[{"author":[{"first_name":"Darja","id":"81dc668a-19fa-11f0-bf31-d56534059ef3","last_name":"Rohden","full_name":"Rohden, Darja"},{"last_name":"Napoli","full_name":"Napoli, Federico","id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b","first_name":"Federico","orcid":"0000-0002-9043-136X"},{"id":"9fb2a840-89e1-11ee-a8b7-cc5c7ba62471","first_name":"Anna","full_name":"Kapitonova, Anna","last_name":"Kapitonova"},{"full_name":"Tatman, Benjamin","last_name":"Tatman","first_name":"Benjamin","id":"71cda2f3-e604-11ee-a1df-da10587eda3f"},{"last_name":"Lichtenecker","full_name":"Lichtenecker, Roman J.","first_name":"Roman J."},{"full_name":"Schanda, Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606"}],"file_date_updated":"2025-12-29T14:51:40Z","scopus_import":"1","publication":"Journal of Molecular Biology","isi":1,"intvolume":"       437","file":[{"access_level":"open_access","relation":"main_file","success":1,"checksum":"90d50594d8ea9860ac5da41297992847","content_type":"application/pdf","date_updated":"2025-12-29T14:51:40Z","creator":"dernst","file_name":"2025_JourMolecularBiology_Rohden.pdf","file_id":"20876","date_created":"2025-12-29T14:51:40Z","file_size":2270555}],"acknowledgement":"This work was supported financially by the Austrian Science Fund (FWF, Grant No. I5812-B, “AlloSpace”). This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support Facility (LSF). We thank Petra Rovò and Margarita Valhondo Falcón for excellent support of the NMR facility.","publication_identifier":{"issn":["0022-2836"],"eissn":["1089-8638"]},"oa":1,"publication_status":"published","external_id":{"isi":["001618289100020"]},"department":[{"_id":"PaSc"}],"date_created":"2025-08-31T22:01:33Z","language":[{"iso":"eng"}],"corr_author":"1","volume":437,"quality_controlled":"1","abstract":[{"lang":"eng","text":"The specific introduction of ^1H-^13C or ^1H-^15N moieties into otherwise deuterated proteins holds great potential for high-resolution solution and magic-angle spinning (MAS) NMR studies of protein structure and dynamics. Arginine residues play key roles for example at active sites of enzymes. Taking advantage of a chemically synthesized Arg with a ^13C-^1H2 group in an otherwise deuterated backbone, we demonstrate here the usefulness of proton-detected MAS NMR approaches to probe arginine dynamics. In experiments with crystalline ubiquitin and the 134 kDa tetrameric enzyme malate dehydrogenase we detected a wide range of motions, from sites that are rigid on time scales of at least tens of milliseconds to residues undergoing predominantly nanosecond motions. Spin-relaxation and dipolar-coupling measurements enabled quantitative determination of these dynamics. We observed microsecond dynamics of residue Arg54 in crystalline ubiquitin, whose backbone is known to sample different β-turn conformations on this time scale. The labeling scheme and experiments presented here expand the toolkit for high-resolution proton-detected MAS NMR."}],"license":"https://creativecommons.org/licenses/by/4.0/","article_number":"169379","acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"project":[{"name":"AlloSpace. The emergence and mechanisms of allostery","grant_number":"I05812","_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf"}],"has_accepted_license":"1","date_published":"2025-12-01T00:00:00Z","oa_version":"Published Version","year":"2025","date_updated":"2025-12-29T14:52:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"day":"01","publisher":"Elsevier","type":"journal_article","issue":"23","ddc":["540"],"doi":"10.1016/j.jmb.2025.169379","OA_place":"publisher","OA_type":"hybrid","article_type":"original","_id":"20258","title":"Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme","month":"12","article_processing_charge":"Yes (via OA deal)","citation":{"ieee":"D. Rohden, F. Napoli, A. Kapitonova, B. Tatman, R. J. Lichtenecker, and P. Schanda, “Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme,” <i>Journal of Molecular Biology</i>, vol. 437, no. 23. Elsevier, 2025.","mla":"Rohden, Darja, et al. “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” <i>Journal of Molecular Biology</i>, vol. 437, no. 23, 169379, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.jmb.2025.169379\">10.1016/j.jmb.2025.169379</a>.","short":"D. Rohden, F. Napoli, A. Kapitonova, B. Tatman, R.J. Lichtenecker, P. Schanda, Journal of Molecular Biology 437 (2025).","chicago":"Rohden, Darja, Federico Napoli, Anna Kapitonova, Benjamin Tatman, Roman J. Lichtenecker, and Paul Schanda. “Arginine Dynamics Probed by Magic-Angle Spinning NMR with a Specific Isotope-Labeling Scheme.” <i>Journal of Molecular Biology</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jmb.2025.169379\">https://doi.org/10.1016/j.jmb.2025.169379</a>.","ista":"Rohden D, Napoli F, Kapitonova A, Tatman B, Lichtenecker RJ, Schanda P. 2025. Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme. Journal of Molecular Biology. 437(23), 169379.","ama":"Rohden D, Napoli F, Kapitonova A, Tatman B, Lichtenecker RJ, Schanda P. Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme. <i>Journal of Molecular Biology</i>. 2025;437(23). doi:<a href=\"https://doi.org/10.1016/j.jmb.2025.169379\">10.1016/j.jmb.2025.169379</a>","apa":"Rohden, D., Napoli, F., Kapitonova, A., Tatman, B., Lichtenecker, R. J., &#38; Schanda, P. (2025). Arginine dynamics probed by magic-angle spinning NMR with a specific isotope-labeling scheme. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2025.169379\">https://doi.org/10.1016/j.jmb.2025.169379</a>"},"related_material":{"record":[{"id":"19956","status":"public","relation":"research_data"}]},"PlanS_conform":"1"},{"article_type":"original","OA_type":"hybrid","OA_place":"publisher","doi":"10.1016/j.jmb.2025.169465","ddc":["540"],"PlanS_conform":"1","citation":{"apa":"Knödlstorfer, S., Toscano, G., Ptaszek, A. L., Kontaxis, G., Napoli, F., Schneider, J., … Konrat, R. (2025). A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2025.169465\">https://doi.org/10.1016/j.jmb.2025.169465</a>","ama":"Knödlstorfer S, Toscano G, Ptaszek AL, et al. A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. <i>Journal of Molecular Biology</i>. 2025;437(23). doi:<a href=\"https://doi.org/10.1016/j.jmb.2025.169465\">10.1016/j.jmb.2025.169465</a>","ista":"Knödlstorfer S, Toscano G, Ptaszek AL, Kontaxis G, Napoli F, Schneider J, Maier K, Kapitonova A, Lichtenecker RJ, Schanda P, Konrat R. 2025. A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0. Journal of Molecular Biology. 437(23), 169465.","chicago":"Knödlstorfer, Sonja, Giorgia Toscano, Aleksandra L. Ptaszek, Georg Kontaxis, Federico Napoli, Jakob Schneider, Katharina Maier, et al. “A Novel HMBC-CC-HMQC NMR Strategy for Methyl Assignment Using Triple-13C-Labeled α-Ketoisovalerate Integrated with UCBShift 2.0.” <i>Journal of Molecular Biology</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jmb.2025.169465\">https://doi.org/10.1016/j.jmb.2025.169465</a>.","mla":"Knödlstorfer, Sonja, et al. “A Novel HMBC-CC-HMQC NMR Strategy for Methyl Assignment Using Triple-13C-Labeled α-Ketoisovalerate Integrated with UCBShift 2.0.” <i>Journal of Molecular Biology</i>, vol. 437, no. 23, 169465, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.jmb.2025.169465\">10.1016/j.jmb.2025.169465</a>.","short":"S. Knödlstorfer, G. Toscano, A.L. Ptaszek, G. Kontaxis, F. Napoli, J. Schneider, K. Maier, A. Kapitonova, R.J. Lichtenecker, P. Schanda, R. Konrat, Journal of Molecular Biology 437 (2025).","ieee":"S. Knödlstorfer <i>et al.</i>, “A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0,” <i>Journal of Molecular Biology</i>, vol. 437, no. 23. Elsevier, 2025."},"article_processing_charge":"Yes (in subscription journal)","month":"12","title":"A novel HMBC-CC-HMQC NMR strategy for methyl assignment using triple-13C-labeled α-ketoisovalerate integrated with UCBShift 2.0","_id":"20538","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-12-30T10:29:20Z","year":"2025","oa_version":"Published Version","project":[{"grant_number":"I06223","_id":"bdb9578d-d553-11ed-ba76-ed5d39fce6f0","name":"Structure and mechanism of the mitochondrial MIM insertase"},{"grant_number":"I05812","_id":"eb9c82eb-77a9-11ec-83b8-aadd536561cf","name":"AlloSpace. The emergence and mechanisms of allostery"}],"has_accepted_license":"1","date_published":"2025-12-01T00:00:00Z","issue":"23","type":"journal_article","publisher":"Elsevier","day":"01","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","language":[{"iso":"eng"}],"date_created":"2025-10-26T23:01:35Z","external_id":{"pmid":["41016549"]},"department":[{"_id":"PaSc"},{"_id":"GradSch"}],"publication_status":"published","acknowledged_ssus":[{"_id":"NMR"},{"_id":"LifeSc"}],"article_number":"169465","abstract":[{"lang":"eng","text":"In this study, we describe an integrated approach for methyl group assignment comprising precursor-based selective methyl group labeling, a novel pulse sequence for methyl to backbone coherence transfer and chemical shift predictions using UCBShift 2.0. The utility of this novel α-ketoacid isotopologue is shown by the adaptation of an HMBC-HMQC pulse sequence that simultaneously connects geminal methyl groups of leucine and valine residues to each other and to the protein backbone. By additional 13C,2H-labeling of residues other than valine and leucine residues of the protein, important chemical shift information about neighboring residues (following valine and leucine residues) can be achieved. Thus, different valine and leucine residues in a protein can be characterized as a specific chemical shift vector. Frequency matching with predicted chemical shifts via UCBShift 2.0 using experimental data taken from a subset of the BMRB database revealed a correct assignment performance of about 90%. With applications to proteins of 60.2 kDa and 134 kDa (4 × 33.5 kDa) in size, we demonstrate that the approach provides valuable information even for very large proteins."}],"quality_controlled":"1","volume":437,"intvolume":"       437","publication":"Journal of Molecular Biology","file_date_updated":"2025-12-30T10:29:08Z","scopus_import":"1","author":[{"last_name":"Knödlstorfer","full_name":"Knödlstorfer, Sonja","first_name":"Sonja"},{"id":"334a5e40-8747-11f0-b671-ba1f5154b4b4","first_name":"Giorgia","last_name":"Toscano","full_name":"Toscano, Giorgia"},{"first_name":"Aleksandra L.","last_name":"Ptaszek","full_name":"Ptaszek, Aleksandra L."},{"full_name":"Kontaxis, Georg","last_name":"Kontaxis","first_name":"Georg"},{"orcid":"0000-0002-9043-136X","first_name":"Federico","id":"d42e08e7-f4fc-11eb-af0a-d71e26138f1b","last_name":"Napoli","full_name":"Napoli, Federico"},{"first_name":"Jakob","id":"64368429-eb97-11eb-a6c2-c980b1f44415","last_name":"Schneider","full_name":"Schneider, Jakob"},{"first_name":"Katharina","full_name":"Maier, Katharina","last_name":"Maier"},{"full_name":"Kapitonova, Anna","last_name":"Kapitonova","id":"9fb2a840-89e1-11ee-a8b7-cc5c7ba62471","first_name":"Anna"},{"first_name":"Roman J.","last_name":"Lichtenecker","full_name":"Lichtenecker, Roman J."},{"orcid":"0000-0002-9350-7606","last_name":"Schanda","full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"first_name":"Robert","full_name":"Konrat, Robert","last_name":"Konrat"}],"publication_identifier":{"eissn":["1089-8638"],"issn":["0022-2836"]},"oa":1,"pmid":1,"acknowledgement":"A.L.P and G.T were funded by the “New Ideas” program by Vienna Doctoral School in Chemistry. S.K. was funded by the Austrian Science Fund FWF P35098-B. This work was supported financially by the Austrian Science Fund (FWF, grant numbers I06223 and I5812-B, “AlloSpace”). This research was supported by the Scientific Service Units (SSU) of Institute of Science and Technology Austria (ISTA) through resources provided by the Nuclear Magnetic Resonance Facility and the Lab Support Facility (LSF). We thank Celina Sailer for assistance with the analysis of the NMR spectrum of HsTom70.","file":[{"checksum":"feb92f9c79032c261165f4ca573f444a","content_type":"application/pdf","date_updated":"2025-12-30T10:29:08Z","date_created":"2025-12-30T10:29:08Z","file_id":"20915","file_name":"2025_JourMolecularBiology_Knoedlstorfer.pdf","creator":"dernst","file_size":3076611,"relation":"main_file","access_level":"open_access","success":1}]},{"day":"01","publisher":"Elsevier","type":"journal_article","issue":"17","status":"public","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","project":[{"_id":"255A6082-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF","name":"Molecular Drug Targets"}],"date_published":"2025-09-01T00:00:00Z","year":"2025","oa_version":"Published Version","date_updated":"2025-12-30T08:18:25Z","article_processing_charge":"Yes (in subscription journal)","citation":{"mla":"Antoney, James, et al. “A F420-Dependent Single Domain Chemogenetic Tool for Protein de-Dimerization.” <i>Journal of Molecular Biology</i>, vol. 437, no. 17, 169184, Elsevier, 2025, doi:<a href=\"https://doi.org/10.1016/j.jmb.2025.169184\">10.1016/j.jmb.2025.169184</a>.","short":"J. Antoney, S. Kainrath, J.G. Dubowsky, F.H. Ahmed, S.W. Kang, E.R.R. Mackie, G. Bracho Granado, T.P. Soares Da Costa, C.J. Jackson, H.L. Janovjak, Journal of Molecular Biology 437 (2025).","ieee":"J. Antoney <i>et al.</i>, “A F420-dependent single domain chemogenetic tool for protein de-dimerization,” <i>Journal of Molecular Biology</i>, vol. 437, no. 17. Elsevier, 2025.","apa":"Antoney, J., Kainrath, S., Dubowsky, J. G., Ahmed, F. H., Kang, S. W., Mackie, E. R. R., … Janovjak, H. L. (2025). A F420-dependent single domain chemogenetic tool for protein de-dimerization. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2025.169184\">https://doi.org/10.1016/j.jmb.2025.169184</a>","ama":"Antoney J, Kainrath S, Dubowsky JG, et al. A F420-dependent single domain chemogenetic tool for protein de-dimerization. <i>Journal of Molecular Biology</i>. 2025;437(17). doi:<a href=\"https://doi.org/10.1016/j.jmb.2025.169184\">10.1016/j.jmb.2025.169184</a>","ista":"Antoney J, Kainrath S, Dubowsky JG, Ahmed FH, Kang SW, Mackie ERR, Bracho Granado G, Soares Da Costa TP, Jackson CJ, Janovjak HL. 2025. A F420-dependent single domain chemogenetic tool for protein de-dimerization. Journal of Molecular Biology. 437(17), 169184.","chicago":"Antoney, James, Stephanie Kainrath, Joshua G. Dubowsky, F. Hafna Ahmed, Suk Woo Kang, Emily R.R. Mackie, Gustavo Bracho Granado, Tatiana P. Soares Da Costa, Colin J. Jackson, and Harald L Janovjak. “A F420-Dependent Single Domain Chemogenetic Tool for Protein de-Dimerization.” <i>Journal of Molecular Biology</i>. Elsevier, 2025. <a href=\"https://doi.org/10.1016/j.jmb.2025.169184\">https://doi.org/10.1016/j.jmb.2025.169184</a>."},"PlanS_conform":"1","_id":"19725","title":"A F420-dependent single domain chemogenetic tool for protein de-dimerization","month":"09","doi":"10.1016/j.jmb.2025.169184","OA_place":"publisher","article_type":"original","OA_type":"hybrid","ddc":["570"],"file":[{"checksum":"fb6e84ba7dc92faee97647fd2bc8cca8","content_type":"application/pdf","date_updated":"2025-12-30T08:18:07Z","file_name":"2025_JourMolecularBiology_Antoney.pdf","creator":"dernst","date_created":"2025-12-30T08:18:07Z","file_id":"20892","file_size":1682721,"access_level":"open_access","relation":"main_file","success":1}],"acknowledgement":"We thank J. Kaczmarski for advice on isothermal titration calorimetry and helpful comments, and Alexandra Tichy, Elliot Gerrard and Rahkesh T Sabapathy for assistance with experiments. This study was supported by grants of the Australian Research Council (FT200100519 and DP200102093, to H.J.; DE190100806, DP220101901, FT230100203, and DP250102939 to T.P.S.D.C; DP200102093, CE200100029 and CE200100012 to C.J.J.), the National Health and Medical Research Council (APP1187638, to H.J.). S.K. was supported by the graduate program MolecularDrugTargets (Austrian Science Fund FWF W1232). The Australian Regenerative Medicine Institute is supported by grants from the State Government of Victoria and the Australian Government. The EMBL Australia Partnership Laboratory (EMBL Australia) is supported by the National Collaborative Research Infrastructure Strategy (NCRIS) of the Australian Government. T.P.S.D.C. acknowledges the University of Adelaide for a Future Making Fellowship. E.R.R.M acknowledges the Grains Research and Development Corporation (9176977) for support through a PhD scholarship and operational funding. J.A. and E.R.R.M. were supported by Australian Research Training Program scholarship. MicroMon of Monash University provided Sanger sequencing services. Imaging was performed in the CellScreen SA screening center of Flinders University. C.J.J. thanks the ARC Centre of Excellence for Innovations in Peptide and Protein Science and the ARC Centre of Excellence in Synthetic Biology. We thank the staff of the MX2 beamline at the Australian Synchrotron, part of ANSTO, which made use of the Australian Cancer Research Foundation (ACRF) detector.","pmid":1,"publication_identifier":{"eissn":["1089-8638"],"issn":["0022-2836"]},"oa":1,"publication":"Journal of Molecular Biology","file_date_updated":"2025-12-30T08:18:07Z","author":[{"first_name":"James","last_name":"Antoney","full_name":"Antoney, James"},{"first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87","last_name":"Kainrath","full_name":"Kainrath, Stephanie","orcid":"0000-0002-6709-2195"},{"first_name":"Joshua G.","last_name":"Dubowsky","full_name":"Dubowsky, Joshua G."},{"last_name":"Ahmed","full_name":"Ahmed, F. Hafna","first_name":"F. Hafna"},{"first_name":"Suk Woo","last_name":"Kang","full_name":"Kang, Suk Woo"},{"first_name":"Emily R.R.","full_name":"Mackie, Emily R.R.","last_name":"Mackie"},{"full_name":"Bracho Granado, Gustavo","last_name":"Bracho Granado","first_name":"Gustavo"},{"first_name":"Tatiana P.","last_name":"Soares Da Costa","full_name":"Soares Da Costa, Tatiana P."},{"last_name":"Jackson","full_name":"Jackson, Colin J.","first_name":"Colin J."},{"orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","intvolume":"       437","isi":1,"abstract":[{"lang":"eng","text":"Protein-protein interactions (PPIs) mediate many fundamental cellular processes. Control of PPIs through optically or chemically responsive protein domains has had a profound impact on basic research and some clinical applications. Most chemogenetic methods induce the association, i.e., dimerization or oligomerization, of target proteins, whilst the few available dissociation approaches either break large oligomeric protein clusters or heteromeric complexes. Here, we have exploited the controlled dissociation of a homodimeric oxidoreductase from mycobacteria (MSMEG_2027) by its native cofactor, F420, which is not present in mammals, as a bioorthogonal monomerization switch. Using X-ray crystallography, we found that in the absence of F420 MSMEG_2027 forms a unique domain-swapped dimer that occludes the cofactor binding site. Rearrangement of the N-terminal helix upon F420 binding results in the dissolution of the dimer. We then showed that MSMEG_2027 can be fused to proteins of interest in human cells and applied it as a tool to induce and release MAPK/ERK signalling downstream of a chimeric fibroblast growth factor receptor 1 (FGFR1) tyrosine kinase. This F420-dependent chemogenetic de-homodimerization tool is stoichiometric and based on a single domain and thus represents a novel mechanism to investigate protein complexes in situ."}],"article_number":"169184","volume":437,"quality_controlled":"1","department":[{"_id":"CaGu"}],"external_id":{"isi":["001494762800001"],"pmid":["40324743"]},"date_created":"2025-05-25T22:16:39Z","language":[{"iso":"eng"}],"publication_status":"published"},{"publication":"Journal of Molecular Biology","keyword":["Molecular Biology","Structural Biology"],"author":[{"first_name":"Higor Vinícius Dias","last_name":"Rosa","full_name":"Rosa, Higor Vinícius Dias"},{"full_name":"Leonardo, Diego Antonio","last_name":"Leonardo","first_name":"Diego Antonio"},{"last_name":"Brognara","full_name":"Brognara, Gabriel","first_name":"Gabriel","id":"D96FFDA0-A884-11E9-9968-DC26E6697425"},{"first_name":"José","last_name":"Brandão-Neto","full_name":"Brandão-Neto, José"},{"first_name":"Humberto","last_name":"D'Muniz Pereira","full_name":"D'Muniz Pereira, Humberto"},{"last_name":"Araújo","full_name":"Araújo, Ana Paula Ulian","first_name":"Ana Paula Ulian"},{"first_name":"Richard Charles","last_name":"Garratt","full_name":"Garratt, Richard Charles"}],"intvolume":"       432","pmid":1,"oa":1,"publication_identifier":{"issn":["0022-2836"]},"main_file_link":[{"url":"https://doi.org/10.1016/j.jmb.2020.09.001","open_access":"1"}],"publication_status":"published","department":[{"_id":"MaLo"}],"external_id":{"pmid":["32910969"]},"date_created":"2024-02-28T08:50:34Z","language":[{"iso":"eng"}],"volume":432,"quality_controlled":"1","abstract":[{"text":"The assembly of a septin filament requires that homologous monomers must distinguish between one another in establishing appropriate interfaces with their neighbors. To understand this phenomenon at the molecular level, we present the first four crystal structures of heterodimeric septin complexes. We describe in detail the two distinct types of G-interface present within the octameric particles, which must polymerize to form filaments. These are formed between SEPT2 and SEPT6 and between SEPT7 and SEPT3, and their description permits an understanding of the structural basis for the selectivity necessary for correct filament assembly. By replacing SEPT6 by SEPT8 or SEPT11, it is possible to rationalize Kinoshita's postulate, which predicts the exchangeability of septins from within a subgroup. Switches I and II, which in classical small GTPases provide a mechanism for nucleotide-dependent conformational change, have been repurposed in septins to play a fundamental role in molecular recognition. Specifically, it is switch I which holds the key to discriminating between the two different G-interfaces. Moreover, residues which are characteristic for a given subgroup play subtle, but pivotal, roles in guaranteeing that the correct interfaces are formed.","lang":"eng"}],"date_published":"2020-10-02T00:00:00Z","oa_version":"Published Version","year":"2020","date_updated":"2024-02-28T12:37:54Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"5784-5801","status":"public","day":"02","type":"journal_article","publisher":"Elsevier","issue":"21","doi":"10.1016/j.jmb.2020.09.001","article_type":"original","_id":"15036","title":"Molecular recognition at septin interfaces: The switches hold the key","month":"10","article_processing_charge":"No","citation":{"apa":"Rosa, H. V. D., Leonardo, D. A., Brognara, G., Brandão-Neto, J., D’Muniz Pereira, H., Araújo, A. P. U., &#38; Garratt, R. C. (2020). Molecular recognition at septin interfaces: The switches hold the key. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">https://doi.org/10.1016/j.jmb.2020.09.001</a>","ama":"Rosa HVD, Leonardo DA, Brognara G, et al. Molecular recognition at septin interfaces: The switches hold the key. <i>Journal of Molecular Biology</i>. 2020;432(21):5784-5801. doi:<a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">10.1016/j.jmb.2020.09.001</a>","ista":"Rosa HVD, Leonardo DA, Brognara G, Brandão-Neto J, D’Muniz Pereira H, Araújo APU, Garratt RC. 2020. Molecular recognition at septin interfaces: The switches hold the key. Journal of Molecular Biology. 432(21), 5784–5801.","chicago":"Rosa, Higor Vinícius Dias, Diego Antonio Leonardo, Gabriel Brognara, José Brandão-Neto, Humberto D’Muniz Pereira, Ana Paula Ulian Araújo, and Richard Charles Garratt. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” <i>Journal of Molecular Biology</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">https://doi.org/10.1016/j.jmb.2020.09.001</a>.","mla":"Rosa, Higor Vinícius Dias, et al. “Molecular Recognition at Septin Interfaces: The Switches Hold the Key.” <i>Journal of Molecular Biology</i>, vol. 432, no. 21, Elsevier, 2020, pp. 5784–801, doi:<a href=\"https://doi.org/10.1016/j.jmb.2020.09.001\">10.1016/j.jmb.2020.09.001</a>.","short":"H.V.D. Rosa, D.A. Leonardo, G. Brognara, J. Brandão-Neto, H. D’Muniz Pereira, A.P.U. Araújo, R.C. Garratt, Journal of Molecular Biology 432 (2020) 5784–5801.","ieee":"H. V. D. Rosa <i>et al.</i>, “Molecular recognition at septin interfaces: The switches hold the key,” <i>Journal of Molecular Biology</i>, vol. 432, no. 21. Elsevier, pp. 5784–5801, 2020."}},{"citation":{"short":"A.-M. Tichy, E.J. Gerrard, J.M.D. Legrand, R.M. Hobbs, H.L. Janovjak, Journal of Molecular Biology 431 (2019) 3046–3055.","mla":"Tichy, Alexandra-Madelaine, et al. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” <i>Journal of Molecular Biology</i>, vol. 431, no. 17, Elsevier, 2019, pp. 3046–55, doi:<a href=\"https://doi.org/10.1016/j.jmb.2019.05.033\">10.1016/j.jmb.2019.05.033</a>.","ieee":"A.-M. Tichy, E. J. Gerrard, J. M. D. Legrand, R. M. Hobbs, and H. L. Janovjak, “Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions,” <i>Journal of Molecular Biology</i>, vol. 431, no. 17. Elsevier, pp. 3046–3055, 2019.","apa":"Tichy, A.-M., Gerrard, E. J., Legrand, J. M. D., Hobbs, R. M., &#38; Janovjak, H. L. (2019). Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2019.05.033\">https://doi.org/10.1016/j.jmb.2019.05.033</a>","ama":"Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. <i>Journal of Molecular Biology</i>. 2019;431(17):3046-3055. doi:<a href=\"https://doi.org/10.1016/j.jmb.2019.05.033\">10.1016/j.jmb.2019.05.033</a>","ista":"Tichy A-M, Gerrard EJ, Legrand JMD, Hobbs RM, Janovjak HL. 2019. Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions. Journal of Molecular Biology. 431(17), 3046–3055.","chicago":"Tichy, Alexandra-Madelaine, Elliot J. Gerrard, Julien M.D. Legrand, Robin M. Hobbs, and Harald L Janovjak. “Engineering Strategy and Vector Library for the Rapid Generation of Modular Light-Controlled Protein–Protein Interactions.” <i>Journal of Molecular Biology</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.jmb.2019.05.033\">https://doi.org/10.1016/j.jmb.2019.05.033</a>."},"article_processing_charge":"No","title":"Engineering strategy and vector library for the rapid generation of modular light-controlled protein–protein interactions","month":"08","_id":"6564","doi":"10.1016/j.jmb.2019.05.033","article_type":"original","day":"09","type":"journal_article","publisher":"Elsevier","issue":"17","status":"public","page":"3046-3055","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2019","oa_version":"Preprint","date_updated":"2025-07-10T11:53:33Z","date_published":"2019-08-09T00:00:00Z","abstract":[{"text":"Optogenetics enables the spatio-temporally precise control of cell and animal behavior. Many optogenetic tools are driven by light-controlled protein–protein interactions (PPIs) that are repurposed from natural light-sensitive domains (LSDs). Applying light-controlled PPIs to new target proteins is challenging because it is difficult to predict which of the many available LSDs, if any, will yield robust light regulation. As a consequence, fusion protein libraries need to be prepared and tested, but methods and platforms to facilitate this process are currently not available. Here, we developed a genetic engineering strategy and vector library for the rapid generation of light-controlled PPIs. The strategy permits fusing a target protein to multiple LSDs efficiently and in two orientations. The public and expandable library contains 29 vectors with blue, green or red light-responsive LSDs, many of which have been previously applied ex vivo and in vivo. We demonstrate the versatility of the approach and the necessity for sampling LSDs by generating light-activated caspase-9 (casp9) enzymes. Collectively, this work provides a new resource for optical regulation of a broad range of target proteins in cell and developmental biology.","lang":"eng"}],"quality_controlled":"1","volume":431,"language":[{"iso":"eng"}],"department":[{"_id":"HaJa"}],"external_id":{"isi":["000482872100002"]},"date_created":"2019-06-16T21:59:14Z","publication_status":"published","main_file_link":[{"url":"http://www.biorxiv.org/content/10.1101/583369v1","open_access":"1"}],"oa":1,"publication_identifier":{"issn":["0022-2836"],"eissn":["1089-8638"]},"intvolume":"       431","isi":1,"scopus_import":"1","author":[{"first_name":"Alexandra-Madelaine","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","full_name":"Tichy, Alexandra-Madelaine","last_name":"Tichy"},{"last_name":"Gerrard","full_name":"Gerrard, Elliot J.","first_name":"Elliot J."},{"first_name":"Julien M.D.","full_name":"Legrand, Julien M.D.","last_name":"Legrand"},{"first_name":"Robin M.","full_name":"Hobbs, Robin M.","last_name":"Hobbs"},{"last_name":"Janovjak","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","orcid":"0000-0002-8023-9315"}],"publication":"Journal of Molecular Biology"},{"publication_status":"published","article_type":"original","language":[{"iso":"eng"}],"doi":"10.1016/j.jmb.2013.04.028","date_created":"2020-09-18T10:09:12Z","month":"08","title":"Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure","quality_controlled":"1","_id":"8462","volume":425,"citation":{"ista":"Rennella E, Cutuil T, Schanda P, Ayala I, Gabel F, Forge V, Corazza A, Esposito G, Brutscher B. 2013. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. Journal of Molecular Biology. 425(15), 2722–2736.","chicago":"Rennella, E., T. Cutuil, Paul Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, and B. Brutscher. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” <i>Journal of Molecular Biology</i>. Elsevier, 2013. <a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">https://doi.org/10.1016/j.jmb.2013.04.028</a>.","apa":"Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Gabel, F., Forge, V., … Brutscher, B. (2013). Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">https://doi.org/10.1016/j.jmb.2013.04.028</a>","ama":"Rennella E, Cutuil T, Schanda P, et al. Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure. <i>Journal of Molecular Biology</i>. 2013;425(15):2722-2736. doi:<a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">10.1016/j.jmb.2013.04.028</a>","ieee":"E. Rennella <i>et al.</i>, “Oligomeric states along the folding pathways of β2-microglobulin: Kinetics, thermodynamics, and structure,” <i>Journal of Molecular Biology</i>, vol. 425, no. 15. Elsevier, pp. 2722–2736, 2013.","mla":"Rennella, E., et al. “Oligomeric States along the Folding Pathways of Β2-Microglobulin: Kinetics, Thermodynamics, and Structure.” <i>Journal of Molecular Biology</i>, vol. 425, no. 15, Elsevier, 2013, pp. 2722–36, doi:<a href=\"https://doi.org/10.1016/j.jmb.2013.04.028\">10.1016/j.jmb.2013.04.028</a>.","short":"E. Rennella, T. Cutuil, P. Schanda, I. Ayala, F. Gabel, V. Forge, A. Corazza, G. Esposito, B. Brutscher, Journal of Molecular Biology 425 (2013) 2722–2736."},"article_processing_charge":"No","abstract":[{"text":"The transition of proteins from their soluble functional state to amyloid fibrils and aggregates is associated with the onset of several human diseases. Protein aggregation often requires some structural reshaping and the subsequent formation of intermolecular contacts. Therefore, the study of the conformation of excited protein states and their ability to form oligomers is of primary importance for understanding the molecular basis of amyloid fibril formation. Here, we investigated the oligomerization processes that occur along the folding of the amyloidogenic human protein β2-microglobulin. The combination of real-time two-dimensional NMR data with real-time small-angle X-ray scattering measurements allowed us to derive thermodynamic and kinetic information on protein oligomerization of different conformational states populated along the folding pathways. In particular, we could demonstrate that a long-lived folding intermediate (I-state) has a higher propensity to oligomerize compared to the native state. Our data agree well with a simple five-state kinetic model that involves only monomeric and dimeric species. The dimers have an elongated shape with the dimerization interface located at the apical side of β2-microglobulin close to Pro32, the residue that has a trans conformation in the I-state and a cis conformation in the native (N) state. Our experimental data suggest that partial unfolding in the apical half of the protein close to Pro32 leads to an excited state conformation with enhanced propensity for oligomerization. This excited state becomes more populated in the transient I-state due to the destabilization of the native conformation by the trans-Pro32 configuration.","lang":"eng"}],"date_updated":"2022-08-25T14:56:24Z","year":"2013","oa_version":"None","date_published":"2013-08-09T00:00:00Z","page":"2722-2736","intvolume":"       425","extern":"1","keyword":["Molecular Biology"],"publication":"Journal of Molecular Biology","author":[{"first_name":"E.","last_name":"Rennella","full_name":"Rennella, E."},{"first_name":"T.","last_name":"Cutuil","full_name":"Cutuil, T."},{"orcid":"0000-0002-9350-7606","full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"first_name":"I.","full_name":"Ayala, I.","last_name":"Ayala"},{"first_name":"F.","last_name":"Gabel","full_name":"Gabel, F."},{"first_name":"V.","full_name":"Forge, V.","last_name":"Forge"},{"full_name":"Corazza, A.","last_name":"Corazza","first_name":"A."},{"first_name":"G.","last_name":"Esposito","full_name":"Esposito, G."},{"full_name":"Brutscher, B.","last_name":"Brutscher","first_name":"B."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0022-2836"]},"status":"public","issue":"15","type":"journal_article","publisher":"Elsevier","day":"09"},{"oa_version":"None","year":"2011","date_updated":"2021-01-12T08:19:30Z","date_published":"2011-01-21T00:00:00Z","extern":"1","page":"765-772","intvolume":"       405","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Van Melckebeke, Hélène","last_name":"Van Melckebeke","first_name":"Hélène"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda"},{"first_name":"Julia","last_name":"Gath","full_name":"Gath, Julia"},{"last_name":"Wasmer","full_name":"Wasmer, Christian","first_name":"Christian"},{"first_name":"René","full_name":"Verel, René","last_name":"Verel"},{"last_name":"Lange","full_name":"Lange, Adam","first_name":"Adam"},{"full_name":"Meier, Beat H.","last_name":"Meier","first_name":"Beat H."},{"first_name":"Anja","last_name":"Böckmann","full_name":"Böckmann, Anja"}],"publication":"Journal of Molecular Biology","publication_identifier":{"issn":["0022-2836"]},"status":"public","type":"journal_article","day":"21","publisher":"Elsevier","issue":"3","publication_status":"published","doi":"10.1016/j.jmb.2010.11.004","language":[{"iso":"eng"}],"article_type":"original","date_created":"2020-09-18T10:11:03Z","title":"Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR","quality_controlled":"1","month":"01","volume":405,"_id":"8471","citation":{"ieee":"H. Van Melckebeke <i>et al.</i>, “Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR,” <i>Journal of Molecular Biology</i>, vol. 405, no. 3. Elsevier, pp. 765–772, 2011.","mla":"Van Melckebeke, Hélène, et al. “Probing Water Accessibility in HET-s(218–289) Amyloid Fibrils by Solid-State NMR.” <i>Journal of Molecular Biology</i>, vol. 405, no. 3, Elsevier, 2011, pp. 765–72, doi:<a href=\"https://doi.org/10.1016/j.jmb.2010.11.004\">10.1016/j.jmb.2010.11.004</a>.","short":"H. Van Melckebeke, P. Schanda, J. Gath, C. Wasmer, R. Verel, A. Lange, B.H. Meier, A. Böckmann, Journal of Molecular Biology 405 (2011) 765–772.","chicago":"Van Melckebeke, Hélène, Paul Schanda, Julia Gath, Christian Wasmer, René Verel, Adam Lange, Beat H. Meier, and Anja Böckmann. “Probing Water Accessibility in HET-s(218–289) Amyloid Fibrils by Solid-State NMR.” <i>Journal of Molecular Biology</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.jmb.2010.11.004\">https://doi.org/10.1016/j.jmb.2010.11.004</a>.","ista":"Van Melckebeke H, Schanda P, Gath J, Wasmer C, Verel R, Lange A, Meier BH, Böckmann A. 2011. Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR. Journal of Molecular Biology. 405(3), 765–772.","ama":"Van Melckebeke H, Schanda P, Gath J, et al. Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR. <i>Journal of Molecular Biology</i>. 2011;405(3):765-772. doi:<a href=\"https://doi.org/10.1016/j.jmb.2010.11.004\">10.1016/j.jmb.2010.11.004</a>","apa":"Van Melckebeke, H., Schanda, P., Gath, J., Wasmer, C., Verel, R., Lange, A., … Böckmann, A. (2011). Probing water accessibility in HET-s(218–289) amyloid fibrils by solid-state NMR. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2010.11.004\">https://doi.org/10.1016/j.jmb.2010.11.004</a>"},"article_processing_charge":"No","abstract":[{"text":"Despite the importance of protein fibrils in the context of conformational diseases, information on their structure is still sparse. Hydrogen/deuterium exchange measurements of backbone amide protons allow the identification hydrogen-bonding patterns and reveal pertinent information on the amyloid β-sheet architecture. However, they provide only little information on the identity of residues exposed to solvent or buried inside the fibril core. NMR spectroscopy is a potent method for identifying solvent-accessible residues in proteins via observation of polarization transfer between chemically exchanging side-chain protons and water protons. We show here that the combined use of highly deuterated samples and fast magic-angle spinning greatly attenuates unwanted spin diffusion and allows identification of polarization exchange with the solvent in a site-specific manner. We apply this measurement protocol to HET-s(218–289) prion fibrils under different conditions (including physiological pH, where protofibrils assemble together into thicker fibrils) and demonstrate that each protofibril of HET-s(218–289), is surrounded by water, thus excluding the existence of extended dry interfibril contacts. We also show that exchangeable side-chain protons inside the hydrophobic core of HET-s(218–289) do not exchange over time intervals of weeks to months. The experiments proposed in this study can provide insight into the detailed structural features of amyloid fibrils in general.","lang":"eng"}]},{"publication_status":"published","date_created":"2020-09-18T10:12:29Z","article_type":"original","doi":"10.1016/j.jmb.2008.05.040","language":[{"iso":"eng"}],"volume":380,"_id":"8480","month":"07","title":"Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy","quality_controlled":"1","abstract":[{"text":"The KIX domain of the transcription co-activator CBP is a three-helix bundle protein that folds via rapid accumulation of an intermediate state, followed by a slower folding phase. Recent NMR relaxation dispersion studies revealed the presence of a low-populated (excited) state of KIX that exists in equilibrium with the natively folded form under non-denaturing conditions, and likely represents the equilibrium analog of the folding intermediate. Here, we combine amide hydrogen/deuterium exchange measurements using rapid NMR data acquisition techniques with backbone 15N and 13C relaxation dispersion experiments to further investigate the equilibrium folding of the KIX domain. Residual structure within the folding intermediate is detected by both methods, and their combination enables reliable quantification of the amount of persistent residual structure. Three well-defined folding subunits are found, which display variable stability and correspond closely to the individual helices in the native state. While two of the three helices (α2 and α3) are partially formed in the folding intermediate (to ∼ 50% and ∼ 80%, respectively, at 20 °C), the third helix is disordered. The observed helical content within the excited state exceeds the helical propensities predicted for the corresponding peptide regions, suggesting that the two helices are weakly mutually stabilized, while methyl 13C relaxation dispersion data indicate that a defined packing arrangement is unlikely. Temperature-dependent experiments reveal that the largest enthalpy and entropy changes along the folding reaction occur during the final transition from the intermediate to the native state. Our experimental data are consistent with a folding mechanism where helices α2 and α3 form rapidly, although to different extents, while helix α1 consolidates only as folding proceeds to complete the native state-structure.","lang":"eng"}],"article_processing_charge":"No","citation":{"mla":"Schanda, Paul, et al. “Folding of the KIX Domain: Characterization of the Equilibrium Analog of a Folding Intermediate Using 15N/13C Relaxation Dispersion and Fast 1H/2H Amide Exchange NMR Spectroscopy.” <i>Journal of Molecular Biology</i>, vol. 380, no. 4, Elsevier, 2008, pp. 726–41, doi:<a href=\"https://doi.org/10.1016/j.jmb.2008.05.040\">10.1016/j.jmb.2008.05.040</a>.","short":"P. Schanda, B. Brutscher, R. Konrat, M. Tollinger, Journal of Molecular Biology 380 (2008) 726–741.","ieee":"P. Schanda, B. Brutscher, R. Konrat, and M. Tollinger, “Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy,” <i>Journal of Molecular Biology</i>, vol. 380, no. 4. Elsevier, pp. 726–741, 2008.","ama":"Schanda P, Brutscher B, Konrat R, Tollinger M. Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. <i>Journal of Molecular Biology</i>. 2008;380(4):726-741. doi:<a href=\"https://doi.org/10.1016/j.jmb.2008.05.040\">10.1016/j.jmb.2008.05.040</a>","apa":"Schanda, P., Brutscher, B., Konrat, R., &#38; Tollinger, M. (2008). Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2008.05.040\">https://doi.org/10.1016/j.jmb.2008.05.040</a>","chicago":"Schanda, Paul, Bernhard Brutscher, Robert Konrat, and Martin Tollinger. “Folding of the KIX Domain: Characterization of the Equilibrium Analog of a Folding Intermediate Using 15N/13C Relaxation Dispersion and Fast 1H/2H Amide Exchange NMR Spectroscopy.” <i>Journal of Molecular Biology</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.jmb.2008.05.040\">https://doi.org/10.1016/j.jmb.2008.05.040</a>.","ista":"Schanda P, Brutscher B, Konrat R, Tollinger M. 2008. Folding of the KIX domain: Characterization of the equilibrium analog of a folding intermediate using 15N/13C relaxation dispersion and fast 1H/2H amide exchange NMR spectroscopy. Journal of Molecular Biology. 380(4), 726–741."},"date_published":"2008-07-18T00:00:00Z","date_updated":"2021-01-12T08:19:34Z","year":"2008","oa_version":"None","keyword":["Molecular Biology"],"publication":"Journal of Molecular Biology","author":[{"last_name":"Schanda","full_name":"Schanda, Paul","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"},{"full_name":"Brutscher, Bernhard","last_name":"Brutscher","first_name":"Bernhard"},{"first_name":"Robert","full_name":"Konrat, Robert","last_name":"Konrat"},{"first_name":"Martin","last_name":"Tollinger","full_name":"Tollinger, Martin"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       380","page":"726-741","extern":"1","status":"public","publication_identifier":{"issn":["0022-2836"]},"issue":"4","day":"18","publisher":"Elsevier","type":"journal_article"},{"keyword":["Molecular Biology"],"publication":"Journal of Molecular Biology","author":[{"first_name":"Beate","last_name":"Bersch","full_name":"Bersch, Beate"},{"last_name":"Favier","full_name":"Favier, Adrien","first_name":"Adrien"},{"full_name":"Schanda, Paul","last_name":"Schanda","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","orcid":"0000-0002-9350-7606"},{"first_name":"Sébastien","last_name":"van Aelst","full_name":"van Aelst, Sébastien"},{"first_name":"Tatiana","full_name":"Vallaeys, Tatiana","last_name":"Vallaeys"},{"first_name":"Jacques","full_name":"Covès, Jacques","last_name":"Covès"},{"first_name":"Max","full_name":"Mergeay, Max","last_name":"Mergeay"},{"last_name":"Wattiez","full_name":"Wattiez, Ruddy","first_name":"Ruddy"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       380","page":"386-403","extern":"1","date_published":"2008-07-04T00:00:00Z","date_updated":"2021-01-12T08:19:34Z","oa_version":"None","year":"2008","issue":"2","type":"journal_article","day":"04","publisher":"Elsevier","status":"public","publication_identifier":{"issn":["0022-2836"]},"date_created":"2020-09-18T10:12:37Z","article_type":"original","language":[{"iso":"eng"}],"doi":"10.1016/j.jmb.2008.05.017","publication_status":"published","abstract":[{"lang":"eng","text":"The copK gene is localized on the pMOL30 plasmid of Cupriavidus metallidurans CH34 within the complex cop cluster of genes, for which 21 genes have been identified. The expression of the corresponding periplasmic CopK protein is strongly upregulated in the presence of copper, leading to a high periplasmic accumulation. The structure and metal-binding properties of CopK were investigated by NMR and mass spectrometry. The protein is dimeric in the apo state with a dissociation constant in the range of 10- 5 M estimated from analytical ultracentrifugation. Mass spectrometry revealed that CopK has two high-affinity Cu(I)-binding sites per monomer with different Cu(I) affinities. Binding of Cu(II) was observed but appeared to be non-specific. The solution structure of apo-CopK revealed an all-β fold formed of two β-sheets in perpendicular orientation with an unstructured C-terminal tail. The dimer interface is formed by the surface of the C-terminal β-sheet. Binding of the first Cu(I)-ion induces a major structural modification involving dissociation of the dimeric apo-protein. Backbone chemical shifts determined for the 1Cu(I)-bound form confirm the conservation of the N-terminal β-sheet, while the last strand of the C-terminal sheet appears in slow conformational exchange. We hypothesize that the partial disruption of the C-terminal β-sheet is related to dimer dissociation. NH-exchange data acquired on the apo-protein are consistent with a lower thermodynamic stability of the C-terminal sheet. CopK contains seven methionine residues, five of which appear highly conserved. Chemical shift data suggest implication of two or three methionines (Met54, Met38, Met28) in the first Cu(I) site. Addition of a second Cu(I) ion further increases protein plasticity. Comparison of the structural and metal-binding properties of CopK with other periplasmic copper-binding proteins reveals two conserved features within these functionally related proteins: the all-β fold and the methionine-rich Cu(I)-binding site."}],"article_processing_charge":"No","citation":{"apa":"Bersch, B., Favier, A., Schanda, P., van Aelst, S., Vallaeys, T., Covès, J., … Wattiez, R. (2008). Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jmb.2008.05.017\">https://doi.org/10.1016/j.jmb.2008.05.017</a>","ama":"Bersch B, Favier A, Schanda P, et al. Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. <i>Journal of Molecular Biology</i>. 2008;380(2):386-403. doi:<a href=\"https://doi.org/10.1016/j.jmb.2008.05.017\">10.1016/j.jmb.2008.05.017</a>","ista":"Bersch B, Favier A, Schanda P, van Aelst S, Vallaeys T, Covès J, Mergeay M, Wattiez R. 2008. Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge. Journal of Molecular Biology. 380(2), 386–403.","chicago":"Bersch, Beate, Adrien Favier, Paul Schanda, Sébastien van Aelst, Tatiana Vallaeys, Jacques Covès, Max Mergeay, and Ruddy Wattiez. “Molecular Structure and Metal-Binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus Metallidurans CH34 during Copper Challenge.” <i>Journal of Molecular Biology</i>. Elsevier, 2008. <a href=\"https://doi.org/10.1016/j.jmb.2008.05.017\">https://doi.org/10.1016/j.jmb.2008.05.017</a>.","short":"B. Bersch, A. Favier, P. Schanda, S. van Aelst, T. Vallaeys, J. Covès, M. Mergeay, R. Wattiez, Journal of Molecular Biology 380 (2008) 386–403.","mla":"Bersch, Beate, et al. “Molecular Structure and Metal-Binding Properties of the Periplasmic CopK Protein Expressed in Cupriavidus Metallidurans CH34 during Copper Challenge.” <i>Journal of Molecular Biology</i>, vol. 380, no. 2, Elsevier, 2008, pp. 386–403, doi:<a href=\"https://doi.org/10.1016/j.jmb.2008.05.017\">10.1016/j.jmb.2008.05.017</a>.","ieee":"B. Bersch <i>et al.</i>, “Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge,” <i>Journal of Molecular Biology</i>, vol. 380, no. 2. Elsevier, pp. 386–403, 2008."},"_id":"8481","volume":380,"month":"07","title":"Molecular structure and metal-binding properties of the periplasmic CopK protein expressed in Cupriavidus metallidurans CH34 during copper challenge","quality_controlled":"1"},{"date_published":"2000-09-15T00:00:00Z","oa_version":"None","year":"2000","date_updated":"2023-05-04T13:23:03Z","user_id":"ea97e931-d5af-11eb-85d4-e6957dddbf17","extern":"1","page":"455 - 464","status":"public","publisher":"Elsevier","day":"15","type":"journal_article","issue":"2","doi":"10.1006/jmbi.2000.4079","publist_id":"5126","article_type":"original","_id":"1957","title":"Cryo-electron crystallography of two sub-complexes of bovine complex I reveals the relationship between the membrane and peripheral arms","month":"09","article_processing_charge":"No","citation":{"ieee":"L. A. Sazanov and J. Walker, “Cryo-electron crystallography of two sub-complexes of bovine complex I reveals the relationship between the membrane and peripheral arms,” <i>Journal of Molecular Biology</i>, vol. 302, no. 2. Elsevier, pp. 455–464, 2000.","short":"L.A. Sazanov, J. Walker, Journal of Molecular Biology 302 (2000) 455–464.","mla":"Sazanov, Leonid A., and John Walker. “Cryo-Electron Crystallography of Two Sub-Complexes of Bovine Complex I Reveals the Relationship between the Membrane and Peripheral Arms.” <i>Journal of Molecular Biology</i>, vol. 302, no. 2, Elsevier, 2000, pp. 455–64, doi:<a href=\"https://doi.org/10.1006/jmbi.2000.4079\">10.1006/jmbi.2000.4079</a>.","chicago":"Sazanov, Leonid A, and John Walker. “Cryo-Electron Crystallography of Two Sub-Complexes of Bovine Complex I Reveals the Relationship between the Membrane and Peripheral Arms.” <i>Journal of Molecular Biology</i>. Elsevier, 2000. <a href=\"https://doi.org/10.1006/jmbi.2000.4079\">https://doi.org/10.1006/jmbi.2000.4079</a>.","ista":"Sazanov LA, Walker J. 2000. Cryo-electron crystallography of two sub-complexes of bovine complex I reveals the relationship between the membrane and peripheral arms. Journal of Molecular Biology. 302(2), 455–464.","ama":"Sazanov LA, Walker J. Cryo-electron crystallography of two sub-complexes of bovine complex I reveals the relationship between the membrane and peripheral arms. <i>Journal of Molecular Biology</i>. 2000;302(2):455-464. doi:<a href=\"https://doi.org/10.1006/jmbi.2000.4079\">10.1006/jmbi.2000.4079</a>","apa":"Sazanov, L. A., &#38; Walker, J. (2000). Cryo-electron crystallography of two sub-complexes of bovine complex I reveals the relationship between the membrane and peripheral arms. <i>Journal of Molecular Biology</i>. Elsevier. <a href=\"https://doi.org/10.1006/jmbi.2000.4079\">https://doi.org/10.1006/jmbi.2000.4079</a>"},"publication":"Journal of Molecular Biology","scopus_import":"1","author":[{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","first_name":"Leonid A","last_name":"Sazanov","full_name":"Sazanov, Leonid A","orcid":"0000-0002-0977-7989"},{"last_name":"Walker","full_name":"Walker, John","first_name":"John"}],"intvolume":"       302","acknowledgement":"We thank Drs I. M. Fearnley and S. Y. Peak-Chew for performing peptide mass mapping. We also thank Drs R. Henderson and G. F. X. Schertler for advice on image processing and for valuable discussions.","pmid":1,"publication_identifier":{"issn":["0022-2836"]},"publication_status":"published","external_id":{"pmid":["10970745"]},"date_created":"2018-12-11T11:54:55Z","language":[{"iso":"eng"}],"volume":302,"quality_controlled":"1","abstract":[{"text":"NADH:ubiquinone oxidoreductase (complex I) is the first and largest enzyme of the mitochondrial respiratory chain. The low-resolution structure of the complex is known from electron microscopy studies. The general shape of the complex is in the form of an L, with one arm in the membrane and the other peripheral. We have purified complex I from beef heart mitochondria and reconstituted the enzyme into lipid bilayers. Under different conditions, several two-dimensional crystal forms were obtained. Crystals belonging to space groups p2221 and c12 (unit cell 488 Å x 79 Å) were obtained at 22°C and contained only the membrane fragment of complex I similar to hydrophobic subcomplex Iβ but lacking the ND5 subunit. A crystal form with larger unit cell (534 Å x 81 Å, space group c12) produced at 4°C contained both the peripheral and membrane arms of the enzyme, except that ND5 was missing. Projection maps from frozen hydrated samples were calculated for all crystal forms. By comparing two different c12 crystal forms, extra electron density in the projection map of large crystal form was assigned to the peripheral arm of the enzyme. One of the features of the map is a deep, channel-like, cleft next to peripheral arm. Comparison with available structures of the intact enzyme indicates that large hydrophobic subunit ND5 is situated at the distal end of the membrane domain. Possible locations of sub-unit ND4 and of other subunits in the membrane domain are proposed. Implications of our findings for the mechanism of proton pumping by complex I are discussed. (C) 2000 Academic Press.","lang":"eng"}]}]