev-genet-071819-103748\">https://doi.org/10.1146/annurev-genet-071819-103748</a>.","ieee":"N. Mishra and C.-P. J. Heisenberg, “Dissecting organismal morphogenesis by bridging genetics and biophysics,” <i>Annual Review of Genetics</i>, vol. 55. Annual Reviews, pp. 209–233, 2021.","ama":"Mishra N, Heisenberg C-PJ. Dissecting organismal morphogenesis by bridging genetics and biophysics. <i>Annual Review of Genetics</i>. 2021;55:209-233. doi:<a href=\"https://doi.org/10.1146/annurev-genet-071819-103748\">10.1146/annurev-genet-071819-103748</a>","apa":"Mishra, N., &#38; Heisenberg, C.-P. J. (2021). Dissecting organismal morphogenesis by bridging genetics and biophysics. <i>Annual Review of Genetics</i>. Annual Reviews. <a href=\"https://doi.org/10.1146/annurev-genet-071819-103748\">https://doi.org/10.1146/annurev-genet-071819-103748</a>"},"isi":1,"external_id":{"pmid":["34460295"],"isi":["000747220900010"]},"publisher":"Annual Reviews","article_type":"original","page":"209-233","quality_controlled":"1","ec_funded":1,"publication_status":"published","department":[{"_id":"CaHe"}],"article_processing_charge":"No","date_created":"2021-12-05T23:01:41Z","title":"Dissecting organismal morphogenesis by bridging genetics and biophysics","intvolume":"        55","pmid":1,"_id":"10406","scopus_import":"1","author":[{"id":"C4D70E82-1081-11EA-B3ED-9A4C3DDC885E","full_name":"Mishra, Nikhil","orcid":"0000-0002-6425-5788","last_name":"Mishra","first_name":"Nikhil"},{"first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"issn":["0066-4197"],"eissn":["1545-2948"]},"date_published":"2021-08-30T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"keyword":["morphogenesis","forward genetics","high-resolution microscopy","biophysics","biochemistry","patterning"],"oa_version":"None","project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"month":"08","publication":"Annual Review of Genetics"},{"date_published":"2020-09-23T00:00:00Z","type":"journal_article","oa":1,"publication_identifier":{"issn":["0006-3495"]},"status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/2020.06.08.140061v1"}],"publication":"Biophysical Journal","month":"09","oa_version":"Published Version","language":[{"iso":"eng"}],"keyword":["biophysics"],"external_id":{"pmid":["33049216"]},"date_updated":"2021-11-26T07:45:24Z","citation":{"ama":"Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. Modeling fibrillogenesis of collagen-mimetic molecules. <i>Biophysical Journal</i>. 2020;119(9):1791-1799. doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.09.013\">10.1016/j.bpj.2020.09.013</a>","apa":"Hafner, A. E., Gyori, N. G., Bench, C. A., Davis, L. K., &#38; Šarić, A. (2020). Modeling fibrillogenesis of collagen-mimetic molecules. <i>Biophysical Journal</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.bpj.2020.09.013\">https://doi.org/10.1016/j.bpj.2020.09.013</a>","chicago":"Hafner, Anne E., Noemi G. Gyori, Ciaran A. Bench, Luke K. Davis, and Anđela Šarić. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” <i>Biophysical Journal</i>. Cell Press, 2020. <a href=\"https://doi.org/10.1016/j.bpj.2020.09.013\">https://doi.org/10.1016/j.bpj.2020.09.013</a>.","ieee":"A. E. Hafner, N. G. Gyori, C. A. Bench, L. K. Davis, and A. Šarić, “Modeling fibrillogenesis of collagen-mimetic molecules,” <i>Biophysical Journal</i>, vol. 119, no. 9. Cell Press, pp. 1791–1799, 2020.","short":"A.E. Hafner, N.G. Gyori, C.A. Bench, L.K. Davis, A. Šarić, Biophysical Journal 119 (2020) 1791–1799.","mla":"Hafner, Anne E., et al. “Modeling Fibrillogenesis of Collagen-Mimetic Molecules.” <i>Biophysical Journal</i>, vol. 119, no. 9, Cell Press, 2020, pp. 1791–99, doi:<a href=\"https://doi.org/10.1016/j.bpj.2020.09.013\">10.1016/j.bpj.2020.09.013</a>.","ista":"Hafner AE, Gyori NG, Bench CA, Davis LK, Šarić A. 2020. Modeling fibrillogenesis of collagen-mimetic molecules. Biophysical Journal. 119(9), 1791–1799."},"year":"2020","abstract":[{"text":"One of the most robust examples of self-assembly in living organisms is the formation of collagen architectures. Collagen type I molecules are a crucial component of the extracellular matrix, where they self-assemble into fibrils of well-defined axial striped patterns. This striped fibrillar pattern is preserved across the animal kingdom and is important for the determination of cell phenotype, cell adhesion, and tissue regulation and signaling. The understanding of the physical processes that determine such a robust morphology of self-assembled collagen fibrils is currently almost completely missing. Here, we develop a minimal coarse-grained computational model to identify the physical principles of the assembly of collagen-mimetic molecules. We find that screened electrostatic interactions can drive the formation of collagen-like filaments of well-defined striped morphologies. The fibril axial pattern is determined solely by the distribution of charges on the molecule and is robust to the changes in protein concentration, monomer rigidity, and environmental conditions. We show that the striped fibrillar pattern cannot be easily predicted from the interactions between two monomers but is an emergent result of multibody interactions. Our results can help address collagen remodeling in diseases and aging and guide the design of collagen scaffolds for biotechnological applications.","lang":"eng"}],"doi":"10.1016/j.bpj.2020.09.013","day":"23","extern":"1","acknowledgement":"We thank Melinda Duer, Patrick Mesquida, Lucy Colwell, Lucie Liu, Daan Frenkel, and Ivan Palaia for helpful discussions. We acknowledge support from the Engineering and Physical Sciences Research Council (A.E.H., L.K.D., and A.Š.), Biotechnology and Biological Sciences Research Council LIDo programme (N.G.G. and C.A.B.), the Royal Society (A.Š.), and the UK Materials and Molecular Modelling Hub for computational resources, which is partially funded by EPSRC ( EP/P020194/1).","volume":119,"author":[{"full_name":"Hafner, Anne E.","last_name":"Hafner","first_name":"Anne E."},{"first_name":"Noemi G.","last_name":"Gyori","full_name":"Gyori, Noemi G."},{"full_name":"Bench, Ciaran A.","last_name":"Bench","first_name":"Ciaran A."},{"last_name":"Davis","first_name":"Luke K.","full_name":"Davis, Luke K."},{"orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","first_name":"Anđela","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b"}],"issue":"9","_id":"10346","pmid":1,"scopus_import":"1","title":"Modeling fibrillogenesis of collagen-mimetic molecules","intvolume":"       119","publication_status":"published","date_created":"2021-11-26T07:27:24Z","article_processing_charge":"No","page":"1791-1799","quality_controlled":"1","article_type":"original","publisher":"Cell Press"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","extern":"1","volume":306,"day":"01","publication_identifier":{"issn":["1090-7807"]},"doi":"10.1016/j.jmr.2019.07.025","external_id":{"pmid":["31350165"]},"type":"journal_article","date_published":"2019-09-01T00:00:00Z","year":"2019","citation":{"ista":"Schanda P. 2019. Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. 306, 180–186.","short":"P. Schanda, Journal of Magnetic Resonance 306 (2019) 180–186.","mla":"Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular Dynamics.” <i>Journal of Magnetic Resonance</i>, vol. 306, Elsevier, 2019, pp. 180–86, doi:<a href=\"https://doi.org/10.1016/j.jmr.2019.07.025\">10.1016/j.jmr.2019.07.025</a>.","chicago":"Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular Dynamics.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.jmr.2019.07.025\">https://doi.org/10.1016/j.jmr.2019.07.025</a>.","ieee":"P. Schanda, “Relaxing with liquids and solids – A perspective on biomolecular dynamics,” <i>Journal of Magnetic Resonance</i>, vol. 306. Elsevier, pp. 180–186, 2019.","ama":"Schanda P. Relaxing with liquids and solids – A perspective on biomolecular dynamics. <i>Journal of Magnetic Resonance</i>. 2019;306:180-186. doi:<a href=\"https://doi.org/10.1016/j.jmr.2019.07.025\">10.1016/j.jmr.2019.07.025</a>","apa":"Schanda, P. (2019). Relaxing with liquids and solids – A perspective on biomolecular dynamics. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2019.07.025\">https://doi.org/10.1016/j.jmr.2019.07.025</a>"},"date_updated":"2021-01-12T08:19:04Z","article_type":"original","publisher":"Elsevier","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"language":[{"iso":"eng"}],"quality_controlled":"1","page":"180-186","intvolume":"       306","month":"09","title":"Relaxing with liquids and solids – A perspective on biomolecular dynamics","date_created":"2020-09-17T10:28:47Z","article_processing_charge":"No","publication_status":"published","oa_version":"Submitted Version","author":[{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"pmid":1,"_id":"8407","publication":"Journal of Magnetic Resonance"},{"language":[{"iso":"eng"}],"keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"has_accepted_license":"1","oa_version":"Published Version","project":[{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573","name":"Design principles underlying genetic switch architecture (DOC Fellowship)"}],"month":"05","file":[{"date_updated":"2021-02-11T11:17:13Z","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","content_type":"application/pdf","embargo":"2020-05-02","date_created":"2019-05-03T11:54:52Z","checksum":"c0085d47c58c9cbcab1b0a783480f6da","file_size":12597663,"file_id":"6373","creator":"cigler","access_level":"open_access","relation":"main_file"},{"date_created":"2019-05-03T11:54:54Z","file_size":34644426,"checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","embargo_to":"open_access","date_updated":"2020-07-14T12:47:28Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","access_level":"closed","relation":"source_file","file_id":"6374","creator":"cigler"}],"status":"public","related_material":{"record":[{"id":"67","relation":"part_of_dissertation","status":"public"},{"relation":"popular_science","id":"5585","status":"public"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2019-05-03T00:00:00Z","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet"}],"oa":1,"page":"152","file_date_updated":"2021-02-11T11:17:13Z","publisher":"Institute of Science and Technology Austria","_id":"6371","author":[{"full_name":"Igler, Claudia","last_name":"Igler","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"CaGu"}],"date_created":"2019-05-03T11:55:51Z","article_processing_charge":"No","title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","alternative_title":["ISTA Thesis"],"ddc":["576","579"],"date_updated":"2024-02-21T13:45:52Z","year":"2019","citation":{"mla":"Igler, Claudia. <i>On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6371\">10.15479/AT:ISTA:6371</a>.","short":"C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.","ista":"Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria.","apa":"Igler, C. (2019). <i>On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6371\">https://doi.org/10.15479/AT:ISTA:6371</a>","ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6371\">10.15479/AT:ISTA:6371</a>","ieee":"C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019.","chicago":"Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6371\">https://doi.org/10.15479/AT:ISTA:6371</a>."},"degree_awarded":"PhD","doi":"10.15479/AT:ISTA:6371","day":"03","abstract":[{"lang":"eng","text":"Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation.   \r\n"}]},{"intvolume":"       113","title":"Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity","month":"12","date_created":"2020-09-18T10:05:54Z","article_processing_charge":"No","oa_version":"None","publication_status":"published","issue":"11","author":[{"full_name":"Dehez, François","first_name":"François","last_name":"Dehez"},{"full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"first_name":"Martin S.","last_name":"King","full_name":"King, Martin S."},{"full_name":"Kunji, Edmund R.S.","first_name":"Edmund R.S.","last_name":"Kunji"},{"last_name":"Chipot","first_name":"Christophe","full_name":"Chipot, Christophe"}],"_id":"8444","publication":"Biophysical Journal","article_type":"original","publisher":"Elsevier","keyword":["Biophysics"],"language":[{"iso":"eng"}],"quality_controlled":"1","page":"2311-2315","abstract":[{"lang":"eng","text":"Biophysical investigation of membrane proteins generally requires their extraction from native sources using detergents, a step that can lead, possibly irreversibly, to protein denaturation. The propensity of dodecylphosphocholine (DPC), a detergent widely utilized in NMR studies of membrane proteins, to distort their structure has been the subject of much controversy. It has been recently proposed that the binding specificity of the yeast mitochondrial ADP/ATP carrier (yAAC3) toward cardiolipins is preserved in DPC, thereby suggesting that DPC is a suitable environment in which to study membrane proteins. In this communication, we used all-atom molecular dynamics simulations to investigate the specific binding of cardiolipins to yAAC3. Our data demonstrate that the interaction interface observed in a native-like environment differs markedly from that inferred from an NMR investigation in DPC, implying that in this detergent, the protein structure is distorted. We further investigated yAAC3 solubilized in DPC and in the milder dodecylmaltoside with thermal-shift assays. The loss of thermal transition observed in DPC confirms that the protein is no longer properly folded in this environment."}],"day":"05","publication_identifier":{"issn":["0006-3495"]},"doi":"10.1016/j.bpj.2017.09.019","type":"journal_article","date_published":"2017-12-05T00:00:00Z","citation":{"mla":"Dehez, François, et al. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-Native Affinity.” <i>Biophysical Journal</i>, vol. 113, no. 11, Elsevier, 2017, pp. 2311–15, doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.09.019\">10.1016/j.bpj.2017.09.019</a>.","short":"F. Dehez, P. Schanda, M.S. King, E.R.S. Kunji, C. Chipot, Biophysical Journal 113 (2017) 2311–2315.","ista":"Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. 2017. Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity. Biophysical Journal. 113(11), 2311–2315.","apa":"Dehez, F., Schanda, P., King, M. S., Kunji, E. R. S., &#38; Chipot, C. (2017). Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2017.09.019\">https://doi.org/10.1016/j.bpj.2017.09.019</a>","ama":"Dehez F, Schanda P, King MS, Kunji ERS, Chipot C. Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity. <i>Biophysical Journal</i>. 2017;113(11):2311-2315. doi:<a href=\"https://doi.org/10.1016/j.bpj.2017.09.019\">10.1016/j.bpj.2017.09.019</a>","chicago":"Dehez, François, Paul Schanda, Martin S. King, Edmund R.S. Kunji, and Christophe Chipot. “Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-Native Affinity.” <i>Biophysical Journal</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.bpj.2017.09.019\">https://doi.org/10.1016/j.bpj.2017.09.019</a>.","ieee":"F. Dehez, P. Schanda, M. S. King, E. R. S. Kunji, and C. Chipot, “Mitochondrial ADP/ATP carrier in dodecylphosphocholine binds cardiolipins with non-native affinity,” <i>Biophysical Journal</i>, vol. 113, no. 11. Elsevier, pp. 2311–2315, 2017."},"year":"2017","date_updated":"2021-01-12T08:19:18Z","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","volume":113},{"volume":281,"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","citation":{"ama":"Franco R, Favier A, Schanda P, Brutscher B. Optimized fast mixing device for real-time NMR applications. <i>Journal of Magnetic Resonance</i>. 2017;281(8):125-129. doi:<a href=\"https://doi.org/10.1016/j.jmr.2017.05.016\">10.1016/j.jmr.2017.05.016</a>","apa":"Franco, R., Favier, A., Schanda, P., &#38; Brutscher, B. (2017). Optimized fast mixing device for real-time NMR applications. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2017.05.016\">https://doi.org/10.1016/j.jmr.2017.05.016</a>","ieee":"R. Franco, A. Favier, P. Schanda, and B. Brutscher, “Optimized fast mixing device for real-time NMR applications,” <i>Journal of Magnetic Resonance</i>, vol. 281, no. 8. Elsevier, pp. 125–129, 2017.","chicago":"Franco, Rémi, Adrien Favier, Paul Schanda, and Bernhard Brutscher. “Optimized Fast Mixing Device for Real-Time NMR Applications.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.jmr.2017.05.016\">https://doi.org/10.1016/j.jmr.2017.05.016</a>.","mla":"Franco, Rémi, et al. “Optimized Fast Mixing Device for Real-Time NMR Applications.” <i>Journal of Magnetic Resonance</i>, vol. 281, no. 8, Elsevier, 2017, pp. 125–29, doi:<a href=\"https://doi.org/10.1016/j.jmr.2017.05.016\">10.1016/j.jmr.2017.05.016</a>.","short":"R. Franco, A. Favier, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 281 (2017) 125–129.","ista":"Franco R, Favier A, Schanda P, Brutscher B. 2017. Optimized fast mixing device for real-time NMR applications. Journal of Magnetic Resonance. 281(8), 125–129."},"year":"2017","date_updated":"2021-01-12T08:19:20Z","type":"journal_article","date_published":"2017-08-01T00:00:00Z","publication_identifier":{"issn":["1090-7807"]},"day":"01","doi":"10.1016/j.jmr.2017.05.016","abstract":[{"text":"We present an improved fast mixing device based on the rapid mixing of two solutions inside the NMR probe, as originally proposed by Hore and coworkers (J. Am. Chem. Soc. 125 (2003) 12484–12492). Such a device is important for off-equilibrium studies of molecular kinetics by multidimensional real-time NMR spectrsocopy. The novelty of this device is that it allows removing the injector from the NMR detection volume after mixing, and thus provides good magnetic field homogeneity independently of the initial sample volume placed in the NMR probe. The apparatus is simple to build, inexpensive, and can be used without any hardware modification on any type of liquid-state NMR spectrometer. We demonstrate the performance of our fast mixing device in terms of improved magnetic field homogeneity, and show an application to the study of protein folding and the structural characterization of transiently populated folding intermediates.","lang":"eng"}],"quality_controlled":"1","page":"125-129","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"language":[{"iso":"eng"}],"publisher":"Elsevier","article_type":"original","publication":"Journal of Magnetic Resonance","_id":"8448","issue":"8","author":[{"last_name":"Franco","first_name":"Rémi","full_name":"Franco, Rémi"},{"last_name":"Favier","first_name":"Adrien","full_name":"Favier, Adrien"},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"first_name":"Bernhard","last_name":"Brutscher","full_name":"Brutscher, Bernhard"}],"date_created":"2020-09-18T10:06:27Z","article_processing_charge":"No","oa_version":"None","publication_status":"published","intvolume":"       281","title":"Optimized fast mixing device for real-time NMR applications","month":"08"},{"publication":"Biophysical Journal","oa_version":"None","month":"02","article_number":"25a","language":[{"iso":"eng"}],"keyword":["Biophysics"],"date_published":"2017-02-03T00:00:00Z","type":"journal_article","publication_identifier":{"issn":["0006-3495"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","_id":"14308","scopus_import":"1","author":[{"last_name":"Praetorius","first_name":"Florian M","full_name":"Praetorius, Florian M","id":"dfec9381-4341-11ee-8fd8-faa02bba7d62"},{"last_name":"Dietz","first_name":"Hendrik","full_name":"Dietz, Hendrik"}],"issue":"3","publication_status":"published","article_processing_charge":"No","date_created":"2023-09-06T13:19:10Z","title":"Genetically encoded DNA-protein hybrid origami","intvolume":"       112","quality_controlled":"1","publisher":"Elsevier","article_type":"original","date_updated":"2023-11-07T11:28:58Z","year":"2017","citation":{"ista":"Praetorius FM, Dietz H. 2017. Genetically encoded DNA-protein hybrid origami. Biophysical Journal. 112(3), 25a.","mla":"Praetorius, Florian M., and Hendrik Dietz. “Genetically Encoded DNA-Protein Hybrid Origami.” <i>Biophysical Journal</i>, vol. 112, no. 3, 25a, Elsevier, 2017, doi:<a href=\"https://doi.org/10.1016/j.bpj.2016.11.171\">10.1016/j.bpj.2016.11.171</a>.","short":"F.M. Praetorius, H. Dietz, Biophysical Journal 112 (2017).","ieee":"F. M. Praetorius and H. Dietz, “Genetically encoded DNA-protein hybrid origami,” <i>Biophysical Journal</i>, vol. 112, no. 3. Elsevier, 2017.","chicago":"Praetorius, Florian M, and Hendrik Dietz. “Genetically Encoded DNA-Protein Hybrid Origami.” <i>Biophysical Journal</i>. Elsevier, 2017. <a href=\"https://doi.org/10.1016/j.bpj.2016.11.171\">https://doi.org/10.1016/j.bpj.2016.11.171</a>.","apa":"Praetorius, F. M., &#38; Dietz, H. (2017). Genetically encoded DNA-protein hybrid origami. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2016.11.171\">https://doi.org/10.1016/j.bpj.2016.11.171</a>","ama":"Praetorius FM, Dietz H. Genetically encoded DNA-protein hybrid origami. <i>Biophysical Journal</i>. 2017;112(3). doi:<a href=\"https://doi.org/10.1016/j.bpj.2016.11.171\">10.1016/j.bpj.2016.11.171</a>"},"doi":"10.1016/j.bpj.2016.11.171","day":"03","abstract":[{"text":"Here we describe an approach to bottom-up fabrication with nanometer-precision that allows integrating the functional diversity of proteins in designed three-dimensional structural frameworks. We reimagined the successful DNA origami design principle using a set of custom staple proteins to fold a double-stranded DNA template into a user-defined shape. Each staple protein recognizes two distinct double-helical DNA sequences and can carry additional functionalities. The staple proteins we present here are based on the transcription activator-like (TAL) effector proteins. Due to their repetitive structure these proteins offer a unique programmability that enables us to construct numerous staple proteins targeting any desired DNA sequence. Our approach is general, meaning that many different objects may be created using the same set of rules, and it is modular, because components can be modified or exchanged individually. We present rules for constructing megadalton-scale DNA-protein hybrid nanostructures; introduce important structural motifs, such as curvature, corners, and vertices; describe principles for creating multi-layer DNA-protein objects with enhanced rigidity; and demonstrate the possibility to combine our DNA-protein hybrid origami with conventional DNA nanotechnology. Since all components can be encoded genetically, our structures should be amenable to biotechnological mass-production. Moreover, since the target objects can self-assemble at room temperature in near-physiological buffer, our hybrid origami may also provide an attractive method to realize positioning and scaffolding tasks in vivo. We expect our method to find application both in scaffolding protein functionalities and in manipulating the spatial arrangement of genomic DNA.","lang":"eng"}],"volume":112,"extern":"1"},{"extern":"1","volume":112,"doi":"10.1016/j.bpj.2016.11.2123","day":"03","date_updated":"2021-11-03T10:02:45Z","citation":{"ama":"Vahid Belarghou A, Šarić A, Idema T. Curvature mediated interactions in highly curved membranes. <i>Biophysical Journal</i>. 2017;112(3). doi:<a href=\"https://doi.org/10.1016/j.bpj.2016.11.2123\">10.1016/j.bpj.2016.11.2123</a>","apa":"Vahid Belarghou, A., Šarić, A., &#38; Idema, T. (2017). Curvature mediated interactions in highly curved membranes. <i>Biophysical Journal</i>. Elsevier . <a href=\"https://doi.org/10.1016/j.bpj.2016.11.2123\">https://doi.org/10.1016/j.bpj.2016.11.2123</a>","chicago":"Vahid Belarghou, Afshin, Anđela Šarić, and Timon Idema. “Curvature Mediated Interactions in Highly Curved Membranes.” <i>Biophysical Journal</i>. Elsevier , 2017. <a href=\"https://doi.org/10.1016/j.bpj.2016.11.2123\">https://doi.org/10.1016/j.bpj.2016.11.2123</a>.","ieee":"A. Vahid Belarghou, A. Šarić, and T. Idema, “Curvature mediated interactions in highly curved membranes,” <i>Biophysical Journal</i>, vol. 112, no. 3. Elsevier , 2017.","mla":"Vahid Belarghou, Afshin, et al. “Curvature Mediated Interactions in Highly Curved Membranes.” <i>Biophysical Journal</i>, vol. 112, no. 3, 391a, Elsevier , 2017, doi:<a href=\"https://doi.org/10.1016/j.bpj.2016.11.2123\">10.1016/j.bpj.2016.11.2123</a>.","short":"A. Vahid Belarghou, A. Šarić, T. Idema, Biophysical Journal 112 (2017).","ista":"Vahid Belarghou A, Šarić A, Idema T. 2017. Curvature mediated interactions in highly curved membranes. Biophysical Journal. 112(3), 391a."},"year":"2017","article_type":"letter_note","publisher":"Elsevier ","quality_controlled":"1","title":"Curvature mediated interactions in highly curved membranes","intvolume":"       112","publication_status":"published","article_processing_charge":"No","date_created":"2021-10-12T07:47:55Z","author":[{"full_name":"Vahid Belarghou, Afshin","last_name":"Vahid Belarghou","first_name":"Afshin"},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","last_name":"Šarić","first_name":"Anđela"},{"last_name":"Idema","first_name":"Timon","full_name":"Idema, Timon"}],"issue":"3","_id":"10126","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","main_file_link":[{"open_access":"1","url":"https://www.cell.com/biophysj/fulltext/S0006-3495(16)33153-8"}],"oa":1,"publication_identifier":{"issn":["0006-3495"]},"date_published":"2017-02-03T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"keyword":["biophysics"],"month":"02","article_number":"391a","oa_version":"Published Version","publication":"Biophysical Journal"},{"author":[{"first_name":"Benjamin M.","last_name":"Regner","full_name":"Regner, Benjamin M."},{"full_name":"Vučinić, Dejan","first_name":"Dejan","last_name":"Vučinić"},{"last_name":"Domnisoru","first_name":"Cristina","full_name":"Domnisoru, Cristina"},{"full_name":"Bartol, Thomas M.","last_name":"Bartol","first_name":"Thomas M."},{"orcid":"0000-0002-2111-992X","full_name":"HETZER, Martin W","first_name":"Martin W","last_name":"HETZER","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed"},{"full_name":"Tartakovsky, Daniel M.","first_name":"Daniel M.","last_name":"Tartakovsky"},{"full_name":"Sejnowski, Terrence J.","first_name":"Terrence J.","last_name":"Sejnowski"}],"issue":"8","pmid":1,"_id":"11088","scopus_import":"1","title":"Anomalous diffusion of single particles in cytoplasm","intvolume":"       104","publication_status":"published","date_created":"2022-04-07T07:51:26Z","article_processing_charge":"No","page":"1652-1660","quality_controlled":"1","article_type":"original","publisher":"Elsevier","external_id":{"pmid":["23601312"]},"date_updated":"2022-07-18T08:51:01Z","year":"2013","citation":{"ieee":"B. M. Regner <i>et al.</i>, “Anomalous diffusion of single particles in cytoplasm,” <i>Biophysical Journal</i>, vol. 104, no. 8. Elsevier, pp. 1652–1660, 2013.","chicago":"Regner, Benjamin M., Dejan Vučinić, Cristina Domnisoru, Thomas M. Bartol, Martin Hetzer, Daniel M. Tartakovsky, and Terrence J. Sejnowski. “Anomalous Diffusion of Single Particles in Cytoplasm.” <i>Biophysical Journal</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.bpj.2013.01.049\">https://doi.org/10.1016/j.bpj.2013.01.049</a>.","apa":"Regner, B. M., Vučinić, D., Domnisoru, C., Bartol, T. M., Hetzer, M., Tartakovsky, D. M., &#38; Sejnowski, T. J. (2013). Anomalous diffusion of single particles in cytoplasm. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2013.01.049\">https://doi.org/10.1016/j.bpj.2013.01.049</a>","ama":"Regner BM, Vučinić D, Domnisoru C, et al. Anomalous diffusion of single particles in cytoplasm. <i>Biophysical Journal</i>. 2013;104(8):1652-1660. doi:<a href=\"https://doi.org/10.1016/j.bpj.2013.01.049\">10.1016/j.bpj.2013.01.049</a>","ista":"Regner BM, Vučinić D, Domnisoru C, Bartol TM, Hetzer M, Tartakovsky DM, Sejnowski TJ. 2013. Anomalous diffusion of single particles in cytoplasm. Biophysical Journal. 104(8), 1652–1660.","mla":"Regner, Benjamin M., et al. “Anomalous Diffusion of Single Particles in Cytoplasm.” <i>Biophysical Journal</i>, vol. 104, no. 8, Elsevier, 2013, pp. 1652–60, doi:<a href=\"https://doi.org/10.1016/j.bpj.2013.01.049\">10.1016/j.bpj.2013.01.049</a>.","short":"B.M. Regner, D. Vučinić, C. Domnisoru, T.M. Bartol, M. Hetzer, D.M. Tartakovsky, T.J. Sejnowski, Biophysical Journal 104 (2013) 1652–1660."},"abstract":[{"lang":"eng","text":"The crowded intracellular environment poses a formidable challenge to experimental and theoretical analyses of intracellular transport mechanisms. Our measurements of single-particle trajectories in cytoplasm and their random-walk interpretations elucidate two of these mechanisms: molecular diffusion in crowded environments and cytoskeletal transport along microtubules. We employed acousto-optic deflector microscopy to map out the three-dimensional trajectories of microspheres migrating in the cytosolic fraction of a cellular extract. Classical Brownian motion (BM), continuous time random walk, and fractional BM were alternatively used to represent these trajectories. The comparison of the experimental and numerical data demonstrates that cytoskeletal transport along microtubules and diffusion in the cytosolic fraction exhibit anomalous (nonFickian) behavior and posses statistically distinct signatures. Among the three random-walk models used, continuous time random walk provides the best representation of diffusion, whereas microtubular transport is accurately modeled with fractional BM."}],"doi":"10.1016/j.bpj.2013.01.049","day":"16","extern":"1","volume":104,"publication":"Biophysical Journal","month":"04","oa_version":"Published Version","language":[{"iso":"eng"}],"keyword":["Biophysics"],"date_published":"2013-04-16T00:00:00Z","type":"journal_article","oa":1,"publication_identifier":{"issn":["0006-3495"]},"user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.bpj.2013.01.049"}]},{"extern":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":210,"date_published":"2011-06-01T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T08:19:29Z","citation":{"ama":"Schanda P, Meier BH, Ernst M. Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR. <i>Journal of Magnetic Resonance</i>. 2011;210(2):246-259. doi:<a href=\"https://doi.org/10.1016/j.jmr.2011.03.015\">10.1016/j.jmr.2011.03.015</a>","apa":"Schanda, P., Meier, B. H., &#38; Ernst, M. (2011). Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2011.03.015\">https://doi.org/10.1016/j.jmr.2011.03.015</a>","ieee":"P. Schanda, B. H. Meier, and M. Ernst, “Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR,” <i>Journal of Magnetic Resonance</i>, vol. 210, no. 2. Elsevier, pp. 246–259, 2011.","chicago":"Schanda, Paul, Beat H. Meier, and Matthias Ernst. “Accurate Measurement of One-Bond H–X Heteronuclear Dipolar Couplings in MAS Solid-State NMR.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.jmr.2011.03.015\">https://doi.org/10.1016/j.jmr.2011.03.015</a>.","mla":"Schanda, Paul, et al. “Accurate Measurement of One-Bond H–X Heteronuclear Dipolar Couplings in MAS Solid-State NMR.” <i>Journal of Magnetic Resonance</i>, vol. 210, no. 2, Elsevier, 2011, pp. 246–59, doi:<a href=\"https://doi.org/10.1016/j.jmr.2011.03.015\">10.1016/j.jmr.2011.03.015</a>.","short":"P. Schanda, B.H. Meier, M. Ernst, Journal of Magnetic Resonance 210 (2011) 246–259.","ista":"Schanda P, Meier BH, Ernst M. 2011. Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR. Journal of Magnetic Resonance. 210(2), 246–259."},"year":"2011","abstract":[{"lang":"eng","text":"The accurate experimental determination of dipolar-coupling constants for one-bond heteronuclear dipolar couplings in solids is a key for the quantification of the amplitudes of motional processes. Averaging of the dipolar coupling reports on motions on time scales up to the inverse of the coupling constant, in our case tens of microseconds. Combining dipolar-coupling derived order parameters that characterize the amplitudes of the motion with relaxation data leads to a more precise characterization of the dynamical parameters and helps to disentangle the amplitudes and the time scales of the motional processes, which impact relaxation rates in a highly correlated way. Here. we describe and characterize an improved experimental protocol – based on REDOR – to measure these couplings in perdeuterated proteins with a reduced sensitivity to experimental missettings. Because such effects are presently the dominant source of systematic errors in experimental dipolar-coupling measurements, these compensated experiments should help to significantly improve the precision of such data. A detailed comparison with other commonly used pulse sequences (T-MREV, phase-inverted CP,R18 5/2, and R18 7/1) is provided."}],"doi":"10.1016/j.jmr.2011.03.015","day":"01","publication_identifier":{"issn":["1090-7807"]},"language":[{"iso":"eng"}],"keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"page":"246-259","quality_controlled":"1","article_type":"original","publisher":"Elsevier","author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul"},{"last_name":"Meier","first_name":"Beat H.","full_name":"Meier, Beat H."},{"last_name":"Ernst","first_name":"Matthias","full_name":"Ernst, Matthias"}],"issue":"2","publication":"Journal of Magnetic Resonance","_id":"8469","month":"06","title":"Accurate measurement of one-bond H–X heteronuclear dipolar couplings in MAS solid-state NMR","intvolume":"       210","publication_status":"published","oa_version":"None","date_created":"2020-09-18T10:10:50Z","article_processing_charge":"No"},{"issue":"2","author":[{"last_name":"Kern","first_name":"Thomas","full_name":"Kern, Thomas"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","first_name":"Paul","last_name":"Schanda"},{"full_name":"Brutscher, Bernhard","first_name":"Bernhard","last_name":"Brutscher"}],"publication":"Journal of Magnetic Resonance","_id":"8482","intvolume":"       190","month":"02","title":"Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load","date_created":"2020-09-18T10:12:46Z","article_processing_charge":"No","publication_status":"published","oa_version":"None","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"language":[{"iso":"eng"}],"quality_controlled":"1","page":"333-338","article_type":"letter_note","publisher":"Elsevier","type":"journal_article","date_published":"2008-02-01T00:00:00Z","year":"2008","citation":{"apa":"Kern, T., Schanda, P., &#38; Brutscher, B. (2008). Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2007.11.015\">https://doi.org/10.1016/j.jmr.2007.11.015</a>","ama":"Kern T, Schanda P, Brutscher B. Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. <i>Journal of Magnetic Resonance</i>. 2008;190(2):333-338. doi:<a href=\"https://doi.org/10.1016/j.jmr.2007.11.015\">10.1016/j.jmr.2007.11.015</a>","chicago":"Kern, Thomas, Paul Schanda, and Bernhard Brutscher. “Sensitivity-Enhanced IPAP-SOFAST-HMQC for Fast-Pulsing 2D NMR with Reduced Radiofrequency Load.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.jmr.2007.11.015\">https://doi.org/10.1016/j.jmr.2007.11.015</a>.","ieee":"T. Kern, P. Schanda, and B. Brutscher, “Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load,” <i>Journal of Magnetic Resonance</i>, vol. 190, no. 2. Elsevier, pp. 333–338, 2008.","short":"T. Kern, P. Schanda, B. Brutscher, Journal of Magnetic Resonance 190 (2008) 333–338.","mla":"Kern, Thomas, et al. “Sensitivity-Enhanced IPAP-SOFAST-HMQC for Fast-Pulsing 2D NMR with Reduced Radiofrequency Load.” <i>Journal of Magnetic Resonance</i>, vol. 190, no. 2, Elsevier, 2008, pp. 333–38, doi:<a href=\"https://doi.org/10.1016/j.jmr.2007.11.015\">10.1016/j.jmr.2007.11.015</a>.","ista":"Kern T, Schanda P, Brutscher B. 2008. Sensitivity-enhanced IPAP-SOFAST-HMQC for fast-pulsing 2D NMR with reduced radiofrequency load. Journal of Magnetic Resonance. 190(2), 333–338."},"date_updated":"2021-01-12T08:19:35Z","abstract":[{"lang":"eng","text":"The SOFAST-HMQC experiment [P. Schanda, B. Brutscher, Very fast two-dimensional NMR spectroscopy for real-time investigation of dynamic events in proteins on the time scale of seconds, J. Am. Chem. Soc. 127 (2005) 8014–8015] allows recording two-dimensional correlation spectra of macromolecules such as proteins in only a few seconds acquisition time. To achieve the highest possible sensitivity, SOFAST-HMQC experiments are preferably performed on high-field NMR spectrometers equipped with cryogenically cooled probes. The duty cycle of over 80% in fast-pulsing SOFAST-HMQC experiments, however, may cause problems when using a cryogenic probe. Here we introduce SE-IPAP-SOFAST-HMQC, a new pulse sequence that provides comparable sensitivity to standard SOFAST-HMQC, while avoiding heteronuclear decoupling during 1H detection, and thus significantly reducing the radiofrequency load of the probe during the experiment. The experiment is also attractive for fast and sensitive measurement of heteronuclear one-bond spin coupling constants."}],"day":"01","publication_identifier":{"issn":["1090-7807"]},"doi":"10.1016/j.jmr.2007.11.015","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","volume":190},{"language":[{"iso":"eng"}],"keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"page":"334-339","article_type":"original","publisher":"Elsevier","author":[{"last_name":"Schanda","first_name":"Paul","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"last_name":"Brutscher","first_name":"Bernhard","full_name":"Brutscher, Bernhard"}],"issue":"2","_id":"8490","publication":"Journal of Magnetic Resonance","title":"Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR","month":"02","intvolume":"       178","oa_version":"None","publication_status":"published","article_processing_charge":"No","date_created":"2020-09-18T10:13:51Z","extern":"1","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":178,"date_published":"2006-02-01T00:00:00Z","type":"journal_article","date_updated":"2021-01-12T08:19:38Z","citation":{"chicago":"Schanda, Paul, and Bernhard Brutscher. “Hadamard Frequency-Encoded SOFAST-HMQC for Ultrafast Two-Dimensional Protein NMR.” <i>Journal of Magnetic Resonance</i>. Elsevier, 2006. <a href=\"https://doi.org/10.1016/j.jmr.2005.10.007\">https://doi.org/10.1016/j.jmr.2005.10.007</a>.","ieee":"P. Schanda and B. Brutscher, “Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR,” <i>Journal of Magnetic Resonance</i>, vol. 178, no. 2. Elsevier, pp. 334–339, 2006.","apa":"Schanda, P., &#38; Brutscher, B. (2006). Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR. <i>Journal of Magnetic Resonance</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmr.2005.10.007\">https://doi.org/10.1016/j.jmr.2005.10.007</a>","ama":"Schanda P, Brutscher B. Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR. <i>Journal of Magnetic Resonance</i>. 2006;178(2):334-339. doi:<a href=\"https://doi.org/10.1016/j.jmr.2005.10.007\">10.1016/j.jmr.2005.10.007</a>","ista":"Schanda P, Brutscher B. 2006. Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR. Journal of Magnetic Resonance. 178(2), 334–339.","short":"P. Schanda, B. Brutscher, Journal of Magnetic Resonance 178 (2006) 334–339.","mla":"Schanda, Paul, and Bernhard Brutscher. “Hadamard Frequency-Encoded SOFAST-HMQC for Ultrafast Two-Dimensional Protein NMR.” <i>Journal of Magnetic Resonance</i>, vol. 178, no. 2, Elsevier, 2006, pp. 334–39, doi:<a href=\"https://doi.org/10.1016/j.jmr.2005.10.007\">10.1016/j.jmr.2005.10.007</a>."},"year":"2006","abstract":[{"lang":"eng","text":"We demonstrate the feasibility of recording 1H–15N correlation spectra of proteins in only one second of acquisition time. The experiment combines recently proposed SOFAST-HMQC with Hadamard-type 15N frequency encoding. This allows site-resolved real-time NMR studies of kinetic processes in proteins with an increased time resolution. The sensitivity of the experiment is sufficient to be applicable to a wide range of molecular systems available at millimolar concentration on a high magnetic field spectrometer."}],"doi":"10.1016/j.jmr.2005.10.007","day":"01","publication_identifier":{"issn":["1090-7807"]}}]