[{"keyword":["nuclear magnetic resonance","NMR","cellwall","structural biology","spectroscopy"],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"year":"2024","type":"research_data","_id":"17042","corr_author":"1","month":"05","date_created":"2024-05-22T12:04:54Z","author":[{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul"}],"doi":"10.15479/AT:ISTA:17042","publisher":"Institute of Science and Technology Austria","day":"22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"date_published":"2024-05-22T00:00:00Z","citation":{"ista":"Schanda P. 2024. Raw data to ‘MAS NMR experiments of corynebacterial cell walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:17042.","ieee":"P. Schanda, “Raw data to ‘MAS NMR experiments of corynebacterial cell walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments.’” Institute of Science and Technology Austria, 2024.","ama":"Schanda P. Raw data to “MAS NMR experiments of corynebacterial cell walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments.” 2024. doi:10.15479/AT:ISTA:17042","short":"P. Schanda, (2024).","chicago":"Schanda, Paul. “Raw Data to ‘MAS NMR Experiments of Corynebacterial Cell Walls: Complementary 1H- and CPMAS CryoProbe-Enhanced 13C-Detected Experiments.’” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/AT:ISTA:17042.","mla":"Schanda, Paul. Raw Data to “MAS NMR Experiments of Corynebacterial Cell Walls: Complementary 1H- and CPMAS CryoProbe-Enhanced 13C-Detected Experiments.” Institute of Science and Technology Austria, 2024, doi:10.15479/AT:ISTA:17042.","apa":"Schanda, P. (2024). Raw data to “MAS NMR experiments of corynebacterial cell walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:17042"},"abstract":[{"lang":"eng","text":"Bacterial cell walls are gigadalton-large cross-linked polymers with a wide range of motional amplitudes, including rather rigid as well as highly flexible parts. Magic-angle spinning NMR is a powerful method to obtain atomic-level information about intact cell walls. Here we investigate sensitivity and information content of different homonuclear 13C-13C and heteronuclear H-N, H-C and N-C correlation experiments. We demonstrate that a CPMAS CryoProbe yields ca. 8-fold increased signal-to-noise over a room-temperature probe, or a ca. 3-4-fold larger per-mass sensitivity. The increased sensitivity allowed to obtain high-resolution spectra even on intact bacteria. Moreover, we compare resolution and sensitivity of 1H MAS experiments obtained at 100 kHz vs. 55 kHz. Our study provides useful hints for choosing experiments to extract atomic-level details on cell-wall samples. "}],"related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"17291"}]},"oa_version":"Published Version","title":"Raw data to \"MAS NMR experiments of corynebacterial cell walls: complementary 1H- and CPMAS CryoProbe-enhanced 13C-detected experiments\"","file":[{"content_type":"text/plain","file_size":2132,"date_updated":"2024-05-22T12:05:13Z","success":1,"relation":"main_file","checksum":"eb55f0988342d927702353b75e07edfa","date_created":"2024-05-22T12:05:13Z","file_id":"17043","file_name":"Read_me.txt","access_level":"open_access","creator":"pschanda"},{"relation":"main_file","date_created":"2024-05-22T12:17:10Z","file_id":"17044","file_name":"raw_data_CryoMAS_cyronebacteria.zip","checksum":"3393592acaf5ee1e032052c236780914","creator":"pschanda","access_level":"open_access","date_updated":"2024-05-22T12:17:10Z","file_size":755704888,"content_type":"application/zip","success":1}],"ddc":["570"],"date_updated":"2025-09-09T12:01:41Z","status":"public","contributor":[{"contributor_type":"data_collector","first_name":"Alicia","last_name":"Vallet"},{"last_name":"Ayala","first_name":"Isabel ","contributor_type":"data_collector"},{"first_name":"Barbara","contributor_type":"data_collector","last_name":"Perrone"},{"contributor_type":"data_collector","first_name":"Alia","last_name":"Hassan"},{"last_name":"Bougault","first_name":"Catherine","contributor_type":"data_collector"}],"file_date_updated":"2024-05-22T12:17:10Z","department":[{"_id":"PaSc"}],"has_accepted_license":"1","article_processing_charge":"No"},{"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"apa":"Datler, J. (2024). Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:18766","ama":"Datler J. Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. 2024. doi:10.15479/at:ista:18766","short":"J. Datler, Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM, Institute of Science and Technology Austria, 2024.","mla":"Datler, Julia. Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:18766.","chicago":"Datler, Julia. “Elucidating the Structural Determinants of the Poxvirus Core Using Multi-Modal Cryo-EM.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:18766.","ieee":"J. Datler, “Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM,” Institute of Science and Technology Austria, 2024.","ista":"Datler J. 2024. Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM. Institute of Science and Technology Austria."},"supervisor":[{"orcid":"0000-0003-4790-8078","last_name":"Schur","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"}],"date_published":"2024-12-30T00:00:00Z","oa":1,"OA_place":"publisher","_id":"18766","doi":"10.15479/at:ista:18766","date_created":"2025-01-07T10:23:12Z","author":[{"orcid":"0000-0002-3616-8580","last_name":"Datler","first_name":"Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","full_name":"Datler, Julia"}],"alternative_title":["ISTA thesis"],"publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-049-7"]},"acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 and ISTA. I\r\nwould like to express my gratitude to the Scientific Service Units, particularly the Lab\r\nSupport Facility, the Scientific Computing Facility and the Electron Microscopy Facility\r\nfor their tremendous support. I want to especially thank Alois for assisting me with the\r\ninstallation of countless new software and for troubleshooting cluster issues. A special\r\nthanks goes to Valentin for his outstanding support in cryo-EM data acquisition and\r\nhis ongoing help in improving the process to ensure that I obtained the best possible\r\ndata from my sample.","file_date_updated":"2025-01-07T12:15:14Z","page":"106","title":"Elucidating the structural determinants of the poxvirus core using multi-modal cryo-EM","oa_version":"Published Version","publication_status":"published","abstract":[{"lang":"eng","text":"Poxviruses are large pleomorphic double-stranded DNA viruses that include well known members such as variola virus, the causative agent of smallpox, Mpox virus, as well as Vaccinia virus (VACV), which serves as a vaccination strain for formerly mentioned viruses. VACV is a valuable model for studying large pleomorphic DNA viruses in general and poxviruses specifically, as many features, such as core morphology and structural proteins, are well conserved within this family. Despite decades of research, our understanding of the structural components and proteins that comprise the poxvirus core in mature virions remains limited. Although major core proteins were identified via indirect experimental evidence, the core's complexity, with its large size, structure and number of involved proteins, has hindered efforts to achieve high-resolution insights and to define the roles of the individual proteins. The specific protein composition of the core's individual layers, including the palisade layer and the inner core wall, has remained unclear. In this study, we have merged multiple approaches, including single particle cryo electron microscopy of purified virus cores, cryo-electron tomography and subtomogram averaging of mature virions and molecular modeling to elucidate the structural determinants of the VACV core. Due to the lack of experimentally derived structures, either in situ or reconstituted in vitro, we used Alphafold to predict models of the putative major core protein candidates, A10, 23k, A3, A4, and L4. Our results show that the VACV core is composed of several layers with varying local symmetries, forming more intricate interactions than observed previously. This allowed us to identify several molecular building blocks forming the viral core lattice. In particular, we identified trimers of protein A10 as a major core structure that forms the palisade layer of the viral core. Additionally, we revealed that six petals of a flower shaped core pore within the core wall are composed of A10 trimers. Furthermore, we obtained a cryo-EM density for the inner core wall that could potentially accommodate an A3 dimer. Integrating descriptions of protein interactions from previous studies enabled us to provide a detailed structural model of the poxvirus core wall, and our findings indicate that the interactions within A10 trimers are likely consistent across orthopox- and parapoxviruses. This combined application of cryo-SPA and cryo-ET can help overcome obstacles in studying complex virus structures in the future, including their key assembly proteins, interactions, and the formation into a core lattice. Our work provides important fundamental new insights into poxvirus core architecture, also considering the recent re-emergence of poxviruses."}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"day":"30","degree_awarded":"PhD","month":"12","corr_author":"1","publisher":"Institute of Science and Technology Austria","year":"2024","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid"}],"type":"dissertation","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"keyword":["cryo-EM","cryo-ET","cryo-SPA","Structural Virology","Poxvirus","Vaccinia Virus","Structural Biology"],"department":[{"_id":"GradSch"},{"_id":"FlSc"}],"has_accepted_license":"1","article_processing_charge":"No","status":"public","ddc":["570"],"date_updated":"2026-04-07T12:59:44Z","file":[{"date_updated":"2025-01-07T12:15:11Z","file_size":38814932,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"18769","file_name":"PhD_thesis_Julia_Datler.docx","checksum":"3e51cab327c754045c3d29c1a50cc9a9","date_created":"2025-01-07T12:15:11Z","creator":"jstanger","access_level":"closed","relation":"source_file"},{"date_updated":"2025-01-07T12:15:14Z","file_size":12044865,"content_type":"application/pdf","success":1,"file_id":"18770","date_created":"2025-01-07T12:15:14Z","file_name":"PhD_thesis_Julia_Datler.pdf","checksum":"22fabe5b97950bf852212f6edb555173","creator":"jstanger","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"id":"12334","status":"public","relation":"part_of_dissertation"},{"status":"public","id":"14979","relation":"part_of_dissertation"}]}},{"pmid":1,"abstract":[{"text":"Poxviruses are among the largest double-stranded DNA viruses, with members such as variola virus, monkeypox virus and the vaccination strain vaccinia virus (VACV). Knowledge about the structural proteins that form the viral core has remained sparse. While major core proteins have been annotated via indirect experimental evidence, their structures have remained elusive and they could not be assigned to individual core features. Hence, which proteins constitute which layers of the core, such as the palisade layer and the inner core wall, has remained enigmatic. Here we show, using a multi-modal cryo-electron microscopy (cryo-EM) approach in combination with AlphaFold molecular modeling, that trimers formed by the cleavage product of VACV protein A10 are the key component of the palisade layer. This allows us to place previously obtained descriptions of protein interactions within the core wall into perspective and to provide a detailed model of poxvirus core architecture. Importantly, we show that interactions within A10 trimers are likely generalizable over members of orthopox- and parapoxviruses.","lang":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"title":"Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores","oa_version":"Published Version","publication_status":"published","page":"1114-1123","quality_controlled":"1","file_date_updated":"2024-07-22T11:27:22Z","intvolume":" 31","acknowledgement":"We thank A. Bergthaler (Research Center for Molecular Medicine of the Austrian Academy of Sciences) for providing VACV WR. We thank A. Nicholas and his team at the ISTA proteomics facility, and S. Elefante at the ISTA Scientific Computing facility for their support. We also thank F. Fäßler, D. Porley, T. Muthspiel and other members of the Schur group for support and helpful discussions. We also thank D. Castaño-Díez for support with Dynamo. We thank D. Farrell for his help optimizing the Rosetta protocol to refine the atomic model into the cryo-EM map with symmetry.\r\n\r\nF.K.M.S. acknowledges support from ISTA and EMBO. F.K.M.S. also received support from the Austrian Science Fund (FWF) grant P31445. This publication has been made possible in part by CZI grant DAF2021-234754 and grant https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (funder https://doi.org/10.13039/100014989) awarded to F.K.M.S.\r\n\r\nThis research was also supported by the Scientific Service Units (SSUs) of ISTA through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We also acknowledge the use of COSMIC45 and Colabfold46.","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"volume":31,"article_type":"original","_id":"14979","OA_place":"publisher","scopus_import":"1","date_created":"2024-02-12T09:59:45Z","doi":"10.1038/s41594-023-01201-6","author":[{"full_name":"Datler, Julia","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","orcid":"0000-0002-3616-8580","last_name":"Datler"},{"full_name":"Hansen, Jesse","id":"1063c618-6f9b-11ec-9123-f912fccded63","first_name":"Jesse","orcid":"0000-0001-7967-2085","last_name":"Hansen"},{"full_name":"Thader, Andreas","id":"3A18A7B8-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Thader"},{"id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","full_name":"Schlögl, Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl","first_name":"Alois"},{"full_name":"Bauer, Lukas W","id":"0c894dcf-897b-11ed-a09c-8186353224b0","first_name":"Lukas W","last_name":"Bauer"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","last_name":"Hodirnau","orcid":"0000-0003-3904-947X"},{"first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2024-07-01T00:00:00Z","oa":1,"citation":{"mla":"Datler, Julia, et al. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology, vol. 31, Springer Nature, 2024, pp. 1114–23, doi:10.1038/s41594-023-01201-6.","chicago":"Datler, Julia, Jesse Hansen, Andreas Thader, Alois Schlögl, Lukas W Bauer, Victor-Valentin Hodirnau, and Florian KM Schur. “Multi-Modal Cryo-EM Reveals Trimers of Protein A10 to Form the Palisade Layer in Poxvirus Cores.” Nature Structural & Molecular Biology. Springer Nature, 2024. https://doi.org/10.1038/s41594-023-01201-6.","short":"J. Datler, J. Hansen, A. Thader, A. Schlögl, L.W. Bauer, V.-V. Hodirnau, F.K. Schur, Nature Structural & Molecular Biology 31 (2024) 1114–1123.","ama":"Datler J, Hansen J, Thader A, et al. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. 2024;31:1114-1123. doi:10.1038/s41594-023-01201-6","apa":"Datler, J., Hansen, J., Thader, A., Schlögl, A., Bauer, L. W., Hodirnau, V.-V., & Schur, F. K. (2024). Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01201-6","ista":"Datler J, Hansen J, Thader A, Schlögl A, Bauer LW, Hodirnau V-V, Schur FK. 2024. Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores. Nature Structural & Molecular Biology. 31, 1114–1123.","ieee":"J. Datler et al., “Multi-modal cryo-EM reveals trimers of protein A10 to form the palisade layer in poxvirus cores,” Nature Structural & Molecular Biology, vol. 31. Springer Nature, pp. 1114–1123, 2024."},"related_material":{"link":[{"description":"News on ISTA Website","url":"https://ista.ac.at/en/news/down-to-the-core-of-poxviruses/","relation":"press_release"}],"record":[{"id":"18766","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"file":[{"success":1,"content_type":"application/pdf","file_size":17485494,"date_updated":"2024-07-22T11:27:22Z","creator":"dernst","access_level":"open_access","file_name":"2024_NatureStrucBio_Datler.pdf","checksum":"bda7bf65d81455480efaed8ca293b0db","file_id":"17307","date_created":"2024-07-22T11:27:22Z","relation":"main_file"}],"ddc":["570"],"date_updated":"2026-04-07T12:59:44Z","status":"public","external_id":{"pmid":["38316877"],"isi":["001158144600002"]},"publication":"Nature Structural & Molecular Biology","has_accepted_license":"1","isi":1,"department":[{"_id":"FlSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"article_processing_charge":"Yes (in subscription journal)","keyword":["Molecular Biology","Structural Biology"],"APC_amount":"11700 EUR","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"year":"2024","type":"journal_article","project":[{"_id":"26736D6A-B435-11E9-9278-68D0E5697425","grant_number":"P31445","call_identifier":"FWF","name":"Structural conservation and diversity in retroviral capsid"}],"corr_author":"1","month":"07","publisher":"Springer Nature","day":"01","OA_type":"hybrid","license":"https://creativecommons.org/licenses/by/4.0/"},{"citation":{"ieee":"D. F. Gauto et al., “Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD,” Journal of Structural Biology: X, vol. 7. Elsevier, 2023.","ista":"Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR, Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.","apa":"Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R., Skrynnikov, N. R., & Schanda, P. (2023). Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. Elsevier. https://doi.org/10.1016/j.yjsbx.2022.100079","chicago":"Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X. Elsevier, 2023. https://doi.org/10.1016/j.yjsbx.2022.100079.","mla":"Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X, vol. 7, 100079, Elsevier, 2023, doi:10.1016/j.yjsbx.2022.100079.","short":"D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R. Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023).","ama":"Gauto DF, Lebedenko OO, Becker LM, et al. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 2023;7. doi:10.1016/j.yjsbx.2022.100079"},"oa":1,"date_published":"2023-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-01-12T11:55:38Z","doi":"10.1016/j.yjsbx.2022.100079","author":[{"last_name":"Gauto","first_name":"Diego F.","full_name":"Gauto, Diego F."},{"first_name":"Olga O.","last_name":"Lebedenko","full_name":"Lebedenko, Olga O."},{"first_name":"Lea Marie","orcid":"0000-0002-6401-5151","last_name":"Becker","full_name":"Becker, Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"},{"full_name":"Ayala, Isabel","last_name":"Ayala","first_name":"Isabel"},{"full_name":"Lichtenecker, Roman","last_name":"Lichtenecker","first_name":"Roman"},{"last_name":"Skrynnikov","first_name":"Nikolai R.","full_name":"Skrynnikov, Nikolai R."},{"last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"}],"scopus_import":"1","_id":"12114","article_type":"original","publication_identifier":{"issn":["2590-1524"]},"volume":7,"acknowledgement":"The NMR platform in Grenoble is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEA-UGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL, financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBH-EUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P.S.) and used the platforms of the Grenoble Instruct Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) with support from FRISBI (ANR-10-INSB-05–02) and GRAL (ANR-10-LABX-49–01) within the Grenoble Partnership for Structural Biology (PSB). We would like to thank Sergei Izmailov for developing and maintaining the pyxmolpp2 library. N.R.S. acknowledges support from St. Petersburg State University in a form of the grant 92425251 and the access to the MRR, MCT and CAMR resource centers. P.S. thanks Malcolm Levitt for pointing out the fact that “tensor asymmetry” is better called “tensor biaxiality”.","intvolume":" 7","file_date_updated":"2023-08-16T09:36:28Z","quality_controlled":"1","publication_status":"published","title":"Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD","oa_version":"Published Version","abstract":[{"text":"Probing the dynamics of aromatic side chains provides important insights into the behavior of a protein because flips of aromatic rings in a protein’s hydrophobic core report on breathing motion involving a large part of the protein. Inherently invisible to crystallography, aromatic motions have been primarily studied by solution NMR. The question how packing of proteins in crystals affects ring flips has, thus, remained largely unexplored. Here we apply magic-angle spinning NMR, advanced phenylalanine 1H-13C/2H isotope labeling and MD simulation to a protein in three different crystal packing environments to shed light onto possible impact of packing on ring flips. The flips of the two Phe residues in ubiquitin, both surface exposed, appear remarkably conserved in the different crystal forms, even though the intermolecular packing is quite different: Phe4 flips on a ca. 10–20 ns time scale, and Phe45 are broadened in all crystals, presumably due to µs motion. Our findings suggest that intramolecular influences are more important for ring flips than intermolecular (packing) effects.","lang":"eng"}],"pmid":1,"day":"01","publisher":"Elsevier","month":"01","corr_author":"1","type":"journal_article","year":"2023","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"keyword":["Structural Biology"],"article_processing_charge":"No","department":[{"_id":"PaSc"}],"has_accepted_license":"1","publication":"Journal of Structural Biology: X","article_number":"100079","external_id":{"pmid":["36578472"]},"status":"public","file":[{"relation":"main_file","date_created":"2023-08-16T09:36:28Z","file_name":"2023_JourStrucBiologyX_Gauto.pdf","checksum":"b4b1c10a31018aafe053b7d55a470e54","file_id":"14064","creator":"dernst","access_level":"open_access","date_updated":"2023-08-16T09:36:28Z","file_size":5132322,"content_type":"application/pdf","success":1}],"date_updated":"2024-10-09T21:04:02Z","ddc":["570"],"language":[{"iso":"eng"}]},{"quality_controlled":"1","file_date_updated":"2023-08-16T08:31:04Z","page":"762-777","publication_status":"published","oa_version":"Published Version","title":"In vitro reconstitution of small GTPase regulation","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"}],"pmid":1,"citation":{"ieee":"M. Loose, A. Auer, G. Brognara, H. R. Budiman, L. M. Kowalski, and I. Matijevic, “In vitro reconstitution of small GTPase regulation,” FEBS Letters, vol. 597, no. 6. Wiley, pp. 762–777, 2023.","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., & Matijevic, I. (2023). In vitro reconstitution of small GTPase regulation. FEBS Letters. Wiley. https://doi.org/10.1002/1873-3468.14540","chicago":"Loose, Martin, Albert Auer, Gabriel Brognara, Hanifatul R Budiman, Lukasz M Kowalski, and Ivana Matijevic. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters. Wiley, 2023. https://doi.org/10.1002/1873-3468.14540.","mla":"Loose, Martin, et al. “In Vitro Reconstitution of Small GTPase Regulation.” FEBS Letters, vol. 597, no. 6, Wiley, 2023, pp. 762–77, doi:10.1002/1873-3468.14540.","short":"M. Loose, A. Auer, G. Brognara, H.R. Budiman, L.M. Kowalski, I. Matijevic, FEBS Letters 597 (2023) 762–777.","ama":"Loose M, Auer A, Brognara G, Budiman HR, Kowalski LM, Matijevic I. In vitro reconstitution of small GTPase regulation. FEBS Letters. 2023;597(6):762-777. doi:10.1002/1873-3468.14540"},"date_published":"2023-03-01T00:00:00Z","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1002/1873-3468.14540","author":[{"full_name":"Loose, Martin","id":"462D4284-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-7309-9724","last_name":"Loose"},{"first_name":"Albert","last_name":"Auer","orcid":"0000-0002-3580-2906","full_name":"Auer, Albert","id":"3018E8C2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gabriel","last_name":"Brognara","full_name":"Brognara, Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425"},{"last_name":"Budiman","first_name":"Hanifatul R","id":"55380f95-15b2-11ec-abd3-aff8e230696b","full_name":"Budiman, Hanifatul R"},{"id":"e3a512e2-4bbe-11eb-a68a-e3857a7844c2","full_name":"Kowalski, Lukasz M","last_name":"Kowalski","first_name":"Lukasz M"},{"last_name":"Matijevic","first_name":"Ivana","id":"83c17ce3-15b2-11ec-abd3-f486545870bd","full_name":"Matijevic, Ivana"}],"date_created":"2023-01-12T12:09:58Z","scopus_import":"1","_id":"12163","article_type":"review","publication_identifier":{"eissn":["1873-3468"],"issn":["0014-5793"]},"volume":597,"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.","intvolume":" 597","article_processing_charge":"Yes (via OA deal)","has_accepted_license":"1","isi":1,"department":[{"_id":"MaLo"}],"publication":"FEBS Letters","external_id":{"pmid":["36448231"],"isi":["000891573000001"]},"status":"public","date_updated":"2024-10-09T21:03:42Z","ddc":["570"],"file":[{"access_level":"open_access","creator":"dernst","file_id":"14063","file_name":"2023_FEBSLetters_Loose.pdf","date_created":"2023-08-16T08:31:04Z","checksum":"7492244d3f9c5faa1347ef03f6e5bc84","relation":"main_file","success":1,"date_updated":"2023-08-16T08:31:04Z","file_size":3148143,"content_type":"application/pdf"}],"language":[{"iso":"eng"}],"day":"01","issue":"6","publisher":"Wiley","month":"03","corr_author":"1","type":"journal_article","year":"2023","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"keyword":["Cell Biology","Genetics","Molecular Biology","Biochemistry","Structural Biology","Biophysics"]},{"keyword":["Molecular Biology","Structural Biology"],"type":"journal_article","year":"2023","publisher":"Springer Nature","month":"06","issue":"7","day":"29","language":[{"iso":"eng"}],"date_updated":"2024-03-25T12:37:20Z","external_id":{"pmid":["37386214"]},"status":"public","article_processing_charge":"No","publication":"Nature Structural & Molecular Biology","intvolume":" 30","volume":30,"publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"article_type":"original","date_created":"2024-03-21T07:53:24Z","doi":"10.1038/s41594-023-01021-8","author":[{"full_name":"Isbel, Luke","last_name":"Isbel","first_name":"Luke"},{"last_name":"Iskar","first_name":"Murat","full_name":"Iskar, Murat"},{"first_name":"Sevi","last_name":"Durdu","full_name":"Durdu, Sevi"},{"full_name":"Weiss, Joscha","last_name":"Weiss","first_name":"Joscha"},{"full_name":"Grand, Ralph S.","first_name":"Ralph S.","last_name":"Grand"},{"full_name":"Hietter-Pfeiffer, Eric","first_name":"Eric","last_name":"Hietter-Pfeiffer"},{"first_name":"Zuzanna","last_name":"Kozicka","full_name":"Kozicka, Zuzanna"},{"last_name":"Michael","orcid":"0000-0002-6080-839X","first_name":"Alicia","id":"6437c950-2a03-11ee-914d-d6476dd7b75c","full_name":"Michael, Alicia"},{"last_name":"Burger","first_name":"Lukas","full_name":"Burger, Lukas"},{"last_name":"Thomä","first_name":"Nicolas H.","full_name":"Thomä, Nicolas H."},{"full_name":"Schübeler, Dirk","first_name":"Dirk","last_name":"Schübeler"}],"extern":"1","_id":"15149","scopus_import":"1","oa":1,"date_published":"2023-06-29T00:00:00Z","citation":{"ieee":"L. Isbel et al., “Readout of histone methylation by Trim24 locally restricts chromatin opening by p53,” Nature Structural & Molecular Biology, vol. 30, no. 7. Springer Nature, pp. 948–957, 2023.","ista":"Isbel L, Iskar M, Durdu S, Weiss J, Grand RS, Hietter-Pfeiffer E, Kozicka Z, Michael AK, Burger L, Thomä NH, Schübeler D. 2023. Readout of histone methylation by Trim24 locally restricts chromatin opening by p53. Nature Structural & Molecular Biology. 30(7), 948–957.","apa":"Isbel, L., Iskar, M., Durdu, S., Weiss, J., Grand, R. S., Hietter-Pfeiffer, E., … Schübeler, D. (2023). Readout of histone methylation by Trim24 locally restricts chromatin opening by p53. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-023-01021-8","ama":"Isbel L, Iskar M, Durdu S, et al. Readout of histone methylation by Trim24 locally restricts chromatin opening by p53. Nature Structural & Molecular Biology. 2023;30(7):948-957. doi:10.1038/s41594-023-01021-8","short":"L. Isbel, M. Iskar, S. Durdu, J. Weiss, R.S. Grand, E. Hietter-Pfeiffer, Z. Kozicka, A.K. Michael, L. Burger, N.H. Thomä, D. Schübeler, Nature Structural & Molecular Biology 30 (2023) 948–957.","mla":"Isbel, Luke, et al. “Readout of Histone Methylation by Trim24 Locally Restricts Chromatin Opening by P53.” Nature Structural & Molecular Biology, vol. 30, no. 7, Springer Nature, 2023, pp. 948–57, doi:10.1038/s41594-023-01021-8.","chicago":"Isbel, Luke, Murat Iskar, Sevi Durdu, Joscha Weiss, Ralph S. Grand, Eric Hietter-Pfeiffer, Zuzanna Kozicka, et al. “Readout of Histone Methylation by Trim24 Locally Restricts Chromatin Opening by P53.” Nature Structural & Molecular Biology. Springer Nature, 2023. https://doi.org/10.1038/s41594-023-01021-8."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"The genomic binding sites of the transcription factor (TF) and tumor suppressor p53 are unusually diverse with regard to their chromatin features, including histone modifications, raising the possibility that the local chromatin environment can contextualize p53 regulation. Here, we show that epigenetic characteristics of closed chromatin, such as DNA methylation, do not influence the binding of p53 across the genome. Instead, the ability of p53 to open chromatin and activate its target genes is locally restricted by its cofactor Trim24. Trim24 binds to both p53 and unmethylated histone 3 lysine 4 (H3K4), thereby preferentially localizing to those p53 sites that reside in closed chromatin, whereas it is deterred from accessible chromatin by H3K4 methylation. The presence of Trim24 increases cell viability upon stress and enables p53 to affect gene expression as a function of the local chromatin state. These findings link H3K4 methylation to p53 function and illustrate how specificity in chromatin can be achieved, not by TF-intrinsic sensitivity to histone modifications, but by employing chromatin-sensitive cofactors that locally modulate TF function."}],"pmid":1,"publication_status":"published","oa_version":"Published Version","title":"Readout of histone methylation by Trim24 locally restricts chromatin opening by p53","page":"948-957","main_file_link":[{"url":"https://doi.org/10.1038/s41594-023-01021-8","open_access":"1"}],"quality_controlled":"1"},{"month":"02","corr_author":"1","publisher":"Institute of Science and Technology Austria","day":"02","degree_awarded":"PhD","keyword":["cryo-EM","cryo-ET","FIB milling","method development","FIBSEM","extracellular matrix","ECM","cell-derived matrices","CDMs","cell culture","high pressure freezing","HPF","structural biology","tomography","collagen"],"year":"2023","type":"dissertation","project":[{"_id":"eba3b5f6-77a9-11ec-83b8-cf0905748aa3","name":"Integrated visual proteomics of reciprocal cell-extracellular matrix interactions"},{"name":"NÃ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"}],"status":"public","has_accepted_license":"1","department":[{"_id":"GradSch"},{"_id":"FlSc"}],"article_processing_charge":"No","language":[{"iso":"eng"}],"related_material":{"record":[{"status":"public","id":"8586","relation":"part_of_dissertation"}]},"file":[{"access_level":"open_access","creator":"bzens","date_created":"2023-02-07T13:07:38Z","file_name":"PhDThesis_BettinaZens_2023_final.pdf","file_id":"12527","checksum":"069d87f025e0799bf9e3c375664264f2","relation":"main_file","embargo":"2024-02-07","file_size":23082464,"date_updated":"2024-02-08T23:30:04Z","content_type":"application/pdf"},{"embargo_to":"open_access","checksum":"8c66ed203495d6e078ed1002a866520c","date_created":"2023-02-07T13:09:05Z","file_id":"12528","file_name":"PhDThesis_BettinaZens_2023_final.docx","access_level":"closed","creator":"bzens","relation":"source_file","date_updated":"2024-02-08T23:30:04Z","file_size":106169509,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document"}],"date_updated":"2026-04-07T13:49:23Z","ddc":["570"],"OA_place":"publisher","_id":"12491","doi":"10.15479/at:ista:12491","date_created":"2023-02-02T14:50:20Z","author":[{"id":"45FD126C-F248-11E8-B48F-1D18A9856A87","full_name":"Zens, Bettina","last_name":"Zens","orcid":"0000-0002-9561-1239","first_name":"Bettina"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","supervisor":[{"orcid":"0000-0003-4790-8078","last_name":"Schur","first_name":"Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM"}],"citation":{"apa":"Zens, B. (2023). Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12491","mla":"Zens, Bettina. Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12491.","chicago":"Zens, Bettina. “Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12491.","short":"B. Zens, Ultrastructural Characterization of Natively Preserved Extracellular Matrix by Cryo-Electron Tomography, Institute of Science and Technology Austria, 2023.","ama":"Zens B. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. 2023. doi:10.15479/at:ista:12491","ieee":"B. Zens, “Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography,” Institute of Science and Technology Austria, 2023.","ista":"Zens B. 2023. Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography. Institute of Science and Technology Austria."},"oa":1,"date_published":"2023-02-02T00:00:00Z","alternative_title":["ISTA Thesis"],"publication_identifier":{"isbn":["978-3-99078-027-5"],"issn":["2663-337X"]},"page":"187","file_date_updated":"2024-02-08T23:30:04Z","abstract":[{"lang":"eng","text":"The extracellular matrix (ECM) is a hydrated and complex three-dimensional network consisting of proteins, polysaccharides, and water. It provides structural scaffolding for the cells embedded within it and is essential in regulating numerous physiological processes, including cell migration and proliferation, wound healing, and stem cell fate. \r\nDespite extensive study, detailed structural knowledge of ECM components in physiologically relevant conditions is still rudimentary. This is due to methodological limitations in specimen preparation protocols which are incompatible with keeping large samples, such as the ECM, in their native state for subsequent imaging. Conventional electron microscopy (EM) techniques rely on fixation, dehydration, contrasting, and sectioning. This results in the alteration of a highly hydrated environment and the potential introduction of artifacts. Other structural biology techniques, such as nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, allow high-resolution analysis of protein structures but only work on homogenous and purified samples, hence lacking contextual information. Currently, no approach exists for the ultrastructural and structural study of extracellular components under native conditions in a physiological, 3D environment. \r\nIn this thesis, I have developed a workflow that allows for the ultrastructural analysis of the ECM in near-native conditions at molecular resolution. The developments I introduced include implementing a novel specimen preparation workflow for cell-derived matrices (CDMs) to render them compatible with ion-beam milling and subsequent high-resolution cryo-electron tomography (ET). \r\nTo this end, I have established protocols to generate CDMs grown over several weeks on EM grids that are compatible with downstream cryo-EM sample preparation and imaging techniques. Characterization of these ECMs confirmed that they contain essential ECM components such as collagen I, collagen VI, and fibronectin I in high abundance and hence represent a bona fide biologically-relevant sample. I successfully optimized vitrification of these specimens by testing various vitrification techniques and cryoprotectants. \r\nIn order to obtain high-resolution molecular insights into the ultrastructure and organization of CDMs, I established cryo-focused ion beam scanning electron microscopy (FIBSEM) on these challenging and complex specimens. I explored different approaches for the creation of thin cryo-lamellae by FIB milling and succeeded in optimizing the cryo-lift-out technique, resulting in high-quality lamellae of approximately 200 nm thickness. \r\nHigh-resolution Cryo-ET of these lamellae revealed for the first time the architecture of native CDM in the context of matrix-secreting cells. This allowed for the in situ visualization of fibrillar matrix proteins such as collagen, laying the foundation for future structural and ultrastructural characterization of these proteins in their near-native environment. \r\nIn summary, in this thesis, I present a novel workflow that combines state-of-the-art cryo-EM specimen preparation and imaging technologies to permit characterization of the ECM, an important tissue component in higher organisms. This innovative and highly versatile workflow will enable addressing far-reaching questions on ECM architecture, composition, and reciprocal ECM-cell interactions."}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"Bio"}],"oa_version":"Published Version","title":"Ultrastructural characterization of natively preserved extracellular matrix by cryo-electron tomography","publication_status":"published"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2022-10-01T00:00:00Z","oa":1,"citation":{"ama":"Gerle C, Kishikawa J, Yamaguchi T, et al. Structures of multisubunit membrane complexes with the CRYO ARM 200. Microscopy. 2022;71(5):249-261. doi:10.1093/jmicro/dfac037","chicago":"Gerle, Christoph, Jun-ichi Kishikawa, Tomoko Yamaguchi, Atsuko Nakanishi, Mehmet Orkun Çoruh, Fumiaki Makino, Tomoko Miyata, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” Microscopy. Oxford University Press, 2022. https://doi.org/10.1093/jmicro/dfac037.","mla":"Gerle, Christoph, et al. “Structures of Multisubunit Membrane Complexes with the CRYO ARM 200.” Microscopy, vol. 71, no. 5, Oxford University Press, 2022, pp. 249–61, doi:10.1093/jmicro/dfac037.","short":"C. Gerle, J. Kishikawa, T. Yamaguchi, A. Nakanishi, M.O. Çoruh, F. Makino, T. Miyata, A. Kawamoto, K. Yokoyama, K. Namba, G. Kurisu, T. Kato, Microscopy 71 (2022) 249–261.","apa":"Gerle, C., Kishikawa, J., Yamaguchi, T., Nakanishi, A., Çoruh, M. O., Makino, F., … Kato, T. (2022). Structures of multisubunit membrane complexes with the CRYO ARM 200. Microscopy. Oxford University Press. https://doi.org/10.1093/jmicro/dfac037","ista":"Gerle C, Kishikawa J, Yamaguchi T, Nakanishi A, Çoruh MO, Makino F, Miyata T, Kawamoto A, Yokoyama K, Namba K, Kurisu G, Kato T. 2022. Structures of multisubunit membrane complexes with the CRYO ARM 200. Microscopy. 71(5), 249–261.","ieee":"C. Gerle et al., “Structures of multisubunit membrane complexes with the CRYO ARM 200,” Microscopy, vol. 71, no. 5. Oxford University Press, pp. 249–261, 2022."},"_id":"11648","scopus_import":"1","author":[{"last_name":"Gerle","first_name":"Christoph","full_name":"Gerle, Christoph"},{"full_name":"Kishikawa, Jun-ichi","last_name":"Kishikawa","first_name":"Jun-ichi"},{"first_name":"Tomoko","last_name":"Yamaguchi","full_name":"Yamaguchi, Tomoko"},{"last_name":"Nakanishi","first_name":"Atsuko","full_name":"Nakanishi, Atsuko"},{"orcid":"0000-0002-3219-2022","last_name":"Çoruh","first_name":"Mehmet Orkun","id":"d25163e5-8d53-11eb-a251-e6dd8ea1b8ef","full_name":"Çoruh, Mehmet Orkun"},{"full_name":"Makino, Fumiaki","last_name":"Makino","first_name":"Fumiaki"},{"last_name":"Miyata","first_name":"Tomoko","full_name":"Miyata, Tomoko"},{"full_name":"Kawamoto, Akihiro","first_name":"Akihiro","last_name":"Kawamoto"},{"last_name":"Yokoyama","first_name":"Ken","full_name":"Yokoyama, Ken"},{"first_name":"Keiichi","last_name":"Namba","full_name":"Namba, Keiichi"},{"full_name":"Kurisu, Genji","last_name":"Kurisu","first_name":"Genji"},{"full_name":"Kato, Takayuki","last_name":"Kato","first_name":"Takayuki"}],"doi":"10.1093/jmicro/dfac037","date_created":"2022-07-25T10:04:58Z","publication_identifier":{"eissn":["2050-5701"],"issn":["2050-5698"]},"volume":71,"article_type":"original","intvolume":" 71","acknowledgement":"Cyclic Innovation for Clinical Empowerment (JP17pc0101020 from Japan Agency for Medical Research and Development (AMED) to K.N. and G.K.); Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research) from AMED (JP20am0101117 to K.N., JP16K07266 to Atsunori Oshima and C.G., JP22ama121001j0001 to Masaki Yamamoto, G.K., T.K. and C.G.); a JSPS KAHKENHI\r\ngrant (20K06514 to J.K.) and a Grant-in-aid for JSPS fellows (20J00162 to A.N.).\r\nWe are grateful for initiation and scientific support from Matthias Rogner, Marc M. Nowaczyk, Anna Frank and ̈Yuko Misumi for the PSI monomer project and also would like to thank Hideki Shigematsu for critical reading of the manuscript. And we are indebted to the two anonymous reviewers who helped us to improve our manuscript.","file_date_updated":"2023-02-03T08:34:48Z","quality_controlled":"1","page":"249-261","oa_version":"Published Version","title":"Structures of multisubunit membrane complexes with the CRYO ARM 200","publication_status":"published","abstract":[{"lang":"eng","text":"Progress in structural membrane biology has been significantly accelerated by the ongoing 'Resolution Revolution' in cryo electron microscopy (cryo-EM). In particular, structure determination by single particle analysis has evolved into the most powerful method for atomic model building of multisubunit membrane protein complexes. This has created an ever increasing demand in cryo-EM machine time, which to satisfy is in need of new and affordable cryo electron microscopes. Here, we review our experience in using the JEOL CRYO ARM 200 prototype for the structure determination by single particle analysis of three different multisubunit membrane complexes: the Thermus thermophilus V-type ATPase VO complex, the Thermosynechococcus elongatus photosystem I monomer and the flagellar motor LP-ring from Salmonella enterica."}],"pmid":1,"issue":"5","day":"01","month":"10","publisher":"Oxford University Press","year":"2022","type":"journal_article","keyword":["Radiology","Nuclear Medicine and imaging","Instrumentation","Structural Biology"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"publication":"Microscopy","has_accepted_license":"1","department":[{"_id":"LeSa"}],"isi":1,"article_processing_charge":"No","status":"public","external_id":{"isi":["000837950900001"],"pmid":["35861182"]},"ddc":["570"],"file":[{"content_type":"application/pdf","file_size":7812696,"date_updated":"2023-02-03T08:34:48Z","success":1,"file_id":"12498","date_created":"2023-02-03T08:34:48Z","file_name":"2022_Microscopy_Gerle.pdf","checksum":"23b51c163636bf9313f7f0818312e67e","creator":"dernst","access_level":"open_access","relation":"main_file"}],"date_updated":"2023-08-03T12:13:37Z","language":[{"iso":"eng"}]},{"quality_controlled":"1","file_date_updated":"2023-01-30T10:00:04Z","page":"942-953","title":"Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1","oa_version":"Published Version","publication_status":"published","abstract":[{"lang":"eng","text":"The AAA-ATPase Drg1 is a key factor in eukaryotic ribosome biogenesis that initiates cytoplasmic maturation of the large ribosomal subunit. Drg1 releases the shuttling maturation factor Rlp24 from pre-60S particles shortly after nuclear export, a strict requirement for downstream maturation. The molecular mechanism of release remained elusive. Here, we report a series of cryo-EM structures that captured the extraction of Rlp24 from pre-60S particles by Saccharomyces cerevisiae Drg1. These structures reveal that Arx1 and the eukaryote-specific rRNA expansion segment ES27 form a joint docking platform that positions Drg1 for efficient extraction of Rlp24 from the pre-ribosome. The tips of the Drg1 N domains thereby guide the Rlp24 C terminus into the central pore of the Drg1 hexamer, enabling extraction by a hand-over-hand translocation mechanism. Our results uncover substrate recognition and processing by Drg1 step by step and provide a comprehensive mechanistic picture of the conserved modus operandi of AAA-ATPases."}],"pmid":1,"acknowledged_ssus":[{"_id":"EM-Fac"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ista":"Prattes M, Grishkovskaya I, Hodirnau V-V, Hetzmannseder C, Zisser G, Sailer C, Kargas V, Loibl M, Gerhalter M, Kofler L, Warren AJ, Stengel F, Haselbach D, Bergler H. 2022. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural & Molecular Biology. 29(9), 942–953.","ieee":"M. Prattes et al., “Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1,” Nature Structural & Molecular Biology, vol. 29, no. 9. Springer Nature, pp. 942–953, 2022.","mla":"Prattes, Michael, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” Nature Structural & Molecular Biology, vol. 29, no. 9, Springer Nature, 2022, pp. 942–53, doi:10.1038/s41594-022-00832-5.","chicago":"Prattes, Michael, Irina Grishkovskaya, Victor-Valentin Hodirnau, Christina Hetzmannseder, Gertrude Zisser, Carolin Sailer, Vasileios Kargas, et al. “Visualizing Maturation Factor Extraction from the Nascent Ribosome by the AAA-ATPase Drg1.” Nature Structural & Molecular Biology. Springer Nature, 2022. https://doi.org/10.1038/s41594-022-00832-5.","short":"M. Prattes, I. Grishkovskaya, V.-V. Hodirnau, C. Hetzmannseder, G. Zisser, C. Sailer, V. Kargas, M. Loibl, M. Gerhalter, L. Kofler, A.J. Warren, F. Stengel, D. Haselbach, H. Bergler, Nature Structural & Molecular Biology 29 (2022) 942–953.","ama":"Prattes M, Grishkovskaya I, Hodirnau V-V, et al. Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural & Molecular Biology. 2022;29(9):942-953. doi:10.1038/s41594-022-00832-5","apa":"Prattes, M., Grishkovskaya, I., Hodirnau, V.-V., Hetzmannseder, C., Zisser, G., Sailer, C., … Bergler, H. (2022). Visualizing maturation factor extraction from the nascent ribosome by the AAA-ATPase Drg1. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-022-00832-5"},"date_published":"2022-09-12T00:00:00Z","oa":1,"scopus_import":"1","_id":"12262","doi":"10.1038/s41594-022-00832-5","author":[{"full_name":"Prattes, Michael","first_name":"Michael","last_name":"Prattes"},{"full_name":"Grishkovskaya, Irina","first_name":"Irina","last_name":"Grishkovskaya"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","first_name":"Victor-Valentin","last_name":"Hodirnau"},{"last_name":"Hetzmannseder","first_name":"Christina","full_name":"Hetzmannseder, Christina"},{"full_name":"Zisser, Gertrude","first_name":"Gertrude","last_name":"Zisser"},{"last_name":"Sailer","first_name":"Carolin","full_name":"Sailer, Carolin"},{"full_name":"Kargas, Vasileios","first_name":"Vasileios","last_name":"Kargas"},{"full_name":"Loibl, Mathias","first_name":"Mathias","last_name":"Loibl"},{"last_name":"Gerhalter","first_name":"Magdalena","full_name":"Gerhalter, Magdalena"},{"full_name":"Kofler, Lisa","last_name":"Kofler","first_name":"Lisa"},{"last_name":"Warren","first_name":"Alan J.","full_name":"Warren, Alan J."},{"full_name":"Stengel, Florian","first_name":"Florian","last_name":"Stengel"},{"first_name":"David","last_name":"Haselbach","full_name":"Haselbach, David"},{"full_name":"Bergler, Helmut","last_name":"Bergler","first_name":"Helmut"}],"date_created":"2023-01-16T09:59:06Z","article_type":"original","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"volume":29,"acknowledgement":"We thank M. Fromont-Racine, A. Johnson, J. Woolford, S. Rospert, J. P. G. Ballesta and\r\nE. Hurt for supplying antibodies. The work was supported by Boehringer Ingelheim (to\r\nD. H.), the Austrian Science Foundation FWF (grants 32536 and 32977 to H. B.), the\r\nUK Medical Research Council (MR/T012412/1 to A. J. W.) and the German Research\r\nFoundation (Emmy Noether Programme STE 2517/1-1 and STE 2517/5-1 to F.S.). We\r\nthank Norberto Escudero-Urquijo, Pablo Castro-Hartmann and K. Dent, Cambridge\r\nInstitute for Medical Research, for their help in cryo-EM during early phases of this\r\nproject. This research was supported by the Scientific Service Units of IST Austria through\r\nresources provided by the Electron Microscopy Facility. We thank S. Keller, Institute of\r\nMolecular Biosciences (Biophysics), University Graz for support with the quantification of\r\nthe SPR particle release assay. We thank I. Schaffner, University of Natural Resources and\r\nLife Sciences, Vienna for her help in early stages of the SPR experiments.","intvolume":" 29","has_accepted_license":"1","isi":1,"department":[{"_id":"EM-Fac"}],"publication":"Nature Structural & Molecular Biology","article_processing_charge":"No","status":"public","external_id":{"pmid":["36097293"],"isi":["000852942100004"]},"ddc":["570"],"file":[{"success":1,"file_size":9935057,"date_updated":"2023-01-30T10:00:04Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","creator":"dernst","checksum":"2d5c3ec01718fefd7553052b0b8a0793","date_created":"2023-01-30T10:00:04Z","file_id":"12447","file_name":"2022_NatureStrucMolecBio_Prattes.pdf"}],"date_updated":"2023-08-04T09:52:20Z","language":[{"iso":"eng"}],"day":"12","issue":"9","month":"09","publisher":"Springer Nature","year":"2022","type":"journal_article","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"keyword":["Molecular Biology","Structural Biology"]},{"keyword":["Molecular Biology","Structural Biology"],"type":"journal_article","year":"2022","publisher":"Springer Nature","month":"12","day":"19","language":[{"iso":"eng"}],"date_updated":"2024-06-04T06:27:09Z","external_id":{"pmid":["36536102"]},"status":"public","article_processing_charge":"Yes (in subscription journal)","publication":"Nature Structural & Molecular Biology","intvolume":" 30","publication_identifier":{"eissn":["1545-9985"],"issn":["1545-9993"]},"volume":30,"article_type":"original","doi":"10.1038/s41594-022-00891-8","date_created":"2024-03-20T10:41:45Z","author":[{"full_name":"Yelland, James N.","last_name":"Yelland","first_name":"James N."},{"last_name":"Bravo","orcid":"0000-0003-0456-0753","first_name":"Jack Peter Kelly","id":"96aecfa5-8931-11ee-af30-aa6a5d6eee0e","full_name":"Bravo, Jack Peter Kelly"},{"full_name":"Black, Joshua J.","last_name":"Black","first_name":"Joshua J."},{"first_name":"David W.","last_name":"Taylor","full_name":"Taylor, David W."},{"full_name":"Johnson, Arlen W.","first_name":"Arlen W.","last_name":"Johnson"}],"extern":"1","_id":"15131","scopus_import":"1","oa":1,"date_published":"2022-12-19T00:00:00Z","citation":{"ieee":"J. N. Yelland, J. P. K. Bravo, J. J. Black, D. W. Taylor, and A. W. Johnson, “A single 2′-O-methylation of ribosomal RNA gates assembly of a functional ribosome,” Nature Structural & Molecular Biology, vol. 30. Springer Nature, pp. 91–98, 2022.","ista":"Yelland JN, Bravo JPK, Black JJ, Taylor DW, Johnson AW. 2022. A single 2′-O-methylation of ribosomal RNA gates assembly of a functional ribosome. Nature Structural & Molecular Biology. 30, 91–98.","apa":"Yelland, J. N., Bravo, J. P. K., Black, J. J., Taylor, D. W., & Johnson, A. W. (2022). A single 2′-O-methylation of ribosomal RNA gates assembly of a functional ribosome. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-022-00891-8","ama":"Yelland JN, Bravo JPK, Black JJ, Taylor DW, Johnson AW. A single 2′-O-methylation of ribosomal RNA gates assembly of a functional ribosome. Nature Structural & Molecular Biology. 2022;30:91-98. doi:10.1038/s41594-022-00891-8","short":"J.N. Yelland, J.P.K. Bravo, J.J. Black, D.W. Taylor, A.W. Johnson, Nature Structural & Molecular Biology 30 (2022) 91–98.","chicago":"Yelland, James N., Jack Peter Kelly Bravo, Joshua J. Black, David W. Taylor, and Arlen W. Johnson. “A Single 2′-O-Methylation of Ribosomal RNA Gates Assembly of a Functional Ribosome.” Nature Structural & Molecular Biology. Springer Nature, 2022. https://doi.org/10.1038/s41594-022-00891-8.","mla":"Yelland, James N., et al. “A Single 2′-O-Methylation of Ribosomal RNA Gates Assembly of a Functional Ribosome.” Nature Structural & Molecular Biology, vol. 30, Springer Nature, 2022, pp. 91–98, doi:10.1038/s41594-022-00891-8."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"abstract":[{"lang":"eng","text":"RNA modifications are widespread in biology and abundant in ribosomal RNA. However, the importance of these modifications is not well understood. We show that methylation of a single nucleotide, in the catalytic center of the large subunit, gates ribosome assembly. Massively parallel mutational scanning of the essential nuclear GTPase Nog2 identified important interactions with rRNA, particularly with the 2′-O-methylated A-site base Gm2922. We found that methylation of G2922 is needed for assembly and efficient nuclear export of the large subunit. Critically, we identified single amino acid changes in Nog2 that completely bypass dependence on G2922 methylation and used cryoelectron microscopy to directly visualize how methylation flips Gm2922 into the active site channel of Nog2. This work demonstrates that a single RNA modification is a critical checkpoint in ribosome biogenesis, suggesting that such modifications can play an important role in regulation and assembly of macromolecular machines."}],"publication_status":"published","title":"A single 2′-O-methylation of ribosomal RNA gates assembly of a functional ribosome","oa_version":"Published Version","page":"91-98","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41594-022-00891-8"}],"quality_controlled":"1"},{"external_id":{"pmid":["34414600"]},"status":"public","article_processing_charge":"No","publication":"Proteins: Structure, Function, and Bioinformatics","department":[{"_id":"MaJö"}],"language":[{"iso":"eng"}],"date_updated":"2024-10-09T21:08:44Z","publisher":"Wiley","corr_author":"1","month":"01","issue":"1","day":"01","keyword":["Molecular Biology","Biochemistry","Structural Biology"],"type":"journal_article","year":"2022","page":"258-269","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.09.18.304337"}],"quality_controlled":"1","pmid":1,"abstract":[{"text":"Apolipoprotein A‐I (apoA‐I) has a key function in the reverse cholesterol transport. However, aggregation of apoA‐I single point mutants can lead to hereditary amyloid pathology. Although several studies have tackled the biophysical and structural consequences introduced by these mutations, there is little information addressing the relationship between the evolutionary and structural features that contribute to the amyloid behavior of apoA‐I. We combined evolutionary studies, in silico mutagenesis and molecular dynamics (MD) simulations to provide a comprehensive analysis of the conservation and pathogenic role of the aggregation‐prone regions (APRs) present in apoA‐I. Sequence analysis demonstrated that among the four amyloidogenic regions described for human apoA‐I, only two (APR1 and APR4) are evolutionary conserved across different species of Sarcopterygii. Moreover, stability analysis carried out with the FoldX engine showed that APR1 contributes to the marginal stability of apoA‐I. Structural properties of full‐length apoA‐I models suggest that aggregation is avoided by placing APRs into highly packed and rigid portions of its native fold. Compared to silent variants extracted from the gnomAD database, the thermodynamic and pathogenic impact of amyloid mutations showed evidence of a higher destabilizing effect. MD simulations of the amyloid variant G26R evidenced the partial unfolding of the alpha‐helix bundle with the concomitant exposure of APR1 to the solvent, suggesting an insight into the early steps involved in its aggregation. Our findings highlight APR1 as a relevant component for apoA‐I structural integrity and emphasize a destabilizing effect of amyloid variants that leads to the exposure of this region.","lang":"eng"}],"publication_status":"published","title":"Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior","oa_version":"Preprint","date_created":"2024-04-03T07:49:53Z","author":[{"last_name":"Gisonno","first_name":"Romina A.","full_name":"Gisonno, Romina A."},{"last_name":"Masson","orcid":"0000-0002-2634-6283","first_name":"Tomas","id":"93ac43e8-8599-11eb-9b86-f6efb0a4c207","full_name":"Masson, Tomas"},{"first_name":"Nahuel A.","last_name":"Ramella","full_name":"Ramella, Nahuel A."},{"full_name":"Barrera, Exequiel E.","last_name":"Barrera","first_name":"Exequiel E."},{"full_name":"Romanowski, Víctor","first_name":"Víctor","last_name":"Romanowski"},{"full_name":"Tricerri, M. Alejandra","last_name":"Tricerri","first_name":"M. Alejandra"}],"doi":"10.1002/prot.26217","_id":"15268","oa":1,"date_published":"2022-01-01T00:00:00Z","citation":{"apa":"Gisonno, R. A., Masson, T., Ramella, N. A., Barrera, E. E., Romanowski, V., & Tricerri, M. A. (2022). Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior. Proteins: Structure, Function, and Bioinformatics. Wiley. https://doi.org/10.1002/prot.26217","ama":"Gisonno RA, Masson T, Ramella NA, Barrera EE, Romanowski V, Tricerri MA. Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior. Proteins: Structure, Function, and Bioinformatics. 2022;90(1):258-269. doi:10.1002/prot.26217","short":"R.A. Gisonno, T. Masson, N.A. Ramella, E.E. Barrera, V. Romanowski, M.A. Tricerri, Proteins: Structure, Function, and Bioinformatics 90 (2022) 258–269.","chicago":"Gisonno, Romina A., Tomas Masson, Nahuel A. Ramella, Exequiel E. Barrera, Víctor Romanowski, and M. Alejandra Tricerri. “Evolutionary and Structural Constraints Influencing Apolipoprotein A‐I Amyloid Behavior.” Proteins: Structure, Function, and Bioinformatics. Wiley, 2022. https://doi.org/10.1002/prot.26217.","mla":"Gisonno, Romina A., et al. “Evolutionary and Structural Constraints Influencing Apolipoprotein A‐I Amyloid Behavior.” Proteins: Structure, Function, and Bioinformatics, vol. 90, no. 1, Wiley, 2022, pp. 258–69, doi:10.1002/prot.26217.","ieee":"R. A. Gisonno, T. Masson, N. A. Ramella, E. E. Barrera, V. Romanowski, and M. A. Tricerri, “Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior,” Proteins: Structure, Function, and Bioinformatics, vol. 90, no. 1. Wiley, pp. 258–269, 2022.","ista":"Gisonno RA, Masson T, Ramella NA, Barrera EE, Romanowski V, Tricerri MA. 2022. Evolutionary and structural constraints influencing apolipoprotein A‐I amyloid behavior. Proteins: Structure, Function, and Bioinformatics. 90(1), 258–269."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 90","publication_identifier":{"eissn":["1097-0134"],"issn":["0887-3585"]},"volume":90,"article_type":"original"},{"language":[{"iso":"eng"}],"date_updated":"2025-04-15T08:24:50Z","file":[{"date_updated":"2022-08-02T11:07:58Z","file_size":7080863,"content_type":"application/pdf","success":1,"file_id":"11722","date_created":"2022-08-02T11:07:58Z","file_name":"2022_JourStructuralBiology_Obr.pdf","checksum":"0b1eb53447aae8e95ae4c12d193b0b00","access_level":"open_access","creator":"dernst","relation":"main_file"}],"ddc":["570"],"article_number":"107852","external_id":{"isi":["000790733600001"],"pmid":["35351542"]},"status":"public","article_processing_charge":"Yes (via OA deal)","department":[{"_id":"FlSc"}],"has_accepted_license":"1","isi":1,"publication":"Journal of Structural Biology","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"keyword":["Structural Biology"],"project":[{"name":"Structural conservation and diversity in retroviral capsid","call_identifier":"FWF","grant_number":"P31445","_id":"26736D6A-B435-11E9-9278-68D0E5697425"}],"type":"journal_article","year":"2022","publisher":"Elsevier","month":"06","corr_author":"1","issue":"2","day":"01","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"}],"pmid":1,"abstract":[{"text":"The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo-EM) has been well documented. Here, we assess the performance of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), an increasingly popular structural determination method for complex 3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs) on two contemporary cryo-EM systems equipped with different energy filters and direct electron detectors (DED), specifically a Krios G4, equipped with a cold field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter, and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG), a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based STA on equally sized datasets acquired on the respective systems. The resulting EIAV CA hexamer reconstructions show that both systems perform comparably in the 4–6 Å resolution range based on Fourier-Shell correlation (FSC). In addition, by employing a recently introduced multiparticle refinement approach, we obtained a reconstruction of the EIAV CA hexamer at 2.9 Å. Our results demonstrate the potential of the new generation of energy filters and DEDs for STA, and the effects of using different processing pipelines on their STA outcomes.","lang":"eng"}],"publication_status":"published","title":"Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs","oa_version":"Published Version","quality_controlled":"1","file_date_updated":"2022-08-02T11:07:58Z","acknowledgement":"This work was funded by the Austrian Science Fund (FWF) grant P31445 to F.K.M.S and the National Institute of Allergy and Infectious Diseases under awards R01AI147890 to R.A.D. This research was also supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), and the Electron Microscopy Facility (EMF). We thank Dustin Morado for providing the software SubTOM for data processing. We also thank William Wan for critical reading of the manuscript and valuable feedback.","intvolume":" 214","article_type":"original","publication_identifier":{"issn":["1047-8477"]},"volume":214,"date_created":"2022-04-15T07:10:26Z","doi":"10.1016/j.jsb.2022.107852","author":[{"orcid":"0000-0003-1756-6564","last_name":"Obr","first_name":"Martin","id":"4741CA5A-F248-11E8-B48F-1D18A9856A87","full_name":"Obr, Martin"},{"last_name":"Hagen","first_name":"Wim J.H.","full_name":"Hagen, Wim J.H."},{"last_name":"Dick","first_name":"Robert A.","full_name":"Dick, Robert A."},{"full_name":"Yu, Lingbo","last_name":"Yu","first_name":"Lingbo"},{"full_name":"Kotecha, Abhay","first_name":"Abhay","last_name":"Kotecha"},{"first_name":"Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur","full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","_id":"11155","citation":{"ista":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. 2022. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. 214(2), 107852.","ieee":"M. Obr, W. J. H. Hagen, R. A. Dick, L. Yu, A. Kotecha, and F. K. Schur, “Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs,” Journal of Structural Biology, vol. 214, no. 2. Elsevier, 2022.","ama":"Obr M, Hagen WJH, Dick RA, Yu L, Kotecha A, Schur FK. Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. 2022;214(2). doi:10.1016/j.jsb.2022.107852","chicago":"Obr, Martin, Wim J.H. Hagen, Robert A. Dick, Lingbo Yu, Abhay Kotecha, and Florian KM Schur. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” Journal of Structural Biology. Elsevier, 2022. https://doi.org/10.1016/j.jsb.2022.107852.","mla":"Obr, Martin, et al. “Exploring High-Resolution Cryo-ET and Subtomogram Averaging Capabilities of Contemporary DEDs.” Journal of Structural Biology, vol. 214, no. 2, 107852, Elsevier, 2022, doi:10.1016/j.jsb.2022.107852.","short":"M. Obr, W.J.H. Hagen, R.A. Dick, L. Yu, A. Kotecha, F.K. Schur, Journal of Structural Biology 214 (2022).","apa":"Obr, M., Hagen, W. J. H., Dick, R. A., Yu, L., Kotecha, A., & Schur, F. K. (2022). Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2022.107852"},"date_published":"2022-06-01T00:00:00Z","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"article_type":"original","volume":74,"publication_identifier":{"issn":["0959-440X"]},"intvolume":" 74","citation":{"mla":"Kampjut, Domen, and Leonid A. Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” Current Opinion in Structural Biology, vol. 74, 102350, Elsevier, 2022, doi:10.1016/j.sbi.2022.102350.","short":"D. Kampjut, L.A. Sazanov, Current Opinion in Structural Biology 74 (2022).","chicago":"Kampjut, Domen, and Leonid A Sazanov. “Structure of Respiratory Complex I – An Emerging Blueprint for the Mechanism.” Current Opinion in Structural Biology. Elsevier, 2022. https://doi.org/10.1016/j.sbi.2022.102350.","ama":"Kampjut D, Sazanov LA. Structure of respiratory complex I – An emerging blueprint for the mechanism. Current Opinion in Structural Biology. 2022;74. doi:10.1016/j.sbi.2022.102350","apa":"Kampjut, D., & Sazanov, L. A. (2022). Structure of respiratory complex I – An emerging blueprint for the mechanism. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2022.102350","ista":"Kampjut D, Sazanov LA. 2022. Structure of respiratory complex I – An emerging blueprint for the mechanism. Current Opinion in Structural Biology. 74, 102350.","ieee":"D. Kampjut and L. A. Sazanov, “Structure of respiratory complex I – An emerging blueprint for the mechanism,” Current Opinion in Structural Biology, vol. 74. Elsevier, 2022."},"date_published":"2022-06-01T00:00:00Z","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","doi":"10.1016/j.sbi.2022.102350","author":[{"last_name":"Kampjut","first_name":"Domen","id":"37233050-F248-11E8-B48F-1D18A9856A87","full_name":"Kampjut, Domen"},{"orcid":"0000-0002-0977-7989","last_name":"Sazanov","first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A"}],"date_created":"2022-04-15T09:32:35Z","scopus_import":"1","_id":"11167","publication_status":"published","title":"Structure of respiratory complex I – An emerging blueprint for the mechanism","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Complex I is one of the major respiratory complexes, conserved from bacteria to mammals. It oxidises NADH, reduces quinone and pumps protons across the membrane, thus playing a central role in the oxidative energy metabolism. In this review we discuss our current state of understanding the structure of complex I from various species of mammals, plants, fungi, and bacteria, as well as of several complex I-related proteins. By comparing the structural evidence from these systems in different redox states and data from mutagenesis and molecular simulations, we formulate the mechanisms of electron transfer and proton pumping and explain how they are conformationally and electrostatically coupled. Finally, we discuss the structural basis of the deactivation phenomenon in mammalian complex I.","lang":"eng"}],"quality_controlled":"1","file_date_updated":"2022-08-05T05:56:03Z","type":"journal_article","year":"2022","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"keyword":["Molecular Biology","Structural Biology"],"day":"01","publisher":"Elsevier","month":"06","corr_author":"1","ddc":["570"],"file":[{"checksum":"72bdde48853643a32d42b75f54965c44","file_name":"2022_CurrentOpStructBiology_Kampjut.pdf","file_id":"11725","date_created":"2022-08-05T05:56:03Z","creator":"dernst","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_size":815607,"date_updated":"2022-08-05T05:56:03Z","success":1}],"date_updated":"2024-10-09T21:02:00Z","language":[{"iso":"eng"}],"article_processing_charge":"Yes (via OA deal)","department":[{"_id":"LeSa"}],"has_accepted_license":"1","isi":1,"publication":"Current Opinion in Structural Biology","article_number":"102350","external_id":{"pmid":["35316665"],"isi":["000829029500020"]},"status":"public"},{"quality_controlled":"1","file_date_updated":"2021-11-15T13:11:27Z","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"abstract":[{"lang":"eng","text":"A precise quantitative description of the ultrastructural characteristics underlying biological mechanisms is often key to their understanding. This is particularly true for dynamic extra- and intracellular filamentous assemblies, playing a role in cell motility, cell integrity, cytokinesis, tissue formation and maintenance. For example, genetic manipulation or modulation of actin regulatory proteins frequently manifests in changes of the morphology, dynamics, and ultrastructural architecture of actin filament-rich cell peripheral structures, such as lamellipodia or filopodia. However, the observed ultrastructural effects often remain subtle and require sufficiently large datasets for appropriate quantitative analysis. The acquisition of such large datasets has been enabled by recent advances in high-throughput cryo-electron tomography (cryo-ET) methods. This also necessitates the development of complementary approaches to maximize the extraction of relevant biological information. We have developed a computational toolbox for the semi-automatic quantification of segmented and vectorized filamentous networks from pre-processed cryo-electron tomograms, facilitating the analysis and cross-comparison of multiple experimental conditions. GUI-based components simplify the processing of data and allow users to obtain a large number of ultrastructural parameters describing filamentous assemblies. We demonstrate the feasibility of this workflow by analyzing cryo-ET data of untreated and chemically perturbed branched actin filament networks and that of parallel actin filament arrays. In principle, the computational toolbox presented here is applicable for data analysis comprising any type of filaments in regular (i.e. parallel) or random arrangement. We show that it can ease the identification of key differences between experimental groups and facilitate the in-depth analysis of ultrastructural data in a time-efficient manner."}],"publication_status":"published","title":"Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data","oa_version":"Published Version","author":[{"id":"38C393BE-F248-11E8-B48F-1D18A9856A87","full_name":"Dimchev, Georgi A","orcid":"0000-0001-8370-6161","last_name":"Dimchev","first_name":"Georgi A"},{"full_name":"Amiri, Behnam","last_name":"Amiri","first_name":"Behnam"},{"full_name":"Fäßler, Florian","id":"404F5528-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","last_name":"Fäßler","orcid":"0000-0001-7149-769X"},{"last_name":"Falcke","first_name":"Martin","full_name":"Falcke, Martin"},{"full_name":"Schur, Florian KM","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","first_name":"Florian KM","orcid":"0000-0003-4790-8078","last_name":"Schur"}],"date_created":"2021-11-15T12:21:42Z","doi":"10.1016/j.jsb.2021.107808","_id":"10290","scopus_import":"1","oa":1,"date_published":"2021-11-03T00:00:00Z","citation":{"mla":"Dimchev, Georgi A., et al. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology, vol. 213, no. 4, 107808, Elsevier , 2021, doi:10.1016/j.jsb.2021.107808.","chicago":"Dimchev, Georgi A, Behnam Amiri, Florian Fäßler, Martin Falcke, and Florian KM Schur. “Computational Toolbox for Ultrastructural Quantitative Analysis of Filament Networks in Cryo-ET Data.” Journal of Structural Biology. Elsevier , 2021. https://doi.org/10.1016/j.jsb.2021.107808.","short":"G.A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, F.K. Schur, Journal of Structural Biology 213 (2021).","ama":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 2021;213(4). doi:10.1016/j.jsb.2021.107808","apa":"Dimchev, G. A., Amiri, B., Fäßler, F., Falcke, M., & Schur, F. K. (2021). Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. Elsevier . https://doi.org/10.1016/j.jsb.2021.107808","ista":"Dimchev GA, Amiri B, Fäßler F, Falcke M, Schur FK. 2021. Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data. Journal of Structural Biology. 213(4), 107808.","ieee":"G. A. Dimchev, B. Amiri, F. Fäßler, M. Falcke, and F. K. Schur, “Computational toolbox for ultrastructural quantitative analysis of filament networks in cryo-ET data,” Journal of Structural Biology, vol. 213, no. 4. Elsevier , 2021."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 213","acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Victor-Valentin Hodirnau for help with cryo-ET data acquisition. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S.","volume":213,"publication_identifier":{"issn":["1047-8477"]},"article_type":"original","external_id":{"isi":["000720259500002"]},"article_number":"107808","status":"public","article_processing_charge":"Yes (via OA deal)","publication":"Journal of Structural Biology","isi":1,"department":[{"_id":"FlSc"}],"has_accepted_license":"1","related_material":{"record":[{"relation":"software","status":"public","id":"14502"}]},"language":[{"iso":"eng"}],"ddc":["572"],"file":[{"date_updated":"2021-11-15T13:11:27Z","file_size":16818304,"content_type":"application/pdf","success":1,"relation":"main_file","file_name":"2021_JournalStructBiol_Dimchev.pdf","date_created":"2021-11-15T13:11:27Z","checksum":"6b209e4d44775d4e02b50f78982c15fa","file_id":"10291","creator":"cchlebak","access_level":"open_access"}],"date_updated":"2025-04-15T08:25:41Z","publisher":"Elsevier ","corr_author":"1","month":"11","issue":"4","day":"03","keyword":["Structural Biology"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png"},"type":"journal_article","project":[{"grant_number":"P33367","name":"Structure and isoform diversity of the Arp2/3 complex","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A"},{"_id":"2674F658-B435-11E9-9278-68D0E5697425","grant_number":"M02495","name":"Protein structure and function in filopodia across scales","call_identifier":"FWF"}],"year":"2021"},{"article_type":"original","volume":432,"publication_identifier":{"issn":["0022-2836"]},"intvolume":" 432","citation":{"apa":"Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira, H., Araújo, A. P. U., & Garratt, R. C. (2020). Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. Elsevier. https://doi.org/10.1016/j.jmb.2020.09.001","mla":"Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” Journal of Molecular Biology, vol. 432, no. 21, Elsevier, 2020, pp. 5784–801, doi:10.1016/j.jmb.2020.09.001.","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.","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.” Journal of Molecular Biology. Elsevier, 2020. https://doi.org/10.1016/j.jmb.2020.09.001.","ama":"Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 2020;432(21):5784-5801. doi:10.1016/j.jmb.2020.09.001","ieee":"H. V. D. Rosa et al., “Molecular recognition at septin interfaces: The switches hold the key,” Journal of Molecular Biology, vol. 432, no. 21. Elsevier, pp. 5784–5801, 2020.","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."},"date_published":"2020-10-02T00:00:00Z","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1016/j.jmb.2020.09.001","author":[{"first_name":"Higor Vinícius Dias","last_name":"Rosa","full_name":"Rosa, Higor Vinícius Dias"},{"first_name":"Diego Antonio","last_name":"Leonardo","full_name":"Leonardo, Diego Antonio"},{"full_name":"Brognara, Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425","first_name":"Gabriel","last_name":"Brognara"},{"full_name":"Brandão-Neto, José","first_name":"José","last_name":"Brandão-Neto"},{"full_name":"D'Muniz Pereira, Humberto","first_name":"Humberto","last_name":"D'Muniz Pereira"},{"last_name":"Araújo","first_name":"Ana Paula Ulian","full_name":"Araújo, Ana Paula Ulian"},{"last_name":"Garratt","first_name":"Richard Charles","full_name":"Garratt, Richard Charles"}],"date_created":"2024-02-28T08:50:34Z","_id":"15036","publication_status":"published","oa_version":"Published Version","title":"Molecular recognition at septin interfaces: The switches hold the key","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"}],"pmid":1,"quality_controlled":"1","page":"5784-5801","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jmb.2020.09.001"}],"type":"journal_article","year":"2020","keyword":["Molecular Biology","Structural Biology"],"day":"02","issue":"21","publisher":"Elsevier","month":"10","date_updated":"2024-02-28T12:37:54Z","language":[{"iso":"eng"}],"article_processing_charge":"No","department":[{"_id":"MaLo"}],"publication":"Journal of Molecular Biology","external_id":{"pmid":["32910969"]},"status":"public"},{"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s12915-019-0733-6"}],"publication_status":"published","DOAJ_listed":"1","title":"The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Background: The mitochondrial pyruvate carrier (MPC) plays a central role in energy metabolism by transporting pyruvate across the inner mitochondrial membrane. Its heterodimeric composition and homology to SWEET and semiSWEET transporters set the MPC apart from the canonical mitochondrial carrier family (named MCF or SLC25). The import of the canonical carriers is mediated by the carrier translocase of the inner membrane (TIM22) pathway and is dependent on their structure, which features an even number of transmembrane segments and both termini in the intermembrane space. The import pathway of MPC proteins has not been elucidated. The odd number of transmembrane segments and positioning of the N-terminus in the matrix argues against an import via the TIM22 carrier pathway but favors an import via the flexible presequence pathway.\r\nResults: Here, we systematically analyzed the import pathways of Mpc2 and Mpc3 and report that, contrary to an expected import via the flexible presequence pathway, yeast MPC proteins with an odd number of transmembrane segments and matrix-exposed N-terminus are imported by the carrier pathway, using the receptor Tom70, small TIM chaperones, and the TIM22 complex. The TIM9·10 complex chaperones MPC proteins through the mitochondrial intermembrane space using conserved hydrophobic motifs that are also required for the interaction with canonical carrier proteins.\r\nConclusions: The carrier pathway can import paired and non-paired transmembrane helices and translocate N-termini to either side of the mitochondrial inner membrane, revealing an unexpected versatility of the mitochondrial import pathway for non-cleavable inner membrane proteins."}],"pmid":1,"citation":{"apa":"Rampelt, H., Sucec, I., Bersch, B., Horten, P., Perschil, I., Martinou, J.-C., … Pfanner, N. (2020). The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. BMC Biology. Springer Nature. https://doi.org/10.1186/s12915-019-0733-6","ama":"Rampelt H, Sucec I, Bersch B, et al. The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. BMC Biology. 2020;18. doi:10.1186/s12915-019-0733-6","mla":"Rampelt, Heike, et al. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates with an Odd Number of Transmembrane Segments.” BMC Biology, vol. 18, 2, Springer Nature, 2020, doi:10.1186/s12915-019-0733-6.","short":"H. Rampelt, I. Sucec, B. Bersch, P. Horten, I. Perschil, J.-C. Martinou, M. van der Laan, N. Wiedemann, P. Schanda, N. Pfanner, BMC Biology 18 (2020).","chicago":"Rampelt, Heike, Iva Sucec, Beate Bersch, Patrick Horten, Inge Perschil, Jean-Claude Martinou, Martin van der Laan, Nils Wiedemann, Paul Schanda, and Nikolaus Pfanner. “The Mitochondrial Carrier Pathway Transports Non-Canonical Substrates with an Odd Number of Transmembrane Segments.” BMC Biology. Springer Nature, 2020. https://doi.org/10.1186/s12915-019-0733-6.","ieee":"H. Rampelt et al., “The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments,” BMC Biology, vol. 18. Springer Nature, 2020.","ista":"Rampelt H, Sucec I, Bersch B, Horten P, Perschil I, Martinou J-C, van der Laan M, Wiedemann N, Schanda P, Pfanner N. 2020. The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments. BMC Biology. 18, 2."},"date_published":"2020-01-06T00:00:00Z","oa":1,"user_id":"0043cee0-e5fc-11ee-9736-f83bc23afbf0","date_created":"2020-09-17T10:26:53Z","doi":"10.1186/s12915-019-0733-6","author":[{"full_name":"Rampelt, Heike","first_name":"Heike","last_name":"Rampelt"},{"first_name":"Iva","last_name":"Sucec","full_name":"Sucec, Iva"},{"first_name":"Beate","last_name":"Bersch","full_name":"Bersch, Beate"},{"first_name":"Patrick","last_name":"Horten","full_name":"Horten, Patrick"},{"full_name":"Perschil, Inge","first_name":"Inge","last_name":"Perschil"},{"first_name":"Jean-Claude","last_name":"Martinou","full_name":"Martinou, Jean-Claude"},{"full_name":"van der Laan, Martin","last_name":"van der Laan","first_name":"Martin"},{"full_name":"Wiedemann, Nils","last_name":"Wiedemann","first_name":"Nils"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul"},{"last_name":"Pfanner","first_name":"Nikolaus","full_name":"Pfanner, Nikolaus"}],"extern":"1","OA_place":"publisher","_id":"8402","article_type":"original","publication_identifier":{"issn":["1741-7007"]},"volume":18,"intvolume":" 18","article_processing_charge":"No","publication":"BMC Biology","article_number":"2","external_id":{"pmid":["31907035"]},"status":"public","date_updated":"2024-10-15T13:23:11Z","language":[{"iso":"eng"}],"OA_type":"gold","day":"06","publisher":"Springer Nature","month":"01","type":"journal_article","year":"2020","keyword":["Biotechnology","Plant Science","General Biochemistry","Genetics and Molecular Biology","Developmental Biology","Cell Biology","Physiology","Ecology","Evolution","Behavior and Systematics","Structural Biology","General Agricultural and Biological Sciences"]},{"pmid":1,"abstract":[{"text":"The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, in which a whole macromolecule is represented by a small number of particles, can be of great value in identifying the main driving forces behind self-organisation in cell biology. Such models can incorporate data from both molecular and continuum scales, and their results can be directly compared to experiments. Here we review the state of the art of models for studying the formation and biological function of macromolecular assemblies in living organisms. We outline the key ingredients of each model and their main findings. We illustrate the contribution of this class of simulations to identifying the physical mechanisms behind life and diseases, and discuss their future developments.","lang":"eng"}],"title":"Minimal coarse-grained models for molecular self-organisation in biology","oa_version":"Preprint","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1906.09349"}],"page":"43-52","quality_controlled":"1","acknowledgement":"We acknowledge funding from EPSRC (A.E.H. and A.Š.), the Academy of Medical Sciences (J.K. and A.Š.), the Wellcome Trust (J.K. and A.Š.), and the Royal Society (A.Š.). We thank Shiladitya Banerjee and Nikola Ojkic for critically reading the manuscript, and Claudia Flandoli for helping us with figures and illustrations.","intvolume":" 58","article_type":"original","volume":58,"publication_identifier":{"issn":["0959-440X"]},"scopus_import":"1","_id":"10355","extern":"1","doi":"10.1016/j.sbi.2019.05.018","date_created":"2021-11-26T11:33:21Z","author":[{"first_name":"Anne E","last_name":"Hafner","full_name":"Hafner, Anne E"},{"full_name":"Krausser, Johannes","first_name":"Johannes","last_name":"Krausser"},{"last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","full_name":"Šarić, Anđela"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ieee":"A. E. Hafner, J. Krausser, and A. Šarić, “Minimal coarse-grained models for molecular self-organisation in biology,” Current Opinion in Structural Biology, vol. 58. Elsevier, pp. 43–52, 2019.","ista":"Hafner AE, Krausser J, Šarić A. 2019. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 58, 43–52.","apa":"Hafner, A. E., Krausser, J., & Šarić, A. (2019). Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2019.05.018","ama":"Hafner AE, Krausser J, Šarić A. Minimal coarse-grained models for molecular self-organisation in biology. Current Opinion in Structural Biology. 2019;58:43-52. doi:10.1016/j.sbi.2019.05.018","mla":"Hafner, Anne E., et al. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural Biology, vol. 58, Elsevier, 2019, pp. 43–52, doi:10.1016/j.sbi.2019.05.018.","chicago":"Hafner, Anne E, Johannes Krausser, and Anđela Šarić. “Minimal Coarse-Grained Models for Molecular Self-Organisation in Biology.” Current Opinion in Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.sbi.2019.05.018.","short":"A.E. Hafner, J. Krausser, A. Šarić, Current Opinion in Structural Biology 58 (2019) 43–52."},"oa":1,"date_published":"2019-06-18T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2021-11-26T11:54:25Z","status":"public","external_id":{"pmid":["31226513"]},"publication":"Current Opinion in Structural Biology","article_processing_charge":"No","keyword":["molecular biology","structural biology"],"year":"2019","type":"journal_article","month":"06","publisher":"Elsevier","day":"18"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Bougault, Catherine, Isabel Ayala, Waldemar Vollmer, Jean-Pierre Simorre, and Paul Schanda. “Studying Intact Bacterial Peptidoglycan by Proton-Detected NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.jsb.2018.07.009.","short":"C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, P. Schanda, Journal of Structural Biology 206 (2019) 66–72.","mla":"Bougault, Catherine, et al. “Studying Intact Bacterial Peptidoglycan by Proton-Detected NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology, vol. 206, no. 1, Elsevier, 2019, pp. 66–72, doi:10.1016/j.jsb.2018.07.009.","ama":"Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. 2019;206(1):66-72. doi:10.1016/j.jsb.2018.07.009","apa":"Bougault, C., Ayala, I., Vollmer, W., Simorre, J.-P., & Schanda, P. (2019). Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2018.07.009","ista":"Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. 2019. Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. 206(1), 66–72.","ieee":"C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, and P. Schanda, “Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency,” Journal of Structural Biology, vol. 206, no. 1. Elsevier, pp. 66–72, 2019."},"date_published":"2019-04-01T00:00:00Z","_id":"8409","extern":"1","author":[{"full_name":"Bougault, Catherine","last_name":"Bougault","first_name":"Catherine"},{"last_name":"Ayala","first_name":"Isabel","full_name":"Ayala, Isabel"},{"full_name":"Vollmer, Waldemar","first_name":"Waldemar","last_name":"Vollmer"},{"last_name":"Simorre","first_name":"Jean-Pierre","full_name":"Simorre, Jean-Pierre"},{"orcid":"0000-0002-9350-7606","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"}],"date_created":"2020-09-17T10:29:10Z","doi":"10.1016/j.jsb.2018.07.009","article_type":"original","publication_identifier":{"issn":["1047-8477"]},"volume":206,"intvolume":" 206","quality_controlled":"1","page":"66-72","oa_version":"Submitted Version","title":"Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency","publication_status":"published","pmid":1,"abstract":[{"text":"The bacterial cell wall is composed of the peptidoglycan (PG), a large polymer that maintains the integrity of the bacterial cell. Due to its multi-gigadalton size, heterogeneity, and dynamics, atomic-resolution studies are inherently complex. Solid-state NMR is an important technique to gain insight into its structure, dynamics and interactions. Here, we explore the possibilities to study the PG with ultra-fast (100 kHz) magic-angle spinning NMR. We demonstrate that highly resolved spectra can be obtained, and show strategies to obtain site-specific resonance assignments and distance information. We also explore the use of proton-proton correlation experiments, thus opening the way for NMR studies of intact cell walls without the need for isotope labeling.","lang":"eng"}],"day":"01","issue":"1","month":"04","publisher":"Elsevier","year":"2019","type":"journal_article","keyword":["Structural Biology"],"publication":"Journal of Structural Biology","article_processing_charge":"No","status":"public","external_id":{"pmid":["30031884"]},"date_updated":"2021-01-12T08:19:05Z","language":[{"iso":"eng"}]},{"volume":25,"publication_identifier":{"issn":["1545-9993","1545-9985"]},"year":"2018","article_type":"letter_note","type":"journal_article","keyword":["Molecular Biology","Structural Biology"],"intvolume":" 25","issue":"9","day":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-09-03T00:00:00Z","citation":{"ieee":"V. Kurauskas, A. Hessel, F. Dehez, C. Chipot, B. Bersch, and P. Schanda, “Dynamics and interactions of AAC3 in DPC are not functionally relevant,” Nature Structural & Molecular Biology, vol. 25, no. 9. Springer Nature, pp. 745–747, 2018.","ista":"Kurauskas V, Hessel A, Dehez F, Chipot C, Bersch B, Schanda P. 2018. Dynamics and interactions of AAC3 in DPC are not functionally relevant. Nature Structural & Molecular Biology. 25(9), 745–747.","apa":"Kurauskas, V., Hessel, A., Dehez, F., Chipot, C., Bersch, B., & Schanda, P. (2018). Dynamics and interactions of AAC3 in DPC are not functionally relevant. Nature Structural & Molecular Biology. Springer Nature. https://doi.org/10.1038/s41594-018-0127-4","chicago":"Kurauskas, Vilius, Audrey Hessel, François Dehez, Christophe Chipot, Beate Bersch, and Paul Schanda. “Dynamics and Interactions of AAC3 in DPC Are Not Functionally Relevant.” Nature Structural & Molecular Biology. Springer Nature, 2018. https://doi.org/10.1038/s41594-018-0127-4.","mla":"Kurauskas, Vilius, et al. “Dynamics and Interactions of AAC3 in DPC Are Not Functionally Relevant.” Nature Structural & Molecular Biology, vol. 25, no. 9, Springer Nature, 2018, pp. 745–47, doi:10.1038/s41594-018-0127-4.","short":"V. Kurauskas, A. Hessel, F. Dehez, C. Chipot, B. Bersch, P. Schanda, Nature Structural & Molecular Biology 25 (2018) 745–747.","ama":"Kurauskas V, Hessel A, Dehez F, Chipot C, Bersch B, Schanda P. Dynamics and interactions of AAC3 in DPC are not functionally relevant. Nature Structural & Molecular Biology. 2018;25(9):745-747. doi:10.1038/s41594-018-0127-4"},"_id":"8438","month":"09","doi":"10.1038/s41594-018-0127-4","date_created":"2020-09-18T10:04:59Z","extern":"1","author":[{"full_name":"Kurauskas, Vilius","last_name":"Kurauskas","first_name":"Vilius"},{"first_name":"Audrey","last_name":"Hessel","full_name":"Hessel, Audrey"},{"first_name":"François","last_name":"Dehez","full_name":"Dehez, François"},{"last_name":"Chipot","first_name":"Christophe","full_name":"Chipot, Christophe"},{"full_name":"Bersch, Beate","last_name":"Bersch","first_name":"Beate"},{"first_name":"Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"publisher":"Springer Nature","title":"Dynamics and interactions of AAC3 in DPC are not functionally relevant","oa_version":"None","date_updated":"2021-01-12T08:19:16Z","publication_status":"published","language":[{"iso":"eng"}],"publication":"Nature Structural & Molecular Biology","quality_controlled":"1","article_processing_charge":"No","status":"public","page":"745-747"}]