[{"has_accepted_license":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","intvolume":" 135","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"abstract":[{"lang":"ger","text":"Aromatische Seitenketten sind wichtige Indikatoren für die Plastizität von Proteinen und bilden oft entscheidende Kontakte bei Protein‐Protein‐Wechselwirkungen. Wir untersuchten aromatische Reste in den beiden strukturell homologen cross‐β Amyloidfibrillen HET‐s und HELLF mit Hilfe eines spezifischen Ansatzes zur Isotopenmarkierung und Festkörper NMR mit Drehung am magischen Winkel. Das dynamische Verhalten der aromatischen Reste Phe und Tyr deutet darauf hin, dass der hydrophobe Amyloidkern starr ist und keine Anzeichen von “atmenden Bewegungen” auf einer Zeitskala von Hunderten von Millisekunden zeigt. Aromatische Reste, die exponiert an der Fibrillenoberfläche sitzen, haben zwar eine starre Ringachse, weisen aber Ringflips auf verschiedenen Zeitskalen von Nanosekunden bis Mikrosekunden auf. Unser Ansatz bietet einen direkten Einblick in die Bewegungen des hydrophoben Kerns und ermöglicht eine bessere Bewertung der Konformationsheterogenität, die aus einem NMR‐Strukturensemble einer solchen Cross‐β‐Amyloidstruktur hervorgeht."}],"file_date_updated":"2024-01-23T08:57:01Z","publication_status":"published","publication_identifier":{"eissn":["1521-3757"],"issn":["0044-8249"]},"day":"02","author":[{"last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","full_name":"Becker, Lea Marie","orcid":"0000-0002-6401-5151","first_name":"Lea Marie"},{"full_name":"Berbon, Mélanie","last_name":"Berbon","first_name":"Mélanie"},{"last_name":"Vallet","full_name":"Vallet, Alicia","first_name":"Alicia"},{"full_name":"Grelard, Axelle","last_name":"Grelard","first_name":"Axelle"},{"first_name":"Estelle","last_name":"Morvan","full_name":"Morvan, Estelle"},{"last_name":"Bardiaux","full_name":"Bardiaux, Benjamin","first_name":"Benjamin"},{"full_name":"Lichtenecker, Roman","last_name":"Lichtenecker","first_name":"Roman"},{"first_name":"Matthias","last_name":"Ernst","full_name":"Ernst, Matthias"},{"first_name":"Antoine","full_name":"Loquet, Antoine","last_name":"Loquet"},{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","first_name":"Paul","orcid":"0000-0002-9350-7606"}],"title":"Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten","oa_version":"Published Version","volume":135,"date_created":"2024-01-18T10:01:01Z","article_type":"original","oa":1,"language":[{"iso":"ger"}],"citation":{"ieee":"L. M. Becker et al., “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten,” Angewandte Chemie, vol. 135, no. 19. Wiley, 2023.","short":"L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie 135 (2023).","ama":"Becker LM, Berbon M, Vallet A, et al. Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. Angewandte Chemie. 2023;135(19). doi:10.1002/ange.202219314","apa":"Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.202219314","mla":"Becker, Lea Marie, et al. “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.” Angewandte Chemie, vol. 135, no. 19, e202219314, Wiley, 2023, doi:10.1002/ange.202219314.","chicago":"Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.” Angewandte Chemie. Wiley, 2023. https://doi.org/10.1002/ange.202219314.","ista":"Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. Angewandte Chemie. 135(19), e202219314."},"issue":"19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","department":[{"_id":"PaSc"}],"file":[{"file_id":"14876","date_updated":"2024-01-23T08:57:01Z","creator":"dernst","file_size":1004676,"date_created":"2024-01-23T08:57:01Z","checksum":"98e68d370159f7be52a3d7c8a8ee1198","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2023_AngewChem_Becker.pdf"}],"article_number":"e202219314","ddc":["540"],"quality_controlled":"1","article_processing_charge":"Yes (in subscription journal)","doi":"10.1002/ange.202219314","publisher":"Wiley","_id":"14835","date_updated":"2024-01-23T12:23:35Z","type":"journal_article","status":"public","publication":"Angewandte Chemie","date_published":"2023-05-02T00:00:00Z","acknowledgement":"Wir danken Albert A. Smith (Leipzig) für aufschlussreiche Diskussionen. Diese Arbeit wurde mit Mitteln des Europäischen Forschungsrats (StG-2012-311318 an P.S.) unterstützt und nutzte die Plattformen des Grenoble Instruct-ERIC Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) im Rahmen der Grenoble Partnership for Structural Biology (PSB) sowie die Einrichtungen und das Fachwissen der Biophysical and Structural Chemistry Platform (BPCS) am IECB, CNRS UAR3033, INSERM US001 und der Universität Bordeaux.","year":"2023","keyword":["General Medicine"]},{"date_created":"2024-01-22T08:04:57Z","volume":29,"oa_version":"Preprint","title":"Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies","day":"01","author":[{"last_name":"Sučec","full_name":"Sučec, I.","first_name":"I."},{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul"}],"publication_identifier":{"isbn":["9781839162824"],"eisbn":["9781839165993"]},"publication_status":"published","abstract":[{"lang":"eng","text":"Understanding the mechanisms of chaperones at the atomic level generally requires producing chaperone–client complexes in vitro. This task comes with significant challenges, because one needs to find conditions in which the client protein is presented to the chaperone in a state that binds and at the same time avoid the pitfalls of protein aggregation that are often inherent to such states. The strategy differs significantly for different client proteins and chaperones, but there are common underlying principles. Here, we discuss these principles and deduce the strategies that can be successfully applied for different chaperone–client complexes. We review successful biochemical strategies applied to making the client protein “binding competent” and illustrate the different strategies with examples of recent biophysical and biochemical studies."}],"intvolume":" 29","department":[{"_id":"PaSc"}],"month":"11","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Sučec, I., and Paul Schanda. “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies.” Biophysics of Molecular Chaperones, edited by Sebastian Hiller et al., vol. 29, Royal Society of Chemistry, 2023, pp. 136–61, doi:10.1039/bk9781839165986-00136.","apa":"Sučec, I., & Schanda, P. (2023). Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In S. Hiller, M. Liu, & L. He (Eds.), Biophysics of Molecular Chaperones (Vol. 29, pp. 136–161). Royal Society of Chemistry. https://doi.org/10.1039/bk9781839165986-00136","chicago":"Sučec, I., and Paul Schanda. “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies.” In Biophysics of Molecular Chaperones, edited by Sebastian Hiller, Maili Liu, and Lichun He, 29:136–61. Royal Society of Chemistry, 2023. https://doi.org/10.1039/bk9781839165986-00136.","ista":"Sučec I, Schanda P. 2023.Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In: Biophysics of Molecular Chaperones. New Developments in NMR, vol. 29, 136–161.","short":"I. Sučec, P. Schanda, in:, S. Hiller, M. Liu, L. He (Eds.), Biophysics of Molecular Chaperones, Royal Society of Chemistry, 2023, pp. 136–161.","ieee":"I. Sučec and P. Schanda, “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies,” in Biophysics of Molecular Chaperones, vol. 29, S. Hiller, M. Liu, and L. He, Eds. Royal Society of Chemistry, 2023, pp. 136–161.","ama":"Sučec I, Schanda P. Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In: Hiller S, Liu M, He L, eds. Biophysics of Molecular Chaperones. Vol 29. Royal Society of Chemistry; 2023:136-161. doi:10.1039/bk9781839165986-00136"},"language":[{"iso":"eng"}],"oa":1,"type":"book_chapter","_id":"14847","date_updated":"2024-01-23T11:50:10Z","publisher":"Royal Society of Chemistry","editor":[{"first_name":"Sebastian","last_name":"Hiller","full_name":"Hiller, Sebastian"},{"first_name":"Maili","last_name":"Liu","full_name":"Liu, Maili"},{"first_name":"Lichun","full_name":"He, Lichun","last_name":"He"}],"alternative_title":["New Developments in NMR"],"article_processing_charge":"No","doi":"10.1039/bk9781839165986-00136","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv-2023-rpn28"}],"page":"136-161","year":"2023","date_published":"2023-11-01T00:00:00Z","publication":"Biophysics of Molecular Chaperones","status":"public"},{"department":[{"_id":"PaSc"}],"article_number":" e202304138","month":"05","citation":{"apa":"Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues. Angewandte Chemie International Edition (Vol. 62). Wiley. https://doi.org/10.1002/anie.202304138","mla":"Becker, Lea Marie, et al. “Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues.” Angewandte Chemie International Edition, vol. 62, no. 19, e202304138, Wiley, 2023, doi:10.1002/anie.202304138.","ista":"Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues, Wiley,p.","chicago":"Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues. Angewandte Chemie International Edition. Vol. 62. Wiley, 2023. https://doi.org/10.1002/anie.202304138.","ieee":"L. M. Becker et al., Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues, vol. 62, no. 19. Wiley, 2023.","short":"L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues, Wiley, 2023.","ama":"Becker LM, Berbon M, Vallet A, et al. Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues. Vol 62. Wiley; 2023. doi:10.1002/anie.202304138"},"issue":"19","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"volume":62,"date_created":"2024-01-22T11:54:34Z","day":"02","author":[{"orcid":"0000-0002-6401-5151","first_name":"Lea Marie","last_name":"Becker","full_name":"Becker, Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"},{"last_name":"Berbon","full_name":"Berbon, Mélanie","first_name":"Mélanie"},{"last_name":"Vallet","full_name":"Vallet, Alicia","first_name":"Alicia"},{"first_name":"Axelle","full_name":"Grelard, Axelle","last_name":"Grelard"},{"last_name":"Morvan","full_name":"Morvan, Estelle","first_name":"Estelle"},{"full_name":"Bardiaux, Benjamin","last_name":"Bardiaux","first_name":"Benjamin"},{"first_name":"Roman","full_name":"Lichtenecker, Roman","last_name":"Lichtenecker"},{"last_name":"Ernst","full_name":"Ernst, Matthias","first_name":"Matthias"},{"full_name":"Loquet, Antoine","last_name":"Loquet","first_name":"Antoine"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"}],"title":"Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues","oa_version":"Published Version","publication_status":"published","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"abstract":[{"text":"Cover Page","lang":"eng"}],"intvolume":" 62","keyword":["General Chemistry","Catalysis"],"year":"2023","related_material":{"link":[{"relation":"translation","url":"https://doi.org/10.1002/ange.202304138"}],"record":[{"status":"public","relation":"other","id":"12675"}]},"date_published":"2023-05-02T00:00:00Z","publication":"Angewandte Chemie International Edition","status":"public","_id":"14861","date_updated":"2024-01-23T08:48:14Z","type":"other_academic_publication","article_processing_charge":"No","doi":"10.1002/anie.202304138","publisher":"Wiley","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/anie.202304138"}]},{"volume":145,"date_created":"2023-05-28T22:01:04Z","article_type":"original","scopus_import":"1","day":"04","author":[{"last_name":"Troussicot","full_name":"Troussicot, Laura","id":"3d9cac31-413c-11eb-9514-d1ec2a7fb7f3","first_name":"Laura"},{"first_name":"Alicia","full_name":"Vallet, Alicia","last_name":"Vallet"},{"first_name":"Mikael","last_name":"Molin","full_name":"Molin, Mikael"},{"first_name":"Björn M.","full_name":"Burmann, Björn M.","last_name":"Burmann"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul"}],"title":"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR","oa_version":"Published Version","file_date_updated":"2023-05-30T07:05:28Z","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"publication_status":"published","has_accepted_license":"1","abstract":[{"text":"Disulfide bond formation is fundamentally important for protein structure and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive μs time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfill other favorable contacts.","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 145","department":[{"_id":"PaSc"}],"file":[{"file_id":"13098","date_updated":"2023-05-30T07:05:28Z","creator":"dernst","file_size":6719299,"date_created":"2023-05-30T07:05:28Z","checksum":"0758a930ef21c62fc91b14e657479f83","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2023_JACS_Troussicot.pdf"}],"month":"05","citation":{"ama":"Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. 2023;145(19):10700–10711. doi:10.1021/jacs.3c01200","ieee":"L. Troussicot, A. Vallet, M. Molin, B. M. Burmann, and P. Schanda, “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR,” Journal of the American Chemical Society, vol. 145, no. 19. American Chemical Society, pp. 10700–10711, 2023.","short":"L. Troussicot, A. Vallet, M. Molin, B.M. Burmann, P. Schanda, Journal of the American Chemical Society 145 (2023) 10700–10711.","chicago":"Troussicot, Laura, Alicia Vallet, Mikael Molin, Björn M. Burmann, and Paul Schanda. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Journal of the American Chemical Society. American Chemical Society, 2023. https://doi.org/10.1021/jacs.3c01200.","ista":"Troussicot L, Vallet A, Molin M, Burmann BM, Schanda P. 2023. Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. 145(19), 10700–10711.","apa":"Troussicot, L., Vallet, A., Molin, M., Burmann, B. M., & Schanda, P. (2023). Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.3c01200","mla":"Troussicot, Laura, et al. “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Journal of the American Chemical Society, vol. 145, no. 19, American Chemical Society, 2023, pp. 10700–10711, doi:10.1021/jacs.3c01200."},"issue":"19","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa":1,"language":[{"iso":"eng"}],"_id":"13095","date_updated":"2023-08-01T14:48:09Z","type":"journal_article","article_processing_charge":"No","doi":"10.1021/jacs.3c01200","publisher":"American Chemical Society","quality_controlled":"1","page":"10700–10711","ddc":["540"],"isi":1,"year":"2023","related_material":{"record":[{"relation":"research_data","status":"public","id":"12820"}]},"external_id":{"pmid":["37140345"],"isi":["000985907400001"]},"pmid":1,"date_published":"2023-05-04T00:00:00Z","acknowledgement":"We thank Albert A. Smith (Univ. Leipzig) for discussions and help with detectors analyses, Undina Guillerm (IST Austria) for gel electrophoresis experiments (Figure S7), and Jens\r\nLidman (Univ. Gothenburg) for a 3Q relaxation analysis script. Intramural funding from Institute of Science and Technology Austria is acknowledged. This work also used the platforms of\r\nthe Grenoble Instruct-ERIC center (ISBG; UMS 3518 CNRSCEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology (PSB), as well as the Swedish NMR Centre\r\nof the University of Gothenburg. Both platforms provided excellent research infrastructures. B.M.B. gratefully acknowledges funding from the Swedish Research Council (Starting grant 2016-04721), the Swedish Cancer Foundation (2019-0415), and the Knut och Alice Wallenberg Foundation through a Wallenberg Academy Fellowship (2016.0163) as well as through the Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, Sweden. ","publication":"Journal of the American Chemical Society","status":"public"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Degen, Morris, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture in Cell Death.” Nature, vol. 618, Springer Nature, 2023, pp. 1065–71, doi:10.1038/s41586-023-05991-z.","apa":"Degen, M., Santos, J. C., Pluhackova, K., Cebrero, G., Ramos, S., Jankevicius, G., … Hiller, S. (2023). Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature. Springer Nature. https://doi.org/10.1038/s41586-023-05991-z","chicago":"Degen, Morris, José Carlos Santos, Kristyna Pluhackova, Gonzalo Cebrero, Saray Ramos, Gytis Jankevicius, Ella Hartenian, et al. “Structural Basis of NINJ1-Mediated Plasma Membrane Rupture in Cell Death.” Nature. Springer Nature, 2023. https://doi.org/10.1038/s41586-023-05991-z.","ista":"Degen M, Santos JC, Pluhackova K, Cebrero G, Ramos S, Jankevicius G, Hartenian E, Guillerm U, Mari SA, Kohl B, Müller DJ, Schanda P, Maier T, Perez C, Sieben C, Broz P, Hiller S. 2023. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature. 618, 1065–1071.","short":"M. Degen, J.C. Santos, K. Pluhackova, G. Cebrero, S. Ramos, G. Jankevicius, E. Hartenian, U. Guillerm, S.A. Mari, B. Kohl, D.J. Müller, P. Schanda, T. Maier, C. Perez, C. Sieben, P. Broz, S. Hiller, Nature 618 (2023) 1065–1071.","ieee":"M. Degen et al., “Structural basis of NINJ1-mediated plasma membrane rupture in cell death,” Nature, vol. 618. Springer Nature, pp. 1065–1071, 2023.","ama":"Degen M, Santos JC, Pluhackova K, et al. Structural basis of NINJ1-mediated plasma membrane rupture in cell death. Nature. 2023;618:1065-1071. doi:10.1038/s41586-023-05991-z"},"language":[{"iso":"eng"}],"oa":1,"file":[{"date_updated":"2023-11-14T11:48:18Z","creator":"dernst","file_size":12292188,"date_created":"2023-11-14T11:48:18Z","file_id":"14533","access_level":"open_access","content_type":"application/pdf","success":1,"file_name":"2023_Nature_Degen.pdf","checksum":"0fab69252453bff1de7f0e2eceb76d34","relation":"main_file"}],"department":[{"_id":"PaSc"}],"month":"06","file_date_updated":"2023-11-14T11:48:18Z","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"publication_status":"published","acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"intvolume":" 618","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Eukaryotic cells can undergo different forms of programmed cell death, many of which culminate in plasma membrane rupture as the defining terminal event1,2,3,4,5,6,7. Plasma membrane rupture was long thought to be driven by osmotic pressure, but it has recently been shown to be in many cases an active process, mediated by the protein ninjurin-18 (NINJ1). Here we resolve the structure of NINJ1 and the mechanism by which it ruptures membranes. Super-resolution microscopy reveals that NINJ1 clusters into structurally diverse assemblies in the membranes of dying cells, in particular large, filamentous assemblies with branched morphology. A cryo-electron microscopy structure of NINJ1 filaments shows a tightly packed fence-like array of transmembrane α-helices. Filament directionality and stability is defined by two amphipathic α-helices that interlink adjacent filament subunits. The NINJ1 filament features a hydrophilic side and a hydrophobic side, and molecular dynamics simulations show that it can stably cap membrane edges. The function of the resulting supramolecular arrangement was validated by site-directed mutagenesis. Our data thus suggest that, during lytic cell death, the extracellular α-helices of NINJ1 insert into the plasma membrane to polymerize NINJ1 monomers into amphipathic filaments that rupture the plasma membrane. The membrane protein NINJ1 is therefore an interactive component of the eukaryotic cell membrane that functions as an in-built breaking point in response to activation of cell death.","lang":"eng"}],"has_accepted_license":"1","date_created":"2023-05-28T22:01:04Z","article_type":"original","volume":618,"title":"Structural basis of NINJ1-mediated plasma membrane rupture in cell death","oa_version":"Published Version","scopus_import":"1","day":"29","author":[{"first_name":"Morris","last_name":"Degen","full_name":"Degen, Morris"},{"last_name":"Santos","full_name":"Santos, José Carlos","first_name":"José Carlos"},{"full_name":"Pluhackova, Kristyna","last_name":"Pluhackova","first_name":"Kristyna"},{"first_name":"Gonzalo","last_name":"Cebrero","full_name":"Cebrero, Gonzalo"},{"first_name":"Saray","last_name":"Ramos","full_name":"Ramos, Saray"},{"first_name":"Gytis","last_name":"Jankevicius","full_name":"Jankevicius, Gytis"},{"last_name":"Hartenian","full_name":"Hartenian, Ella","first_name":"Ella"},{"full_name":"Guillerm, Undina","id":"bb74f472-ae54-11eb-9835-bc9c22fb1183","last_name":"Guillerm","first_name":"Undina"},{"first_name":"Stefania A.","last_name":"Mari","full_name":"Mari, Stefania A."},{"first_name":"Bastian","full_name":"Kohl, Bastian","last_name":"Kohl"},{"first_name":"Daniel J.","last_name":"Müller","full_name":"Müller, Daniel J."},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul"},{"full_name":"Maier, Timm","last_name":"Maier","first_name":"Timm"},{"full_name":"Perez, Camilo","last_name":"Perez","first_name":"Camilo"},{"full_name":"Sieben, Christian","last_name":"Sieben","first_name":"Christian"},{"first_name":"Petr","last_name":"Broz","full_name":"Broz, Petr"},{"first_name":"Sebastian","full_name":"Hiller, Sebastian","last_name":"Hiller"}],"date_published":"2023-06-29T00:00:00Z","acknowledgement":"This work was supported by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy EXC 2075–390740016 and the Stuttgart Center for Simulation Science (SC SimTech) to K.P., by ERC-CoG 770988 (InflamCellDeath) and SNF Project funding (310030B_198005, 310030B_192523) to P.B., by the Swiss Nanoscience Institute and the Swiss National Science Foundation via the NCCR AntiResist (180541) to S.H. and the NCCR Molecular Systems Engineering (51NF40-205608) to D.J.M., by the Helmholtz Young Investigator Program of the Helmholtz Association to C.S., by the SNF Professorship funding (PP00P3_198903) to C.P., EMBO postdoctoral fellowship ALTF 27-2022 to E.H. and by the Scientific Service Units of IST Austria through resources provided by the NMR and Life Science Facilities to P.S. Molecular dynamics simulations were performed on the HoreKa supercomputer funded by the Ministry of Science, Research and the Arts Baden-Württemberg and by the Federal Ministry of Education and Research. The authors thank the BioEM Lab of the Biozentrum, University of Basel for support; V. Mack, K. Shkarina and J. Fricke for technical support; D. Ricklin and S. Vogt for peptide synthesis; P. Pelczar for support with animals; S.-J. Marrink and P. Telles de Souza for supply with Martini3 parameters and scripts; and P. Radler und M. Loose for help with QCM. Fig. 4g and Extended Data Fig. 1a were in part created with BioRender.com.\r\nOpen access funding provided by University of Basel.","publication":"Nature","status":"public","external_id":{"isi":["000991386800011"]},"isi":1,"year":"2023","quality_controlled":"1","ddc":["570"],"page":"1065-1071","type":"journal_article","_id":"13096","date_updated":"2023-11-14T11:49:21Z","publisher":"Springer Nature","article_processing_charge":"Yes (via OA deal)","doi":"10.1038/s41586-023-05991-z"},{"ddc":["570"],"quality_controlled":"1","publisher":"Elsevier","doi":"10.1016/j.sbi.2023.102660","article_processing_charge":"Yes (via OA deal)","type":"journal_article","date_updated":"2024-01-30T12:37:36Z","_id":"14036","project":[{"_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","name":"AlloSpace. The emergence and mechanisms of allostery","grant_number":"I05812"}],"publication":"Current Opinion in Structural Biology","status":"public","date_published":"2023-10-01T00:00:00Z","acknowledgement":"We thank Petra Rovó for critical reading of this manuscript. We acknowledge the Austrian Science Foundation FWF (project AlloSpace, number I5812–B) and funding by the Institute of Science and Technology Austria.","pmid":1,"external_id":{"isi":["001053616200001"],"pmid":["37536064"]},"year":"2023","isi":1,"abstract":[{"lang":"eng","text":"Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) is establishing itself as a powerful method for the characterization of protein dynamics at the atomic scale. We discuss here how R1ρ MAS relaxation dispersion NMR can explore microsecond-to-millisecond motions. Progress in instrumentation, isotope labeling, and pulse sequence design has paved the way for quantitative analyses of even rare structural fluctuations. In addition to isotropic chemical-shift fluctuations exploited in solution-state NMR relaxation dispersion experiments, MAS NMR has a wider arsenal of observables, allowing to see motions even if the exchanging states do not differ in their chemical shifts. We demonstrate the potential of the technique for probing motions in challenging large enzymes, membrane proteins, and protein assemblies."}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"intvolume":" 82","publication_identifier":{"issn":["0959-440X"],"eissn":["1879-033X"]},"publication_status":"published","file_date_updated":"2024-01-30T12:36:39Z","oa_version":"Published Version","title":"Protein dynamics detected by magic-angle spinning relaxation dispersion NMR","author":[{"id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b","full_name":"Napoli, Federico","last_name":"Napoli","orcid":"0000-0002-9043-136X","first_name":"Federico"},{"orcid":"0000-0002-6401-5151","first_name":"Lea Marie","last_name":"Becker","full_name":"Becker, Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul"}],"scopus_import":"1","day":"01","article_type":"original","date_created":"2023-08-13T22:01:11Z","volume":82,"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"10","citation":{"ista":"Napoli F, Becker LM, Schanda P. 2023. Protein dynamics detected by magic-angle spinning relaxation dispersion NMR. Current Opinion in Structural Biology. 82(10), 102660.","chicago":"Napoli, Federico, Lea Marie Becker, and Paul Schanda. “Protein Dynamics Detected by Magic-Angle Spinning Relaxation Dispersion NMR.” Current Opinion in Structural Biology. Elsevier, 2023. https://doi.org/10.1016/j.sbi.2023.102660.","apa":"Napoli, F., Becker, L. M., & Schanda, P. (2023). Protein dynamics detected by magic-angle spinning relaxation dispersion NMR. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2023.102660","mla":"Napoli, Federico, et al. “Protein Dynamics Detected by Magic-Angle Spinning Relaxation Dispersion NMR.” Current Opinion in Structural Biology, vol. 82, no. 10, 102660, Elsevier, 2023, doi:10.1016/j.sbi.2023.102660.","ama":"Napoli F, Becker LM, Schanda P. Protein dynamics detected by magic-angle spinning relaxation dispersion NMR. Current Opinion in Structural Biology. 2023;82(10). doi:10.1016/j.sbi.2023.102660","ieee":"F. Napoli, L. M. Becker, and P. Schanda, “Protein dynamics detected by magic-angle spinning relaxation dispersion NMR,” Current Opinion in Structural Biology, vol. 82, no. 10. Elsevier, 2023.","short":"F. Napoli, L.M. Becker, P. Schanda, Current Opinion in Structural Biology 82 (2023)."},"month":"10","file":[{"file_id":"14907","date_created":"2024-01-30T12:36:39Z","file_size":1231998,"creator":"dernst","date_updated":"2024-01-30T12:36:39Z","relation":"main_file","checksum":"c850f7ac8a4234319755b672c1df69ae","success":1,"file_name":"2023_CurrentOpinionStrucBio_Napoli.pdf","access_level":"open_access","content_type":"application/pdf"}],"article_number":"102660","department":[{"_id":"PaSc"}]},{"file_date_updated":"2023-08-16T09:36:28Z","publication_identifier":{"issn":["2590-1524"]},"publication_status":"published","has_accepted_license":"1","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","intvolume":" 7","abstract":[{"lang":"eng","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."}],"volume":7,"date_created":"2023-01-12T11:55:38Z","article_type":"original","day":"01","scopus_import":"1","author":[{"first_name":"Diego F.","last_name":"Gauto","full_name":"Gauto, Diego F."},{"last_name":"Lebedenko","full_name":"Lebedenko, Olga O.","first_name":"Olga O."},{"orcid":"0000-0002-6401-5151","first_name":"Lea Marie","last_name":"Becker","full_name":"Becker, Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79"},{"first_name":"Isabel","last_name":"Ayala","full_name":"Ayala, Isabel"},{"first_name":"Roman","last_name":"Lichtenecker","full_name":"Lichtenecker, Roman"},{"full_name":"Skrynnikov, Nikolai R.","last_name":"Skrynnikov","first_name":"Nikolai R."},{"first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda"}],"title":"Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD","oa_version":"Published Version","citation":{"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.","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","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.","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","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.","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)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"PaSc"}],"file":[{"file_size":5132322,"date_created":"2023-08-16T09:36:28Z","creator":"dernst","date_updated":"2023-08-16T09:36:28Z","file_id":"14064","file_name":"2023_JourStrucBiologyX_Gauto.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"b4b1c10a31018aafe053b7d55a470e54"}],"article_number":"100079","month":"01","quality_controlled":"1","ddc":["570"],"_id":"12114","date_updated":"2023-08-16T09:37:25Z","type":"journal_article","article_processing_charge":"No","doi":"10.1016/j.yjsbx.2022.100079","publisher":"Elsevier","pmid":1,"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”.","date_published":"2023-01-01T00:00:00Z","publication":"Journal of Structural Biology: X","status":"public","keyword":["Structural Biology"],"year":"2023","external_id":{"pmid":["36578472"]}},{"status":"public","oa":1,"date_published":"2023-03-23T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Becker, Lea Marie, and Paul Schanda. Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12497.","apa":"Becker, L. M., & Schanda, P. (2023). Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12497","chicago":"Becker, Lea Marie, and Paul Schanda. “Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12497.","ista":"Becker LM, Schanda P. 2023. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12497.","short":"L.M. Becker, P. Schanda, (2023).","ieee":"L. M. Becker and P. Schanda, “Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues.” Institute of Science and Technology Austria, 2023.","ama":"Becker LM, Schanda P. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. 2023. doi:10.15479/AT:ISTA:12497"},"month":"03","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"12675"}]},"year":"2023","keyword":["aromatic side chains","isotopic labeling","protein dynamics","ring flips","spin relaxation"],"file":[{"file_id":"12743","date_updated":"2023-03-24T09:34:20Z","creator":"lbecker","date_created":"2023-03-23T10:03:16Z","file_size":87018103,"checksum":"fd9a28620a81a82991fb70f4fd6591d9","relation":"main_file","access_level":"open_access","content_type":"application/zip","file_name":"Research_Data.zip"},{"file_size":747,"date_created":"2023-03-24T07:13:55Z","date_updated":"2023-03-24T09:42:03Z","creator":"dernst","file_id":"12755","file_name":"README.txt","content_type":"text/plain","access_level":"open_access","relation":"main_file","checksum":"30ebdfb600af118fcf8518b6efe0b7e9"}],"department":[{"_id":"GradSch"},{"_id":"PaSc"}],"abstract":[{"lang":"eng","text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein–protein interactions. We studied aromatic residues in the two structurally homologous cross-β amyloid fibrils HET-s, and HELLF by employing a specific isotope-labeling approach and magic-angle-spinning NMR. The dynamic behavior of the aromatic residues Phe and Tyr indicates that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips on a variety of time scales from nanoseconds to microseconds. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from an NMR structural ensemble of such amyloid cross-β architecture."}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"ddc":["572"],"has_accepted_license":"1","file_date_updated":"2023-03-24T09:42:03Z","title":"Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues","publisher":"Institute of Science and Technology Austria","oa_version":"Published Version","doi":"10.15479/AT:ISTA:12497","author":[{"orcid":"0000-0002-6401-5151","first_name":"Lea Marie","last_name":"Becker","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","full_name":"Becker, Lea Marie"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul"}],"contributor":[{"first_name":"Mélanie","contributor_type":"researcher","last_name":"Berbon"},{"last_name":"Vallet","contributor_type":"researcher","first_name":"Alicia"},{"last_name":"Grelard","first_name":"Axelle","contributor_type":"researcher"},{"last_name":"Morvan","contributor_type":"researcher","first_name":"Estelle"},{"first_name":"Benjamin","contributor_type":"researcher","last_name":"Bardiaux"},{"last_name":"Lichtenecker","first_name":"Roman","contributor_type":"researcher"},{"last_name":"Ernst","first_name":"Matthias","contributor_type":"researcher"},{"last_name":"Loquet","first_name":"Antoine","contributor_type":"researcher"},{"id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","orcid":"0000-0002-9350-7606","first_name":"Paul","contributor_type":"contact_person"},{"id":"36336939-eb97-11eb-a6c2-c83f1214ca79","last_name":"Becker","contributor_type":"researcher","first_name":"Lea Marie","orcid":"0000-0002-6401-5151"}],"article_processing_charge":"No","day":"23","type":"research_data","date_created":"2023-02-03T08:08:02Z","date_updated":"2024-02-21T12:14:06Z","_id":"12497"},{"keyword":["General Chemistry","Catalysis"],"related_material":{"record":[{"relation":"other","status":"public","id":"14861"},{"relation":"research_data","status":"public","id":"12497"}],"link":[{"relation":"press_release","url":"https://ista.ac.at/en/news/dancing-styles-of-atoms/","description":"News on ISTA website"}]},"external_id":{"pmid":["36738230"],"isi":["000956919900001"]},"isi":1,"year":"2023","date_published":"2023-05-01T00:00:00Z","acknowledgement":"We thank AlbertA. Smith (Leipzig)for insightful discussions. This work was supported by funding from the European Research Council (StG-2012-311318 to P.S.) and used the platforms of the Grenoble Instruct-ERIC center (ISBG;UMS 3518 CNRS-CEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology(PSB) and facilities and expertiseof the Biophysical and Structural Chemistry platform (BPCS) at IECB,CNRSUAR3033,INSERMUS001 and Bordeaux University.","pmid":1,"publication":"Angewandte Chemie International Edition","status":"public","type":"journal_article","_id":"12675","date_updated":"2024-02-21T12:14:06Z","publisher":"Wiley","article_processing_charge":"Yes (via OA deal)","doi":"10.1002/anie.202219314","quality_controlled":"1","ddc":["540"],"file":[{"date_created":"2023-08-16T12:33:31Z","file_size":1422445,"creator":"dernst","date_updated":"2023-08-16T12:33:31Z","file_id":"14072","file_name":"2023_AngewChemInt_Becker.pdf","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"7dd083ed8850faa55c34e411ed390de9"}],"article_number":"e202219314","department":[{"_id":"GradSch"},{"_id":"PaSc"}],"month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"L. M. Becker et al., “The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues,” Angewandte Chemie International Edition, vol. 62, no. 19. Wiley, 2023.","short":"L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie International Edition 62 (2023).","ama":"Becker LM, Berbon M, Vallet A, et al. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. 2023;62(19). doi:10.1002/anie.202219314","apa":"Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202219314","mla":"Becker, Lea Marie, et al. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” Angewandte Chemie International Edition, vol. 62, no. 19, e202219314, Wiley, 2023, doi:10.1002/anie.202219314.","ista":"Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. 62(19), e202219314.","chicago":"Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” Angewandte Chemie International Edition. Wiley, 2023. https://doi.org/10.1002/anie.202219314."},"issue":"19","language":[{"iso":"eng"}],"oa":1,"date_created":"2023-02-24T10:45:01Z","article_type":"original","volume":62,"title":"The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues","oa_version":"Published Version","day":"01","author":[{"full_name":"Becker, Lea Marie","id":"36336939-eb97-11eb-a6c2-c83f1214ca79","last_name":"Becker","first_name":"Lea Marie","orcid":"0000-0002-6401-5151"},{"first_name":"Mélanie","last_name":"Berbon","full_name":"Berbon, Mélanie"},{"last_name":"Vallet","full_name":"Vallet, Alicia","first_name":"Alicia"},{"first_name":"Axelle","full_name":"Grelard, Axelle","last_name":"Grelard"},{"first_name":"Estelle","full_name":"Morvan, Estelle","last_name":"Morvan"},{"last_name":"Bardiaux","full_name":"Bardiaux, Benjamin","first_name":"Benjamin"},{"first_name":"Roman","full_name":"Lichtenecker, Roman","last_name":"Lichtenecker"},{"last_name":"Ernst","full_name":"Ernst, Matthias","first_name":"Matthias"},{"first_name":"Antoine","last_name":"Loquet","full_name":"Loquet, Antoine"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda"}],"file_date_updated":"2023-08-16T12:33:31Z","publication_identifier":{"eissn":["1521-3773"],"issn":["1433-7851"]},"publication_status":"published","tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"intvolume":" 62","abstract":[{"text":"Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein--protein interactions. By studying a pair of structurally homologous cross-β amyloid fibrils, HET-s and HELLF, with a specific isotope-labeling approach and magic-angle-spinning (MAS) NMR, we have characterized the dynamic behavior of Phe and Tyr aromatic rings to show that the hydrophobic amyloid core is rigid, without any sign of \"breathing motions\" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips, on a variety of time scales from ns to µs. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from a NMR structural ensemble of such amyloid cross-β architecture.","lang":"eng"}],"has_accepted_license":"1"},{"department":[{"_id":"PaSc"}],"file":[{"file_size":54184807,"date_created":"2023-04-14T09:39:33Z","creator":"pschanda","date_updated":"2023-04-14T09:39:33Z","file_id":"12823","file_name":"data_deposition.zip","success":1,"content_type":"application/zip","access_level":"open_access","relation":"main_file","checksum":"54a619605e44c871214fb0e07b05c6bf"},{"relation":"main_file","checksum":"8dede9fc78399d13144eb05c62bf5750","file_name":"README","success":1,"content_type":"application/octet-stream","access_level":"open_access","file_id":"12824","date_created":"2023-04-14T09:39:58Z","file_size":4978,"date_updated":"2023-04-14T09:39:58Z","creator":"pschanda"}],"year":"2023","month":"04","related_material":{"record":[{"id":"13095","relation":"used_in_publication","status":"public"}]},"citation":{"ama":"Schanda P. Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” 2023. doi:10.15479/AT:ISTA:12820","ieee":"P. Schanda, “Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023.","short":"P. Schanda, (2023).","ista":"Schanda P. 2023. Research data of the publication ‘Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12820.","chicago":"Schanda, Paul. “Research Data of the Publication ‘Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12820.","apa":"Schanda, P. (2023). Research data of the publication “Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12820","mla":"Schanda, Paul. Research Data of the Publication “Disulfide-Bond-Induced Structural Frustration and Dynamic Disorder in a Peroxiredoxin from MAS NMR.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12820."},"date_published":"2023-04-18T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"status":"public","date_updated":"2023-08-01T14:48:08Z","_id":"12820","type":"research_data","date_created":"2023-04-10T05:55:56Z","author":[{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606"}],"doi":"10.15479/AT:ISTA:12820","contributor":[{"last_name":"Troussicot","first_name":"Laura","contributor_type":"researcher"},{"last_name":"Burmann","contributor_type":"researcher","first_name":"Björn M."}],"day":"18","article_processing_charge":"No","oa_version":"Published Version","title":"Research data of the publication \"Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR\"","publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-04-14T09:39:58Z","has_accepted_license":"1","abstract":[{"text":"Disulfide bond formation is fundamentally important for protein structure, and constitutes a key mechanism by which cells regulate the intracellular oxidation state. Peroxiredoxins (PRDXs) eliminate reactive oxygen species such as hydrogen peroxide through a catalytic cycle of Cys oxidation and reduction. Additionally, upon Cys oxidation PRDXs undergo extensive conformational rearrangements that may underlie their presently structurally poorly defined functions as molecular chaperones. Rearrangements include high molecular-weight oligomerization, the dynamics of which are, however, poorly understood, as is the impact of disulfide bond formation on these properties. Here we show that formation of disulfide bonds along the catalytic cycle induces extensive microsecond time scale dynamics, as monitored by magic-angle spinning NMR of the 216 kDa-large Tsa1 decameric assembly and solution-NMR of a designed dimeric mutant. We ascribe the conformational dynamics to structural frustration, resulting from conflicts between the disulfide-constrained reduction of mobility and the desire to fulfil other favorable contacts. \r\n\r\nThis data repository contains NMR data presented in the associated manuscript","lang":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"ddc":["570"]},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"mla":"Gauto, Diego F., et al. “Functional Control of a 0.5 MDa TET Aminopeptidase by a Flexible Loop Revealed by MAS NMR.” Nature Communications, vol. 13, 1927, Springer Nature, 2022, doi:10.1038/s41467-022-29423-0.","apa":"Gauto, D. F., Macek, P., Malinverni, D., Fraga, H., Paloni, M., Sučec, I., … Schanda, P. (2022). Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-022-29423-0","ista":"Gauto DF, Macek P, Malinverni D, Fraga H, Paloni M, Sučec I, Hessel A, Bustamante JP, Barducci A, Schanda P. 2022. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. Nature Communications. 13, 1927.","chicago":"Gauto, Diego F., Pavel Macek, Duccio Malinverni, Hugo Fraga, Matteo Paloni, Iva Sučec, Audrey Hessel, Juan Pablo Bustamante, Alessandro Barducci, and Paul Schanda. “Functional Control of a 0.5 MDa TET Aminopeptidase by a Flexible Loop Revealed by MAS NMR.” Nature Communications. Springer Nature, 2022. https://doi.org/10.1038/s41467-022-29423-0.","short":"D.F. Gauto, P. Macek, D. Malinverni, H. Fraga, M. Paloni, I. Sučec, A. Hessel, J.P. Bustamante, A. Barducci, P. Schanda, Nature Communications 13 (2022).","ieee":"D. F. Gauto et al., “Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR,” Nature Communications, vol. 13. Springer Nature, 2022.","ama":"Gauto DF, Macek P, Malinverni D, et al. Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR. Nature Communications. 2022;13. doi:10.1038/s41467-022-29423-0"},"language":[{"iso":"eng"}],"oa":1,"article_number":"1927","file":[{"file_id":"11348","file_size":2637590,"date_created":"2022-05-02T08:48:00Z","date_updated":"2022-05-02T08:48:00Z","creator":"dernst","relation":"main_file","checksum":"db61d5534e988743d6266d3675d77b08","success":1,"file_name":"2022_NatureCommunications_Gauto.pdf","access_level":"open_access","content_type":"application/pdf"}],"department":[{"_id":"PaSc"}],"month":"04","file_date_updated":"2022-05-02T08:48:00Z","publication_identifier":{"eissn":["2041-1723"]},"publication_status":"published","intvolume":" 13","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Large oligomeric enzymes control a myriad of cellular processes, from protein synthesis and degradation to metabolism. The 0.5 MDa large TET2 aminopeptidase, a prototypical protease important for cellular homeostasis, degrades peptides within a ca. 60 Å wide tetrahedral chamber with four lateral openings. The mechanisms of substrate trafficking and processing remain debated. Here, we integrate magic-angle spinning (MAS) NMR, mutagenesis, co-evolution analysis and molecular dynamics simulations and reveal that a loop in the catalytic chamber is a key element for enzymatic function. The loop is able to stabilize ligands in the active site and may additionally have a direct role in activating the catalytic water molecule whereby a conserved histidine plays a key role. Our data provide a strong case for the functional importance of highly dynamic - and often overlooked - parts of an enzyme, and the potential of MAS NMR to investigate their dynamics at atomic resolution.","lang":"eng"}],"has_accepted_license":"1","date_created":"2022-04-17T22:01:45Z","article_type":"original","volume":13,"oa_version":"Published Version","title":"Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR","day":"08","scopus_import":"1","author":[{"first_name":"Diego F.","last_name":"Gauto","full_name":"Gauto, Diego F."},{"last_name":"Macek","full_name":"Macek, Pavel","first_name":"Pavel"},{"first_name":"Duccio","last_name":"Malinverni","full_name":"Malinverni, Duccio"},{"first_name":"Hugo","last_name":"Fraga","full_name":"Fraga, Hugo"},{"full_name":"Paloni, Matteo","last_name":"Paloni","first_name":"Matteo"},{"first_name":"Iva","last_name":"Sučec","full_name":"Sučec, Iva"},{"last_name":"Hessel","full_name":"Hessel, Audrey","first_name":"Audrey"},{"first_name":"Juan Pablo","last_name":"Bustamante","full_name":"Bustamante, Juan Pablo"},{"first_name":"Alessandro","full_name":"Barducci, Alessandro","last_name":"Barducci"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"date_published":"2022-04-08T00:00:00Z","acknowledgement":"We are grateful to Bernhard Brutscher, Alicia Vallet, and Adrien Favier for excellent NMR\r\nplatform operation and management. The plasmid coding for TET2 was kindly provided\r\nby Bruno Franzetti and Jerome Boisbouvier (IBS Grenoble). We thank Anne-Marie Villard\r\nand the RoBioMol platform for preparing the loop deletion construct. The RoBioMol\r\nplatform is part of the Grenoble Instruct-ERIC center (ISBG; UAR 3518 CNRS-CEAUGA-EMBL) within the Grenoble Partnership for Structural Biology (PSB), supported by FRISBI (ANR-10-INBS-0005-02) and GRAL (ANR-10-LABX-49-01), financed within the University Grenoble Alpes graduate school (Ecoles Universitaires de Recherche) CBHEUR-GS (ANR-17-EURE-0003). This work was supported by the European Research Council (StG-2012-311318-ProtDyn2Function to P. S.) and the French Agence Nationale de la Recherche (ANR), under grant ANR-14-ACHN-0016 (M.P. and A.B.).","status":"public","publication":"Nature Communications","related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41467-022-31243-1"}]},"external_id":{"isi":["000781498700009"]},"year":"2022","isi":1,"quality_controlled":"1","ddc":["570"],"type":"journal_article","_id":"11179","date_updated":"2023-08-03T06:54:56Z","publisher":"Springer Nature","article_processing_charge":"No","doi":"10.1038/s41467-022-29423-0"},{"publication":"Frontiers in Molecular Biosciences","status":"public","acknowledgement":"We thank Juan C. Fontecilla-Camps for insightful discussions related to ATP-driven machineries, and Elif Karagöz for providing the structural model of the Hsp90-Tau complex. This study was supported by the European Research Council (StG-2012-311318-ProtDyn2Function) and the Agence Nationale de la Recherche (ANR-18-CE92-0032-MitoMemProtImp).","date_published":"2021-10-25T00:00:00Z","pmid":1,"external_id":{"isi":["000717241700001"],"pmid":["34760928"]},"isi":1,"year":"2021","ddc":["547"],"quality_controlled":"1","publisher":"Frontiers","article_processing_charge":"Yes (via OA deal)","doi":"10.3389/fmolb.2021.762005","type":"journal_article","_id":"10323","date_updated":"2023-08-14T11:55:04Z","language":[{"iso":"eng"}],"oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"ama":"Sučec I, Bersch B, Schanda P. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 2021;8. doi:10.3389/fmolb.2021.762005","short":"I. Sučec, B. Bersch, P. Schanda, Frontiers in Molecular Biosciences 8 (2021).","ieee":"I. Sučec, B. Bersch, and P. Schanda, “How do chaperones bind (partly) unfolded client proteins?,” Frontiers in Molecular Biosciences, vol. 8. Frontiers, 2021.","chicago":"Sučec, Iva, Beate Bersch, and Paul Schanda. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” Frontiers in Molecular Biosciences. Frontiers, 2021. https://doi.org/10.3389/fmolb.2021.762005.","ista":"Sučec I, Bersch B, Schanda P. 2021. How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. 8, 762005.","mla":"Sučec, Iva, et al. “How Do Chaperones Bind (Partly) Unfolded Client Proteins?” Frontiers in Molecular Biosciences, vol. 8, 762005, Frontiers, 2021, doi:10.3389/fmolb.2021.762005.","apa":"Sučec, I., Bersch, B., & Schanda, P. (2021). How do chaperones bind (partly) unfolded client proteins? Frontiers in Molecular Biosciences. Frontiers. https://doi.org/10.3389/fmolb.2021.762005"},"month":"10","article_number":"762005","file":[{"relation":"main_file","checksum":"a5c9dbf80dc2c5aaa737f456c941d964","success":1,"file_name":"2021_FrontiersMolBioSc_Sučec.pdf","access_level":"open_access","content_type":"application/pdf","file_id":"10333","file_size":4700798,"date_created":"2021-11-23T15:06:58Z","date_updated":"2021-11-23T15:06:58Z","creator":"cchlebak"}],"department":[{"_id":"PaSc"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"abstract":[{"text":"Molecular chaperones are central to cellular protein homeostasis. Dynamic disorder is a key feature of the complexes of molecular chaperones and their client proteins, and it facilitates the client release towards a folded state or the handover to downstream components. The dynamic nature also implies that a given chaperone can interact with many different client proteins, based on physico-chemical sequence properties rather than on structural complementarity of their (folded) 3D structure. Yet, the balance between this promiscuity and some degree of client specificity is poorly understood. Here, we review recent atomic-level descriptions of chaperones with client proteins, including chaperones in complex with intrinsically disordered proteins, with membrane-protein precursors, or partially folded client proteins. We focus hereby on chaperone-client interactions that are independent of ATP. The picture emerging from these studies highlights the importance of dynamics in these complexes, whereby several interaction types, not only hydrophobic ones, contribute to the complex formation. We discuss these features of chaperone-client complexes and possible factors that may contribute to this balance of promiscuity and specificity.","lang":"eng"}],"intvolume":" 8","has_accepted_license":"1","file_date_updated":"2021-11-23T15:06:58Z","publication_status":"published","publication_identifier":{"eissn":["2296-889X"]},"oa_version":"Published Version","title":"How do chaperones bind (partly) unfolded client proteins?","day":"25","scopus_import":"1","author":[{"first_name":"Iva","last_name":"Sučec","full_name":"Sučec, Iva"},{"first_name":"Beate","last_name":"Bersch","full_name":"Bersch, Beate"},{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","first_name":"Paul","orcid":"0000-0002-9350-7606"}],"date_created":"2021-11-21T23:01:29Z","article_type":"original","volume":8},{"publication_status":"published","publication_identifier":{"issn":["1741-7007"]},"abstract":[{"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.","lang":"eng"}],"intvolume":" 18","article_type":"original","date_created":"2020-09-17T10:26:53Z","volume":18,"oa_version":"Published Version","title":"The mitochondrial carrier pathway transports non-canonical substrates with an odd number of transmembrane segments","author":[{"last_name":"Rampelt","full_name":"Rampelt, Heike","first_name":"Heike"},{"first_name":"Iva","last_name":"Sucec","full_name":"Sucec, Iva"},{"first_name":"Beate","last_name":"Bersch","full_name":"Bersch, Beate"},{"last_name":"Horten","full_name":"Horten, Patrick","first_name":"Patrick"},{"first_name":"Inge","full_name":"Perschil, Inge","last_name":"Perschil"},{"full_name":"Martinou, Jean-Claude","last_name":"Martinou","first_name":"Jean-Claude"},{"full_name":"van der Laan, Martin","last_name":"van der Laan","first_name":"Martin"},{"last_name":"Wiedemann","full_name":"Wiedemann, Nils","first_name":"Nils"},{"full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","first_name":"Paul","orcid":"0000-0002-9350-7606"},{"last_name":"Pfanner","full_name":"Pfanner, Nikolaus","first_name":"Nikolaus"}],"day":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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).","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.","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.","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","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.","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."},"language":[{"iso":"eng"}],"oa":1,"article_number":"2","month":"01","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1186/s12915-019-0733-6","open_access":"1"}],"type":"journal_article","date_updated":"2021-01-12T08:19:02Z","_id":"8402","publisher":"Springer Nature","doi":"10.1186/s12915-019-0733-6","article_processing_charge":"No","date_published":"2020-01-06T00:00:00Z","pmid":1,"publication":"BMC Biology","status":"public","extern":"1","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"],"external_id":{"pmid":["31907035"]},"year":"2020"},{"publication":"bioRxiv","extern":"1","language":[{"iso":"eng"}],"status":"public","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2020-09-17T00:00:00Z","citation":{"ama":"Sučec I, Wang Y, Dakhlaoui O, et al. Structural basis of client specificity in mitochondrial membrane-protein chaperones. bioRxiv. doi:10.1101/2020.06.08.140772","ieee":"I. Sučec et al., “Structural basis of client specificity in mitochondrial membrane-protein chaperones,” bioRxiv. Cold Spring Harbor Laboratory.","short":"I. Sučec, Y. Wang, O. Dakhlaoui, K. Weinhäupl, T. Jores, D. Costa, A. Hessel, M. Brennich, D. Rapaport, K. Lindorff-Larsen, B. Bersch, P. Schanda, BioRxiv (n.d.).","ista":"Sučec I, Wang Y, Dakhlaoui O, Weinhäupl K, Jores T, Costa D, Hessel A, Brennich M, Rapaport D, Lindorff-Larsen K, Bersch B, Schanda P. Structural basis of client specificity in mitochondrial membrane-protein chaperones. bioRxiv, 10.1101/2020.06.08.140772.","chicago":"Sučec, Iva, Yong Wang, Ons Dakhlaoui, Katharina Weinhäupl, Tobias Jores, Doriane Costa, Audrey Hessel, et al. “Structural Basis of Client Specificity in Mitochondrial Membrane-Protein Chaperones.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.06.08.140772.","apa":"Sučec, I., Wang, Y., Dakhlaoui, O., Weinhäupl, K., Jores, T., Costa, D., … Schanda, P. (n.d.). Structural basis of client specificity in mitochondrial membrane-protein chaperones. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.06.08.140772","mla":"Sučec, Iva, et al. “Structural Basis of Client Specificity in Mitochondrial Membrane-Protein Chaperones.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.06.08.140772."},"month":"09","year":"2020","abstract":[{"text":"Chaperones are essential for assisting protein folding, and for transferring poorly soluble proteins to their functional locations within cells. Hydrophobic interactions drive promiscuous chaperone–client binding, but our understanding of how additional interactions enable client specificity is sparse. Here we decipher what determines binding of two chaperones (TIM8·13, TIM9·10) to different integral membrane proteins, the all-transmembrane mitochondrial carrier Ggc1, and Tim23 which has an additional disordered hydrophilic domain. Combining NMR, SAXS and molecular dynamics simulations, we determine the structures of Tim23/TIM8·13 and Tim23/TIM9·10 complexes. TIM8·13 uses transient salt bridges to interact with the hydrophilic part of its client, but its interactions to the transmembrane part are weaker than in TIM9·10. Consequently, TIM9·10 outcompetes TIM8·13 in binding hydrophobic clients, while TIM8·13 is tuned to few clients with both hydrophilic and hydrophobic parts. Our study exemplifies how chaperones fine-tune the balance of promiscuity vs. specificity.","lang":"eng"}],"publication_status":"submitted","main_file_link":[{"url":"https://doi.org/10.1101/2020.06.08.140772","open_access":"1"}],"publisher":"Cold Spring Harbor Laboratory","oa_version":"Preprint","title":"Structural basis of client specificity in mitochondrial membrane-protein chaperones","article_processing_charge":"No","day":"17","author":[{"last_name":"Sučec","full_name":"Sučec, Iva","first_name":"Iva"},{"full_name":"Wang, Yong","last_name":"Wang","first_name":"Yong"},{"first_name":"Ons","last_name":"Dakhlaoui","full_name":"Dakhlaoui, Ons"},{"first_name":"Katharina","last_name":"Weinhäupl","full_name":"Weinhäupl, Katharina"},{"full_name":"Jores, Tobias","last_name":"Jores","first_name":"Tobias"},{"first_name":"Doriane","full_name":"Costa, Doriane","last_name":"Costa"},{"full_name":"Hessel, Audrey","last_name":"Hessel","first_name":"Audrey"},{"full_name":"Brennich, Martha","last_name":"Brennich","first_name":"Martha"},{"full_name":"Rapaport, Doron","last_name":"Rapaport","first_name":"Doron"},{"first_name":"Kresten","full_name":"Lindorff-Larsen, Kresten","last_name":"Lindorff-Larsen"},{"full_name":"Bersch, Beate","last_name":"Bersch","first_name":"Beate"},{"first_name":"Paul","orcid":"0000-0002-9350-7606","last_name":"Schanda","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"doi":"10.1101/2020.06.08.140772","date_created":"2020-09-17T10:27:47Z","type":"preprint","_id":"8403","date_updated":"2021-01-12T08:19:02Z"},{"abstract":[{"lang":"eng","text":"The mitochondrial Tim chaperones are responsible for the transport of membrane proteins across the inter-membrane space to the inner and outer mitochondrial membranes. TIM9·10, a hexameric 70 kDa protein complex formed by 3 copies of Tim9 and Tim10, guides its clients across the aqueous compartment. The TIM9·10·12 complex is the anchor point at the inner-membrane insertase complex TIM22. The mechanism of client transport by TIM9·10 has been resolved recently, but the structure and subunit composition of the TIM9·10·12 complex remains largely unresolved. Furthermore, the assembly process of the hexameric TIM chaperones from its subunits remained elusive. We investigate the structural and dynamical properties of the Tim subunits, and show that they are highly dynamic. In their non-assembled form, the subunits behave as intrinsically disordered proteins; when the conserved cysteines of the CX3C-Xn-CX3C motifs are formed, short marginally stable α-helices are formed, which are only fully stabilized upon hexamer formation to the mature chaperone. Subunits are in equilibrium between their hexamer-embedded and a free form, with exchange kinetics on a minutes time scale. Joint NMR, small-angle X-ray scattering and MD simulation data allow us to derive a structural model of the TIM9·10·12 assembly, which has a 2:3:1 stoichiometry (Tim9:Tim10:Tim12) with a conserved hydrophobic client-binding groove and flexible N- and C-terminal tentacles."}],"main_file_link":[{"url":"https://doi.org/10.1101/2020.03.13.990150","open_access":"1"}],"publication_status":"submitted","doi":"10.1101/2020.03.13.990150","author":[{"last_name":"Weinhäupl","full_name":"Weinhäupl, Katharina","first_name":"Katharina"},{"last_name":"Wang","full_name":"Wang, Yong","first_name":"Yong"},{"last_name":"Hessel","full_name":"Hessel, Audrey","first_name":"Audrey"},{"last_name":"Brennich","full_name":"Brennich, Martha","first_name":"Martha"},{"first_name":"Kresten","last_name":"Lindorff-Larsen","full_name":"Lindorff-Larsen, Kresten"},{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606","first_name":"Paul"}],"article_processing_charge":"No","day":"14","title":"Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone","publisher":"Cold Spring Harbor Laboratory","oa_version":"Preprint","date_updated":"2021-01-12T08:19:03Z","_id":"8404","type":"preprint","date_created":"2020-09-17T10:27:59Z","oa":1,"language":[{"iso":"eng"}],"publication":"bioRxiv","extern":"1","status":"public","citation":{"ista":"Weinhäupl K, Wang Y, Hessel A, Brennich M, Lindorff-Larsen K, Schanda P. Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone. bioRxiv, 10.1101/2020.03.13.990150.","chicago":"Weinhäupl, Katharina, Yong Wang, Audrey Hessel, Martha Brennich, Kresten Lindorff-Larsen, and Paul Schanda. “Architecture and Subunit Dynamics of the Mitochondrial TIM9·10·12 Chaperone.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/2020.03.13.990150.","mla":"Weinhäupl, Katharina, et al. “Architecture and Subunit Dynamics of the Mitochondrial TIM9·10·12 Chaperone.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/2020.03.13.990150.","apa":"Weinhäupl, K., Wang, Y., Hessel, A., Brennich, M., Lindorff-Larsen, K., & Schanda, P. (n.d.). Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.03.13.990150","ama":"Weinhäupl K, Wang Y, Hessel A, Brennich M, Lindorff-Larsen K, Schanda P. Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone. bioRxiv. doi:10.1101/2020.03.13.990150","short":"K. Weinhäupl, Y. Wang, A. Hessel, M. Brennich, K. Lindorff-Larsen, P. Schanda, BioRxiv (n.d.).","ieee":"K. Weinhäupl, Y. Wang, A. Hessel, M. Brennich, K. Lindorff-Larsen, and P. Schanda, “Architecture and subunit dynamics of the mitochondrial TIM9·10·12 chaperone,” bioRxiv. Cold Spring Harbor Laboratory."},"date_published":"2020-03-14T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2020","month":"03"},{"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"external_id":{"pmid":["31217444"]},"year":"2019","date_published":"2019-06-19T00:00:00Z","pmid":1,"extern":"1","publication":"Nature Communications","status":"public","type":"journal_article","date_updated":"2021-01-12T08:19:03Z","_id":"8405","publisher":"Springer Nature","doi":"10.1038/s41467-019-10490-9","article_processing_charge":"No","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41467-019-10490-9","open_access":"1"}],"article_number":"2697","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Gauto DF, Estrozi LF, Schwieters CD, et al. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. 2019;10. doi:10.1038/s41467-019-10490-9","short":"D.F. Gauto, L.F. Estrozi, C.D. Schwieters, G. Effantin, P. Macek, R. Sounier, A.C. Sivertsen, E. Schmidt, R. Kerfah, G. Mas, J.-P. Colletier, P. Güntert, A. Favier, G. Schoehn, P. Schanda, J. Boisbouvier, Nature Communications 10 (2019).","ieee":"D. F. Gauto et al., “Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex,” Nature Communications, vol. 10. Springer Nature, 2019.","chicago":"Gauto, Diego F., Leandro F. Estrozi, Charles D. Schwieters, Gregory Effantin, Pavel Macek, Remy Sounier, Astrid C. Sivertsen, et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-10490-9.","ista":"Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen AC, Schmidt E, Kerfah R, Mas G, Colletier J-P, Güntert P, Favier A, Schoehn G, Schanda P, Boisbouvier J. 2019. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. 10, 2697.","mla":"Gauto, Diego F., et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.” Nature Communications, vol. 10, 2697, Springer Nature, 2019, doi:10.1038/s41467-019-10490-9.","apa":"Gauto, D. F., Estrozi, L. F., Schwieters, C. D., Effantin, G., Macek, P., Sounier, R., … Boisbouvier, J. (2019). Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-10490-9"},"language":[{"iso":"eng"}],"oa":1,"article_type":"original","date_created":"2020-09-17T10:28:25Z","volume":10,"oa_version":"Published Version","title":"Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex","author":[{"first_name":"Diego F.","full_name":"Gauto, Diego F.","last_name":"Gauto"},{"last_name":"Estrozi","full_name":"Estrozi, Leandro F.","first_name":"Leandro F."},{"full_name":"Schwieters, Charles D.","last_name":"Schwieters","first_name":"Charles D."},{"first_name":"Gregory","full_name":"Effantin, Gregory","last_name":"Effantin"},{"first_name":"Pavel","full_name":"Macek, Pavel","last_name":"Macek"},{"full_name":"Sounier, Remy","last_name":"Sounier","first_name":"Remy"},{"full_name":"Sivertsen, Astrid C.","last_name":"Sivertsen","first_name":"Astrid C."},{"full_name":"Schmidt, Elena","last_name":"Schmidt","first_name":"Elena"},{"full_name":"Kerfah, Rime","last_name":"Kerfah","first_name":"Rime"},{"full_name":"Mas, Guillaume","last_name":"Mas","first_name":"Guillaume"},{"first_name":"Jacques-Philippe","full_name":"Colletier, Jacques-Philippe","last_name":"Colletier"},{"full_name":"Güntert, Peter","last_name":"Güntert","first_name":"Peter"},{"first_name":"Adrien","full_name":"Favier, Adrien","last_name":"Favier"},{"first_name":"Guy","full_name":"Schoehn, Guy","last_name":"Schoehn"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda"},{"last_name":"Boisbouvier","full_name":"Boisbouvier, Jerome","first_name":"Jerome"}],"day":"19","publication_identifier":{"issn":["2041-1723"]},"publication_status":"published","intvolume":" 10","abstract":[{"lang":"eng","text":"Atomic-resolution structure determination is crucial for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely give access to atomic-level structural data, and, generally, NMR structure determination is restricted to small (<30 kDa) proteins. We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods. The approach enables structure determination of the 468 kDa large dodecameric aminopeptidase TET2 to a precision and accuracy below 1 Å by combining secondary-structure information obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large subunits, distance restraints from backbone amides and ILV methyl groups, and a 4.1 Å resolution EM map. The resulting structure exceeds current standards of NMR and EM structure determination in terms of molecular weight and precision. Importantly, the approach is successful even in cases where only medium-resolution cryo-EM data are available."}]},{"_id":"8406","date_updated":"2021-01-12T08:19:03Z","type":"journal_article","article_processing_charge":"No","doi":"10.1126/sciadv.aaw3818","publisher":"American Association for the Advancement of Science","main_file_link":[{"url":" https://doi.org/10.1126/sciadv.aaw3818","open_access":"1"}],"quality_controlled":"1","year":"2019","date_published":"2019-09-04T00:00:00Z","publication":"Science Advances","status":"public","extern":"1","volume":5,"date_created":"2020-09-17T10:28:36Z","article_type":"original","day":"04","author":[{"last_name":"Felix","full_name":"Felix, Jan","first_name":"Jan"},{"first_name":"Katharina","last_name":"Weinhäupl","full_name":"Weinhäupl, Katharina"},{"first_name":"Christophe","last_name":"Chipot","full_name":"Chipot, Christophe"},{"last_name":"Dehez","full_name":"Dehez, François","first_name":"François"},{"first_name":"Audrey","last_name":"Hessel","full_name":"Hessel, Audrey"},{"last_name":"Gauto","full_name":"Gauto, Diego F.","first_name":"Diego F."},{"last_name":"Morlot","full_name":"Morlot, Cecile","first_name":"Cecile"},{"full_name":"Abian, Olga","last_name":"Abian","first_name":"Olga"},{"full_name":"Gutsche, Irina","last_name":"Gutsche","first_name":"Irina"},{"full_name":"Velazquez-Campoy, Adrian","last_name":"Velazquez-Campoy","first_name":"Adrian"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda"},{"last_name":"Fraga","full_name":"Fraga, Hugo","first_name":"Hugo"}],"title":"Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors","oa_version":"Published Version","publication_identifier":{"issn":["2375-2548"]},"publication_status":"published","intvolume":" 5","abstract":[{"lang":"eng","text":"Coordinated conformational transitions in oligomeric enzymatic complexes modulate function in response to substrates and play a crucial role in enzyme inhibition and activation. Caseinolytic protease (ClpP) is a tetradecameric complex, which has emerged as a drug target against multiple pathogenic bacteria. Activation of different ClpPs by inhibitors has been independently reported from drug development efforts, but no rationale for inhibitor-induced activation has been hitherto proposed. Using an integrated approach that includes x-ray crystallography, solid- and solution-state nuclear magnetic resonance, molecular dynamics simulations, and isothermal titration calorimetry, we show that the proteasome inhibitor bortezomib binds to the ClpP active-site serine, mimicking a peptide substrate, and induces a concerted allosteric activation of the complex. The bortezomib-activated conformation also exhibits a higher affinity for its cognate unfoldase ClpX. We propose a universal allosteric mechanism, where substrate binding to a single subunit locks ClpP into an active conformation optimized for chaperone association and protein processive degradation."}],"article_number":"eaaw3818","month":"09","citation":{"ista":"Felix J, Weinhäupl K, Chipot C, Dehez F, Hessel A, Gauto DF, Morlot C, Abian O, Gutsche I, Velazquez-Campoy A, Schanda P, Fraga H. 2019. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. 5(9), eaaw3818.","chicago":"Felix, Jan, Katharina Weinhäupl, Christophe Chipot, François Dehez, Audrey Hessel, Diego F. Gauto, Cecile Morlot, et al. “Mechanism of the Allosteric Activation of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” Science Advances. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/sciadv.aaw3818.","mla":"Felix, Jan, et al. “Mechanism of the Allosteric Activation of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” Science Advances, vol. 5, no. 9, eaaw3818, American Association for the Advancement of Science, 2019, doi:10.1126/sciadv.aaw3818.","apa":"Felix, J., Weinhäupl, K., Chipot, C., Dehez, F., Hessel, A., Gauto, D. F., … Fraga, H. (2019). Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw3818","ama":"Felix J, Weinhäupl K, Chipot C, et al. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. 2019;5(9). doi:10.1126/sciadv.aaw3818","short":"J. Felix, K. Weinhäupl, C. Chipot, F. Dehez, A. Hessel, D.F. Gauto, C. Morlot, O. Abian, I. Gutsche, A. Velazquez-Campoy, P. Schanda, H. Fraga, Science Advances 5 (2019).","ieee":"J. Felix et al., “Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors,” Science Advances, vol. 5, no. 9. American Association for the Advancement of Science, 2019."},"issue":"9","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"language":[{"iso":"eng"}]},{"page":"180-186","intvolume":" 306","quality_controlled":"1","publication_status":"published","publication_identifier":{"issn":["1090-7807"]},"author":[{"first_name":"Paul","orcid":"0000-0002-9350-7606","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda"}],"doi":"10.1016/j.jmr.2019.07.025","article_processing_charge":"No","day":"01","oa_version":"Submitted Version","publisher":"Elsevier","title":"Relaxing with liquids and solids – A perspective on biomolecular dynamics","date_updated":"2021-01-12T08:19:04Z","volume":306,"_id":"8407","article_type":"original","type":"journal_article","date_created":"2020-09-17T10:28:47Z","publication":"Journal of Magnetic Resonance","extern":"1","status":"public","language":[{"iso":"eng"}],"pmid":1,"citation":{"apa":"Schanda, P. (2019). Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2019.07.025","mla":"Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular Dynamics.” Journal of Magnetic Resonance, vol. 306, Elsevier, 2019, pp. 180–86, doi:10.1016/j.jmr.2019.07.025.","chicago":"Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular Dynamics.” Journal of Magnetic Resonance. Elsevier, 2019. https://doi.org/10.1016/j.jmr.2019.07.025.","ista":"Schanda P. 2019. Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. 306, 180–186.","ieee":"P. Schanda, “Relaxing with liquids and solids – A perspective on biomolecular dynamics,” Journal of Magnetic Resonance, vol. 306. Elsevier, pp. 180–186, 2019.","short":"P. Schanda, Journal of Magnetic Resonance 306 (2019) 180–186.","ama":"Schanda P. Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. 2019;306:180-186. doi:10.1016/j.jmr.2019.07.025"},"date_published":"2019-09-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","external_id":{"pmid":["31350165"]},"month":"09","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"]},{"abstract":[{"text":"Aromatic residues are located at structurally important sites of many proteins. Probing their interactions and dynamics can provide important functional insight but is challenging in large proteins. Here, we introduce approaches to characterize dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning (MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields isolated two-spin systems that are ideally suited for artefact-free dynamics measurements, and allows probing motions effectively without molecular-weight limitations. The application to the TET2 enzyme assembly of ~0.5 MDa size, the currently largest protein assigned by MAS NMR, provides insights into motions occurring on a wide range of time scales (ps-ms). We quantitatively probe ring flip motions, and show the temperature dependence by MAS NMR measurements down to 100 K. Interestingly, favorable line widths are observed down to 100 K, with potential implications for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion measurements and detect structural excursions occurring on a microsecond time scale in the entry pore to the catalytic chamber and at a trimer interface that was proposed as exit pore. We show that the labeling scheme with deuteration at ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments with protonated, uniformly 13C-labeled samples.","lang":"eng"}],"intvolume":" 141","publication_identifier":{"issn":["0002-7863","1520-5126"]},"publication_status":"published","title":"Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR","oa_version":"Submitted Version","author":[{"full_name":"Gauto, Diego F.","last_name":"Gauto","first_name":"Diego F."},{"first_name":"Pavel","full_name":"Macek, Pavel","last_name":"Macek"},{"first_name":"Alessandro","last_name":"Barducci","full_name":"Barducci, Alessandro"},{"last_name":"Fraga","full_name":"Fraga, Hugo","first_name":"Hugo"},{"first_name":"Audrey","last_name":"Hessel","full_name":"Hessel, Audrey"},{"first_name":"Tsutomu","full_name":"Terauchi, Tsutomu","last_name":"Terauchi"},{"first_name":"David","last_name":"Gajan","full_name":"Gajan, David"},{"last_name":"Miyanoiri","full_name":"Miyanoiri, Yohei","first_name":"Yohei"},{"full_name":"Boisbouvier, Jerome","last_name":"Boisbouvier","first_name":"Jerome"},{"last_name":"Lichtenecker","full_name":"Lichtenecker, Roman","first_name":"Roman"},{"last_name":"Kainosho","full_name":"Kainosho, Masatsune","first_name":"Masatsune"},{"last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","first_name":"Paul","orcid":"0000-0002-9350-7606"}],"day":"14","article_type":"original","date_created":"2020-09-17T10:29:00Z","volume":141,"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"28","citation":{"ama":"Gauto DF, Macek P, Barducci A, et al. Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. 2019;141(28):11183-11195. doi:10.1021/jacs.9b04219","short":"D.F. Gauto, P. Macek, A. Barducci, H. Fraga, A. Hessel, T. Terauchi, D. Gajan, Y. Miyanoiri, J. Boisbouvier, R. Lichtenecker, M. Kainosho, P. Schanda, Journal of the American Chemical Society 141 (2019) 11183–11195.","ieee":"D. F. Gauto et al., “Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR,” Journal of the American Chemical Society, vol. 141, no. 28. American Chemical Society, pp. 11183–11195, 2019.","ista":"Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P. 2019. Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. 141(28), 11183–11195.","chicago":"Gauto, Diego F., Pavel Macek, Alessandro Barducci, Hugo Fraga, Audrey Hessel, Tsutomu Terauchi, David Gajan, et al. “Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 KDa Enzyme by Specific 1H–13C Labeling and Fast Magic-Angle Spinning NMR.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.9b04219.","mla":"Gauto, Diego F., et al. “Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 KDa Enzyme by Specific 1H–13C Labeling and Fast Magic-Angle Spinning NMR.” Journal of the American Chemical Society, vol. 141, no. 28, American Chemical Society, 2019, pp. 11183–95, doi:10.1021/jacs.9b04219.","apa":"Gauto, D. F., Macek, P., Barducci, A., Fraga, H., Hessel, A., Terauchi, T., … Schanda, P. (2019). Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.9b04219"},"month":"06","page":"11183-11195","quality_controlled":"1","publisher":"American Chemical Society","doi":"10.1021/jacs.9b04219","article_processing_charge":"No","type":"journal_article","date_updated":"2021-01-12T08:19:04Z","_id":"8408","publication":"Journal of the American Chemical Society","status":"public","extern":"1","date_published":"2019-06-14T00:00:00Z","pmid":1,"external_id":{"pmid":["31199882"]},"year":"2019","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"]},{"page":"66-72","quality_controlled":"1","publisher":"Elsevier","article_processing_charge":"No","doi":"10.1016/j.jsb.2018.07.009","type":"journal_article","_id":"8409","date_updated":"2021-01-12T08:19:05Z","extern":"1","status":"public","publication":"Journal of Structural Biology","date_published":"2019-04-01T00:00:00Z","pmid":1,"external_id":{"pmid":["30031884"]},"year":"2019","keyword":["Structural Biology"],"intvolume":" 206","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"}],"publication_identifier":{"issn":["1047-8477"]},"publication_status":"published","oa_version":"Submitted Version","title":"Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency","day":"01","author":[{"full_name":"Bougault, Catherine","last_name":"Bougault","first_name":"Catherine"},{"first_name":"Isabel","last_name":"Ayala","full_name":"Ayala, Isabel"},{"first_name":"Waldemar","full_name":"Vollmer, Waldemar","last_name":"Vollmer"},{"first_name":"Jean-Pierre","full_name":"Simorre, Jean-Pierre","last_name":"Simorre"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"}],"date_created":"2020-09-17T10:29:10Z","article_type":"original","volume":206,"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","short":"C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, P. Schanda, Journal of Structural Biology 206 (2019) 66–72.","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","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.","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.","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."},"issue":"1","month":"04"}]