--- _id: '13095' abstract: - lang: eng 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. 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. " article_processing_charge: No article_type: original author: - first_name: Laura full_name: Troussicot, Laura id: 3d9cac31-413c-11eb-9514-d1ec2a7fb7f3 last_name: Troussicot - first_name: Alicia full_name: Vallet, Alicia last_name: Vallet - first_name: Mikael full_name: Molin, Mikael last_name: Molin - first_name: Björn M. full_name: Burmann, Björn M. last_name: Burmann - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 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 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 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. 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. 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. 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. short: L. Troussicot, A. Vallet, M. Molin, B.M. Burmann, P. Schanda, Journal of the American Chemical Society 145 (2023) 10700–10711. date_created: 2023-05-28T22:01:04Z date_published: 2023-05-04T00:00:00Z date_updated: 2023-08-01T14:48:09Z day: '04' ddc: - '540' department: - _id: PaSc doi: 10.1021/jacs.3c01200 external_id: isi: - '000985907400001' pmid: - '37140345' file: - access_level: open_access checksum: 0758a930ef21c62fc91b14e657479f83 content_type: application/pdf creator: dernst date_created: 2023-05-30T07:05:28Z date_updated: 2023-05-30T07:05:28Z file_id: '13098' file_name: 2023_JACS_Troussicot.pdf file_size: 6719299 relation: main_file success: 1 file_date_updated: 2023-05-30T07:05:28Z has_accepted_license: '1' intvolume: ' 145' isi: 1 issue: '19' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 10700–10711 pmid: 1 publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' related_material: record: - id: '12820' relation: research_data status: public scopus_import: '1' status: public title: Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 145 year: '2023' ... --- _id: '12820' abstract: - lang: eng 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" article_processing_charge: No author: - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 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 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 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. 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. 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. 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. short: P. Schanda, (2023). contributor: - contributor_type: researcher first_name: Laura last_name: Troussicot - contributor_type: researcher first_name: Björn M. last_name: Burmann date_created: 2023-04-10T05:55:56Z date_published: 2023-04-18T00:00:00Z date_updated: 2023-08-01T14:48:08Z day: '18' ddc: - '570' department: - _id: PaSc doi: 10.15479/AT:ISTA:12820 file: - access_level: open_access checksum: 54a619605e44c871214fb0e07b05c6bf content_type: application/zip creator: pschanda date_created: 2023-04-14T09:39:33Z date_updated: 2023-04-14T09:39:33Z file_id: '12823' file_name: data_deposition.zip file_size: 54184807 relation: main_file success: 1 - access_level: open_access checksum: 8dede9fc78399d13144eb05c62bf5750 content_type: application/octet-stream creator: pschanda date_created: 2023-04-14T09:39:58Z date_updated: 2023-04-14T09:39:58Z file_id: '12824' file_name: README file_size: 4978 relation: main_file success: 1 file_date_updated: 2023-04-14T09:39:58Z has_accepted_license: '1' month: '04' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '13095' relation: used_in_publication status: public status: public title: Research data of the publication "Disulfide-bond-induced structural frustration and dynamic disorder in a peroxiredoxin from MAS NMR" tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12114' 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.' 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”. article_number: '100079' article_processing_charge: No article_type: original author: - first_name: Diego F. full_name: Gauto, Diego F. last_name: Gauto - first_name: Olga O. full_name: Lebedenko, Olga O. last_name: Lebedenko - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Isabel full_name: Ayala, Isabel last_name: Ayala - first_name: Roman full_name: Lichtenecker, Roman last_name: Lichtenecker - first_name: Nikolai R. full_name: Skrynnikov, Nikolai R. last_name: Skrynnikov - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: 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' apa: 'Gauto, D. F., Lebedenko, O. O., Becker, L. M., Ayala, I., Lichtenecker, R., Skrynnikov, N. R., & Schanda, P. (2023). Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. Elsevier. https://doi.org/10.1016/j.yjsbx.2022.100079' chicago: 'Gauto, Diego F., Olga O. Lebedenko, Lea Marie Becker, Isabel Ayala, Roman Lichtenecker, Nikolai R. Skrynnikov, and Paul Schanda. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X. Elsevier, 2023. https://doi.org/10.1016/j.yjsbx.2022.100079.' ieee: 'D. F. Gauto et al., “Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD,” Journal of Structural Biology: X, vol. 7. Elsevier, 2023.' ista: 'Gauto DF, Lebedenko OO, Becker LM, Ayala I, Lichtenecker R, Skrynnikov NR, Schanda P. 2023. Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD. Journal of Structural Biology: X. 7, 100079.' mla: 'Gauto, Diego F., et al. “Aromatic Ring Flips in Differently Packed Ubiquitin Protein Crystals from MAS NMR and MD.” Journal of Structural Biology: X, vol. 7, 100079, Elsevier, 2023, doi:10.1016/j.yjsbx.2022.100079.' short: 'D.F. Gauto, O.O. Lebedenko, L.M. Becker, I. Ayala, R. Lichtenecker, N.R. Skrynnikov, P. Schanda, Journal of Structural Biology: X 7 (2023).' date_created: 2023-01-12T11:55:38Z date_published: 2023-01-01T00:00:00Z date_updated: 2023-08-16T09:37:25Z day: '01' ddc: - '570' department: - _id: PaSc doi: 10.1016/j.yjsbx.2022.100079 external_id: pmid: - '36578472' file: - access_level: open_access checksum: b4b1c10a31018aafe053b7d55a470e54 content_type: application/pdf creator: dernst date_created: 2023-08-16T09:36:28Z date_updated: 2023-08-16T09:36:28Z file_id: '14064' file_name: 2023_JourStrucBiologyX_Gauto.pdf file_size: 5132322 relation: main_file success: 1 file_date_updated: 2023-08-16T09:36:28Z has_accepted_license: '1' intvolume: ' 7' keyword: - Structural Biology language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '01' oa: 1 oa_version: Published Version pmid: 1 publication: 'Journal of Structural Biology: X' publication_identifier: issn: - 2590-1524 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Aromatic ring flips in differently packed ubiquitin protein crystals from MAS NMR and MD tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2023' ... --- _id: '13096' abstract: - lang: eng 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. acknowledged_ssus: - _id: NMR - _id: LifeSc 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." article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Morris full_name: Degen, Morris last_name: Degen - first_name: José Carlos full_name: Santos, José Carlos last_name: Santos - first_name: Kristyna full_name: Pluhackova, Kristyna last_name: Pluhackova - first_name: Gonzalo full_name: Cebrero, Gonzalo last_name: Cebrero - first_name: Saray full_name: Ramos, Saray last_name: Ramos - first_name: Gytis full_name: Jankevicius, Gytis last_name: Jankevicius - first_name: Ella full_name: Hartenian, Ella last_name: Hartenian - first_name: Undina full_name: Guillerm, Undina id: bb74f472-ae54-11eb-9835-bc9c22fb1183 last_name: Guillerm - first_name: Stefania A. full_name: Mari, Stefania A. last_name: Mari - first_name: Bastian full_name: Kohl, Bastian last_name: Kohl - first_name: Daniel J. full_name: Müller, Daniel J. last_name: Müller - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - first_name: Timm full_name: Maier, Timm last_name: Maier - first_name: Camilo full_name: Perez, Camilo last_name: Perez - first_name: Christian full_name: Sieben, Christian last_name: Sieben - first_name: Petr full_name: Broz, Petr last_name: Broz - first_name: Sebastian full_name: Hiller, Sebastian last_name: Hiller citation: 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 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. 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. 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. 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. 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. date_created: 2023-05-28T22:01:04Z date_published: 2023-06-29T00:00:00Z date_updated: 2023-11-14T11:49:21Z day: '29' ddc: - '570' department: - _id: PaSc doi: 10.1038/s41586-023-05991-z external_id: isi: - '000991386800011' file: - access_level: open_access checksum: 0fab69252453bff1de7f0e2eceb76d34 content_type: application/pdf creator: dernst date_created: 2023-11-14T11:48:18Z date_updated: 2023-11-14T11:48:18Z file_id: '14533' file_name: 2023_Nature_Degen.pdf file_size: 12292188 relation: main_file success: 1 file_date_updated: 2023-11-14T11:48:18Z has_accepted_license: '1' intvolume: ' 618' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1065-1071 publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Structural basis of NINJ1-mediated plasma membrane rupture in cell death tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 618 year: '2023' ... --- _id: '14861' abstract: - lang: eng text: Cover Page article_number: ' e202304138' article_processing_charge: No author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Mélanie full_name: Berbon, Mélanie last_name: Berbon - first_name: Alicia full_name: Vallet, Alicia last_name: Vallet - first_name: Axelle full_name: Grelard, Axelle last_name: Grelard - first_name: Estelle full_name: Morvan, Estelle last_name: Morvan - first_name: Benjamin full_name: Bardiaux, Benjamin last_name: Bardiaux - first_name: Roman full_name: Lichtenecker, Roman last_name: Lichtenecker - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst - first_name: Antoine full_name: Loquet, Antoine last_name: Loquet - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: 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' 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' 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.' 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.' 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.' 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.' date_created: 2024-01-22T11:54:34Z date_published: 2023-05-02T00:00:00Z date_updated: 2024-01-23T08:48:14Z day: '02' department: - _id: PaSc doi: 10.1002/anie.202304138 intvolume: ' 62' issue: '19' keyword: - General Chemistry - Catalysis language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/anie.202304138 month: '05' oa: 1 oa_version: Published Version publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: published publisher: Wiley related_material: link: - relation: translation url: https://doi.org/10.1002/ange.202304138 record: - id: '12675' relation: other status: public status: public title: 'Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues' type: other_academic_publication user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2023' ... --- _id: '14835' 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. 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. article_number: e202219314 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Mélanie full_name: Berbon, Mélanie last_name: Berbon - first_name: Alicia full_name: Vallet, Alicia last_name: Vallet - first_name: Axelle full_name: Grelard, Axelle last_name: Grelard - first_name: Estelle full_name: Morvan, Estelle last_name: Morvan - first_name: Benjamin full_name: Bardiaux, Benjamin last_name: Bardiaux - first_name: Roman full_name: Lichtenecker, Roman last_name: Lichtenecker - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst - first_name: Antoine full_name: Loquet, Antoine last_name: Loquet - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: 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 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. 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. 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. 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. 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). date_created: 2024-01-18T10:01:01Z date_published: 2023-05-02T00:00:00Z date_updated: 2024-01-23T12:23:35Z day: '02' ddc: - '540' department: - _id: PaSc doi: 10.1002/ange.202219314 file: - access_level: open_access checksum: 98e68d370159f7be52a3d7c8a8ee1198 content_type: application/pdf creator: dernst date_created: 2024-01-23T08:57:01Z date_updated: 2024-01-23T08:57:01Z file_id: '14876' file_name: 2023_AngewChem_Becker.pdf file_size: 1004676 relation: main_file success: 1 file_date_updated: 2024-01-23T08:57:01Z has_accepted_license: '1' intvolume: ' 135' issue: '19' keyword: - General Medicine language: - iso: ger month: '05' oa: 1 oa_version: Published Version publication: Angewandte Chemie publication_identifier: eissn: - 1521-3757 issn: - 0044-8249 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2023' ... --- _id: '14847' 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. alternative_title: - New Developments in NMR article_processing_charge: No author: - first_name: I. full_name: Sučec, I. last_name: Sučec - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: 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' 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. 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. 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.' 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. 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. date_created: 2024-01-22T08:04:57Z date_published: 2023-11-01T00:00:00Z date_updated: 2024-01-23T11:50:10Z day: '01' department: - _id: PaSc doi: 10.1039/bk9781839165986-00136 editor: - first_name: Sebastian full_name: Hiller, Sebastian last_name: Hiller - first_name: Maili full_name: Liu, Maili last_name: Liu - first_name: Lichun full_name: He, Lichun last_name: He intvolume: ' 29' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.26434/chemrxiv-2023-rpn28 month: '11' oa: 1 oa_version: Preprint page: 136-161 publication: Biophysics of Molecular Chaperones publication_identifier: eisbn: - '9781839165993' isbn: - '9781839162824' publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2023' ... --- _id: '14036' 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. 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. article_number: '102660' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Federico full_name: Napoli, Federico id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b last_name: Napoli orcid: 0000-0002-9043-136X - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: 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 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 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. 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. 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. 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. short: F. Napoli, L.M. Becker, P. Schanda, Current Opinion in Structural Biology 82 (2023). date_created: 2023-08-13T22:01:11Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-30T12:37:36Z day: '01' ddc: - '570' department: - _id: PaSc doi: 10.1016/j.sbi.2023.102660 external_id: isi: - '001053616200001' pmid: - '37536064' file: - access_level: open_access checksum: c850f7ac8a4234319755b672c1df69ae content_type: application/pdf creator: dernst date_created: 2024-01-30T12:36:39Z date_updated: 2024-01-30T12:36:39Z file_id: '14907' file_name: 2023_CurrentOpinionStrucBio_Napoli.pdf file_size: 1231998 relation: main_file success: 1 file_date_updated: 2024-01-30T12:36:39Z intvolume: ' 82' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 project: - _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf grant_number: I05812 name: AlloSpace. The emergence and mechanisms of allostery publication: Current Opinion in Structural Biology publication_identifier: eissn: - 1879-033X issn: - 0959-440X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Protein dynamics detected by magic-angle spinning relaxation dispersion NMR tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 82 year: '2023' ... --- _id: '12675' abstract: - lang: eng 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. 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. article_number: e202219314 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Mélanie full_name: Berbon, Mélanie last_name: Berbon - first_name: Alicia full_name: Vallet, Alicia last_name: Vallet - first_name: Axelle full_name: Grelard, Axelle last_name: Grelard - first_name: Estelle full_name: Morvan, Estelle last_name: Morvan - first_name: Benjamin full_name: Bardiaux, Benjamin last_name: Bardiaux - first_name: Roman full_name: Lichtenecker, Roman last_name: Lichtenecker - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst - first_name: Antoine full_name: Loquet, Antoine last_name: Loquet - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: 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 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. 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. 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. 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. 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). date_created: 2023-02-24T10:45:01Z date_published: 2023-05-01T00:00:00Z date_updated: 2024-02-21T12:14:06Z day: '01' ddc: - '540' department: - _id: GradSch - _id: PaSc doi: 10.1002/anie.202219314 external_id: isi: - '000956919900001' pmid: - '36738230' file: - access_level: open_access checksum: 7dd083ed8850faa55c34e411ed390de9 content_type: application/pdf creator: dernst date_created: 2023-08-16T12:33:31Z date_updated: 2023-08-16T12:33:31Z file_id: '14072' file_name: 2023_AngewChemInt_Becker.pdf file_size: 1422445 relation: main_file success: 1 file_date_updated: 2023-08-16T12:33:31Z has_accepted_license: '1' intvolume: ' 62' isi: 1 issue: '19' keyword: - General Chemistry - Catalysis language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/dancing-styles-of-atoms/ record: - id: '14861' relation: other status: public - id: '12497' relation: research_data status: public status: public title: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2023' ... --- _id: '12497' 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. article_processing_charge: No author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: 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' 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.' 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.' 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.' 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.' short: L.M. Becker, P. Schanda, (2023). contributor: - contributor_type: researcher first_name: Mélanie last_name: Berbon - contributor_type: researcher first_name: Alicia last_name: Vallet - contributor_type: researcher first_name: Axelle last_name: Grelard - contributor_type: researcher first_name: Estelle last_name: Morvan - contributor_type: researcher first_name: Benjamin last_name: Bardiaux - contributor_type: researcher first_name: Roman last_name: Lichtenecker - contributor_type: researcher first_name: Matthias last_name: Ernst - contributor_type: researcher first_name: Antoine last_name: Loquet - contributor_type: contact_person first_name: Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - contributor_type: researcher first_name: Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 date_created: 2023-02-03T08:08:02Z date_published: 2023-03-23T00:00:00Z date_updated: 2024-02-21T12:14:06Z day: '23' ddc: - '572' department: - _id: GradSch - _id: PaSc doi: 10.15479/AT:ISTA:12497 file: - access_level: open_access checksum: fd9a28620a81a82991fb70f4fd6591d9 content_type: application/zip creator: lbecker date_created: 2023-03-23T10:03:16Z date_updated: 2023-03-24T09:34:20Z file_id: '12743' file_name: Research_Data.zip file_size: 87018103 relation: main_file - access_level: open_access checksum: 30ebdfb600af118fcf8518b6efe0b7e9 content_type: text/plain creator: dernst date_created: 2023-03-24T07:13:55Z date_updated: 2023-03-24T09:42:03Z file_id: '12755' file_name: README.txt file_size: 747 relation: main_file file_date_updated: 2023-03-24T09:42:03Z has_accepted_license: '1' keyword: - aromatic side chains - isotopic labeling - protein dynamics - ring flips - spin relaxation month: '03' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '12675' relation: used_in_publication status: public status: public title: 'Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues' tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '11179' abstract: - lang: eng 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. 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.)." article_number: '1927' article_processing_charge: No article_type: original author: - first_name: Diego F. full_name: Gauto, Diego F. last_name: Gauto - first_name: Pavel full_name: Macek, Pavel last_name: Macek - first_name: Duccio full_name: Malinverni, Duccio last_name: Malinverni - first_name: Hugo full_name: Fraga, Hugo last_name: Fraga - first_name: Matteo full_name: Paloni, Matteo last_name: Paloni - first_name: Iva full_name: Sučec, Iva last_name: Sučec - first_name: Audrey full_name: Hessel, Audrey last_name: Hessel - first_name: Juan Pablo full_name: Bustamante, Juan Pablo last_name: Bustamante - first_name: Alessandro full_name: Barducci, Alessandro last_name: Barducci - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: 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 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 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. 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. 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. 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. 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). date_created: 2022-04-17T22:01:45Z date_published: 2022-04-08T00:00:00Z date_updated: 2023-08-03T06:54:56Z day: '08' ddc: - '570' department: - _id: PaSc doi: 10.1038/s41467-022-29423-0 external_id: isi: - '000781498700009' file: - access_level: open_access checksum: db61d5534e988743d6266d3675d77b08 content_type: application/pdf creator: dernst date_created: 2022-05-02T08:48:00Z date_updated: 2022-05-02T08:48:00Z file_id: '11348' file_name: 2022_NatureCommunications_Gauto.pdf file_size: 2637590 relation: main_file success: 1 file_date_updated: 2022-05-02T08:48:00Z has_accepted_license: '1' intvolume: ' 13' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Nature Communications publication_identifier: eissn: - 2041-1723 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41467-022-31243-1 scopus_import: '1' status: public title: Functional control of a 0.5 MDa TET aminopeptidase by a flexible loop revealed by MAS NMR tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 13 year: '2022' ... --- _id: '10323' abstract: - lang: eng 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. 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). article_number: '762005' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Iva full_name: Sučec, Iva last_name: Sučec - first_name: Beate full_name: Bersch, Beate last_name: Bersch - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 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 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 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. ieee: I. Sučec, B. Bersch, and P. Schanda, “How do chaperones bind (partly) unfolded client proteins?,” Frontiers in Molecular Biosciences, vol. 8. Frontiers, 2021. 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. short: I. Sučec, B. Bersch, P. Schanda, Frontiers in Molecular Biosciences 8 (2021). date_created: 2021-11-21T23:01:29Z date_published: 2021-10-25T00:00:00Z date_updated: 2023-08-14T11:55:04Z day: '25' ddc: - '547' department: - _id: PaSc doi: 10.3389/fmolb.2021.762005 external_id: isi: - '000717241700001' pmid: - '34760928' file: - access_level: open_access checksum: a5c9dbf80dc2c5aaa737f456c941d964 content_type: application/pdf creator: cchlebak date_created: 2021-11-23T15:06:58Z date_updated: 2021-11-23T15:06:58Z file_id: '10333' file_name: 2021_FrontiersMolBioSc_Sučec.pdf file_size: 4700798 relation: main_file success: 1 file_date_updated: 2021-11-23T15:06:58Z has_accepted_license: '1' intvolume: ' 8' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Frontiers in Molecular Biosciences publication_identifier: eissn: - 2296-889X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: How do chaperones bind (partly) unfolded client proteins? tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 8 year: '2021' ...