Becker, Stefan T.

[["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","13"],["dc.contributor.author","Frieg, Benedikt"],["dc.contributor.author","Antonschmidt, Leif"],["dc.contributor.author","Dienemann, Christian"],["dc.contributor.author","Geraets, James A."],["dc.contributor.author","Najbauer, Eszter E."],["dc.contributor.author","Matthes, Dirk"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Andreas, Loren B."],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Schröder, Gunnar F."],["dc.date.accessioned","2022-12-01T08:30:50Z"],["dc.date.available","2022-12-01T08:30:50Z"],["dc.date.issued","2022"],["dc.description.abstract","Abstract\n α-synuclein misfolding and aggregation into fibrils is a common feature of α-synucleinopathies, such as Parkinson’s disease, in which α-synuclein fibrils are a characteristic hallmark of neuronal inclusions called Lewy bodies. Studies on the composition of Lewy bodies extracted postmortem from brain tissue of Parkinson’s patients revealed that lipids and membranous organelles are also a significant component. Interactions between α-synuclein and lipids have been previously identified as relevant for Parkinson’s disease pathology, however molecular insights into their interactions have remained elusive. Here we present cryo-electron microscopy structures of six α-synuclein fibrils in complex with lipids, revealing specific lipid-fibril interactions. We observe that phospholipids promote an alternative protofilament fold, mediate an unusual arrangement of protofilaments, and fill the central cavities of the fibrils. Together with our previous studies, these structures also indicate a mechanism for fibril-induced lipid extraction, which is likely to be involved in the development of α-synucleinopathies. Specifically, one potential mechanism for the cellular toxicity is the disruption of intracellular vesicles mediated by fibrils and oligomers, and therefore the modulation of these interactions may provide a promising strategy for future therapeutic interventions."],["dc.identifier.doi","10.1038/s41467-022-34552-7"],["dc.identifier.pii","34552"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/117993"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-621"],["dc.relation.eissn","2041-1723"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","The 3D structure of lipidic fibrils of α-synuclein"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","12404"],["dc.bibliographiccitation.issue","82"],["dc.bibliographiccitation.journal","Chemical Communications"],["dc.bibliographiccitation.lastpage","12407"],["dc.bibliographiccitation.volume","55"],["dc.contributor.author","Rezaei-Ghaleh, Nasrollah"],["dc.contributor.author","Munari, Francesca"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Assfalg, Michael"],["dc.contributor.author","Griesinger, Christian"],["dc.date.accessioned","2020-12-10T18:11:26Z"],["dc.date.available","2020-12-10T18:11:26Z"],["dc.date.issued","2019"],["dc.description.abstract","This NMR probe of water dynamics enables viscosity determination in concentrated and crowded solutions and allows quantifying internal fluidity within biological condensates."],["dc.description.abstract","We present an NMR method based on natural abundance 17 O relaxation of water to determine effective viscosity in biological aqueous samples. The method accurately captures viscosity of dilute and crowded protein solutions and offers a fairly simple way to quantify the internal fluidity of biological condensates formed through phase separation."],["dc.description.abstract","This NMR probe of water dynamics enables viscosity determination in concentrated and crowded solutions and allows quantifying internal fluidity within biological condensates."],["dc.description.abstract","We present an NMR method based on natural abundance 17 O relaxation of water to determine effective viscosity in biological aqueous samples. The method accurately captures viscosity of dilute and crowded protein solutions and offers a fairly simple way to quantify the internal fluidity of biological condensates formed through phase separation."],["dc.identifier.doi","10.1039/C9CC06124J"],["dc.identifier.eissn","1364-548X"],["dc.identifier.issn","1359-7345"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/16666"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/74010"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.notes.intern","Merged from goescholar"],["dc.relation.eissn","1364-548X"],["dc.relation.issn","1359-7345"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","A facile oxygen-17 NMR method to determine effective viscosity in dilute, molecularly crowded and confined aqueous media"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","109"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","The European Physical Journal E - Soft Matter"],["dc.bibliographiccitation.volume","36"],["dc.contributor.author","Jain, R."],["dc.contributor.author","Petri, M."],["dc.contributor.author","Kirschbaum, S."],["dc.contributor.author","Feindt, H."],["dc.contributor.author","Steltenkamp, Siegfried"],["dc.contributor.author","Sonnenkalb, S."],["dc.contributor.author","Becker, S."],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Menzel, A."],["dc.contributor.author","Burg, T. P."],["dc.contributor.author","Techert, S."],["dc.date.accessioned","2017-09-07T11:47:08Z"],["dc.date.available","2017-09-07T11:47:08Z"],["dc.date.issued","2013"],["dc.description.abstract","Small-angle X-ray scattering provides global, shape-sensitive structural information about macromolecules in solution. Its extension to time dimension in the form of time-resolved SAXS investigations and combination with other time-resolved biophysical methods contributes immensely to the study of protein dynamics. TR-SAXS can also provide unique information about the global structures of transient intermediates during protein dynamics. An experimental set-up with low protein consumption is essential for an extensive use of TR-SAXS experiments on protein dynamics. In this direction, a newly developed 20-microchannel microfluidic continuous-flow mixer was combined with SAXS. With this set-up, we demonstrate ubiquitin unfolding dynamics after rapid mixing with the chaotropic agent Guanidinium-HCl within milliseconds using only similar to 40 nanoliters of the protein sample per scattering image. It is suggested that, in the future, this new TR-SAXS platform will help to increase the use of time-resolved small-angle X-ray scattering, wide-angle X-ray scattering and neutron scattering experiments for studying protein dynamics in the early millisecond regime. The potential research field for this set-up includes protein folding, protein misfolding, aggregation in amyloidogenic diseases, function of intrinsically disordered proteins and various protein-ligand interactions."],["dc.identifier.doi","10.1140/epje/i2013-13109-9"],["dc.identifier.gro","3142281"],["dc.identifier.isi","000325224100001"],["dc.identifier.pmid","24092048"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/6542"],["dc.notes.intern","WoS Import 2017-03-10 / Funder: Nanoscale Photon Imaging of the DFG [SFB 755]"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","1292-8941"],["dc.relation.orgunit","Institut für Röntgenphysik"],["dc.relation.workinggroup","RG Techert (Structural Dynamics in Chemical Systems)"],["dc.title","X-ray scattering experiments with high-flux X-ray source coupled rapid mixing microchannel device and their potential for high-flux neutron scattering investigations"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","13010"],["dc.bibliographiccitation.issue","53"],["dc.bibliographiccitation.journal","Chemistry - A European Journal"],["dc.bibliographiccitation.lastpage","13014"],["dc.bibliographiccitation.volume","23"],["dc.contributor.author","Fonseca-Ornelas, Luis"],["dc.contributor.author","Schmidt, Carla"],["dc.contributor.author","Camacho-Zarco, Aldo R."],["dc.contributor.author","Fernandez, Claudio O."],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Zweckstetter, Markus"],["dc.date.accessioned","2020-12-10T14:05:47Z"],["dc.date.available","2020-12-10T14:05:47Z"],["dc.date.issued","2017"],["dc.identifier.doi","10.1002/chem.201703001"],["dc.identifier.issn","0947-6539"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/69658"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.title","Small-Molecule-Induced Soluble Oligomers of α-Synuclein with Helical Structure"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.issue","15"],["dc.bibliographiccitation.journal","Science Advances"],["dc.bibliographiccitation.volume","8"],["dc.contributor.author","Luebben, Anna V."],["dc.contributor.author","Bender, Daniel"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Crowther, Lisa M."],["dc.contributor.author","Erven, Ilka"],["dc.contributor.author","Hofmann, Kay"],["dc.contributor.author","Söding, Johannes"],["dc.contributor.author","Klemp, Henry"],["dc.contributor.author","Bellotti, Cristina"],["dc.contributor.author","Stäuble, Andreas"],["dc.contributor.author","Steinfeld, Robert"],["dc.date.accessioned","2022-05-02T08:02:30Z"],["dc.date.available","2022-05-02T08:02:30Z"],["dc.date.issued","2022"],["dc.description.abstract","Genetic CLN5 variants are associated with childhood neurodegeneration and Alzheimer’s disease; however, the molecular function of ceroid lipofuscinosis neuronal protein 5 (Cln5) is unknown. We solved the Cln5 crystal structure and identified a region homologous to the catalytic domain of members of the N1pC/P60 superfamily of papain-like enzymes. However, we observed no protease activity for Cln5; and instead, we discovered that Cln5 and structurally related PPPDE1 and PPPDE2 have efficient cysteine palmitoyl thioesterase ( S -depalmitoylation) activity using fluorescent substrates. Mutational analysis revealed that the predicted catalytic residues histidine-166 and cysteine-280 are critical for Cln5 thioesterase activity, uncovering a new cysteine-based catalytic mechanism for S -depalmitoylation enzymes. Last, we found that Cln5-deficient neuronal progenitor cells showed reduced thioesterase activity, confirming live cell function of Cln5 in setting S -depalmitoylation levels. Our results provide new insight into the function of Cln5, emphasize the importance of S -depalmitoylation in neuronal homeostasis, and disclose a new, unexpected enzymatic function for the N1pC/P60 superfamily of proteins.\r\nCln5 structure reveals thioesterase activity among N1pC/P60 proteins, stressing the role of S -depalmitoylation in neurodegeneration."],["dc.identifier.doi","10.1126/sciadv.abj8633"],["dc.identifier.pmid","35427157"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/107343"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/476"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-561"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.eissn","2375-2548"],["dc.relation.workinggroup","RG Gärtner"],["dc.relation.workinggroup","RG Söding (Quantitative and Computational Biology)"],["dc.title","Cln5 represents a new type of cysteine-based S -depalmitoylase linked to neurodegeneration"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","10"],["dc.contributor.author","Strohäker, Timo"],["dc.contributor.author","Jung, Byung Chul"],["dc.contributor.author","Liou, Shu-Hao"],["dc.contributor.author","Fernandez, Claudio O."],["dc.contributor.author","Riedel, Dietmar"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Halliday, Glenda M."],["dc.contributor.author","Bennati, Marina"],["dc.contributor.author","Kim, Woojin S."],["dc.contributor.author","Lee, Seung-Jae"],["dc.contributor.author","Zweckstetter, Markus"],["dc.date.accessioned","2020-12-10T18:09:52Z"],["dc.date.available","2020-12-10T18:09:52Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1038/s41467-019-13564-w"],["dc.identifier.eissn","2041-1723"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/17027"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/73784"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.notes.intern","Merged from goescholar"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Structural heterogeneity of α-synuclein fibrils amplified from patient brain extracts"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","23"],["dc.bibliographiccitation.issue","1-2"],["dc.bibliographiccitation.journal","Journal of Biomolecular NMR"],["dc.bibliographiccitation.lastpage","44"],["dc.bibliographiccitation.volume","45"],["dc.contributor.author","Farès, Christophe"],["dc.contributor.author","Lakomek, Nils-Alexander"],["dc.contributor.author","Walter, Korvin F. A."],["dc.contributor.author","Frank, Benedikt T. C."],["dc.contributor.author","Meiler, Jens"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Griesinger, Christian"],["dc.date.accessioned","2017-09-07T11:46:50Z"],["dc.date.available","2017-09-07T11:46:50Z"],["dc.date.issued","2009"],["dc.description.abstract","This study presents the first application of the model-free analysis (MFA) (Meiler in J Am Chem Soc 123:6098-6107, 2001; Lakomek in J Biomol NMR 34:101-115, 2006) to methyl group RDCs measured in 13 different alignment media in order to describe their supra-tau (c) dynamics in ubiquitin. Our results indicate that methyl groups vary from rigid to very mobile with good correlation to residue type, distance to backbone and solvent exposure, and that considerable additional dynamics are effective at rates slower than the correlation time tau (c). In fact, the average amplitude of motion expressed in terms of order parameters S (2) associated with the supra-tau (c) window brings evidence to the existence of fluctuations contributing as much additional mobility as those already present in the faster ps-ns time scale measured from relaxation data. Comparison to previous results on ubiquitin demonstrates that the RDC-derived order parameters are dominated both by rotameric interconversions and faster libration-type motions around equilibrium positions. They match best with those derived from a combined J-coupling and residual dipolar coupling approach (Chou in J Am Chem Soc 125:8959-8966, 2003) taking backbone motion into account. In order to appreciate the dynamic scale of side chains over the entire protein, the methyl group order parameters are compared to existing dynamic ensembles of ubiquitin. Of those recently published, the broadest one, namely the EROS ensemble (Lange in Science 320:1471-1475, 2008), fits the collection of methyl group order parameters presented here best. Last, we used the MFA-derived averaged spherical harmonics to perform highly-parameterized rotameric searches of the side chains conformation and find expanded rotamer distributions with excellent fit to our data. These rotamer distributions suggest the presence of concerted motions along the side chains."],["dc.identifier.doi","10.1007/s10858-009-9354-7"],["dc.identifier.gro","3143062"],["dc.identifier.isi","000269079100005"],["dc.identifier.pmid","19652920"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/534"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","0925-2738"],["dc.title","Accessing ns-mu s side chain dynamics in ubiquitin with methyl RDCs"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3115"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","Proceedings of the National Academy of Sciences of the United States of America : PNAS"],["dc.bibliographiccitation.lastpage","3120"],["dc.bibliographiccitation.volume","114"],["dc.contributor.author","Salvi, Michele"],["dc.contributor.author","Schomburg, Benjamin"],["dc.contributor.author","Giller, Karin"],["dc.contributor.author","Graf, Sabrina"],["dc.contributor.author","Unden, Gottfried"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Lange, Adam"],["dc.contributor.author","Griesinger, Christian"],["dc.date.accessioned","2018-01-17T11:33:34Z"],["dc.date.available","2018-01-17T11:33:34Z"],["dc.date.issued","2017"],["dc.description.abstract","Bacteria use membrane-integral sensor histidine kinases (HK) to perceive stimuli and transduce signals from the environment to the cytosol. Information on how the signal is transmitted across the membrane by HKs is still scarce. Combining both liquid- and solid-state NMR, we demonstrate that structural rearrangements in the extracytoplasmic, citrate-sensing Per-Arnt-Sim (PAS) domain of HK CitA are identical for the isolated domain in solution and in a longer construct containing the membrane-embedded HK and lacking only the kinase core. We show that upon citrate binding, the PAS domain contracts, resulting in a shortening of the C-terminal β-strand. We demonstrate that this contraction of the PAS domain, which is well characterized for the isolated domain, is the signal transmitted to the transmembrane (TM) helices in a CitA construct in liposomes. Putting the extracytoplasmic PAS domain into context of the membrane-embedded CitA construct slows down citrate-binding kinetics by at least a factor of 60, confirming that TM helix motions are linked to the citrate-binding event. Our results are confirmation of a hallmark of the HK signal transduction mechanism with atomic resolution on a full-length construct lacking only the kinase core domain."],["dc.identifier.doi","10.1073/pnas.1620286114"],["dc.identifier.pmid","28265100"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/11680"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1091-6490"],["dc.title","Sensory domain contraction in histidine kinase CitA triggers transmembrane signaling in the membrane-bound sensor"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","Angewandte Chemie International Edition"],["dc.contributor.author","Tekwani Movellan, Kumar"],["dc.contributor.author","Dervişoğlu, Rıza"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Andreas, Loren"],["dc.date.accessioned","2021-10-01T09:58:08Z"],["dc.date.available","2021-10-01T09:58:08Z"],["dc.date.issued","2021"],["dc.identifier.doi","10.1002/anie.202103955"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/89996"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-469"],["dc.relation.eissn","1521-3773"],["dc.relation.issn","1433-7851"],["dc.title","Pore bound water at the key residue histidine 37 in Influenza A M2"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","2162"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","Structure"],["dc.bibliographiccitation.lastpage","2174"],["dc.bibliographiccitation.volume","21"],["dc.contributor.author","Xiang, Shengqi"],["dc.contributor.author","Gapsys, Vytautas"],["dc.contributor.author","Kim, Hai-Young"],["dc.contributor.author","Bessonov, Sergey"],["dc.contributor.author","Hsiao, He-Hsuan"],["dc.contributor.author","Moehlmann, Sina"],["dc.contributor.author","Klaukien, Volker"],["dc.contributor.author","Ficner, Ralf"],["dc.contributor.author","Becker, Stefan"],["dc.contributor.author","Urlaub, Henning"],["dc.contributor.author","Luehrmann, Reinhard"],["dc.contributor.author","Groot, Bert L. de"],["dc.contributor.author","Zweckstetter, Markus"],["dc.date.accessioned","2017-09-07T11:46:59Z"],["dc.date.available","2017-09-07T11:46:59Z"],["dc.date.issued","2013"],["dc.description.abstract","Serine/arginine-rich (SR) proteins are important players in RNA metabolism and are extensively phosphorylated at serine residues in RS repeats. Here, we show that phosphorylation switches the RS domain of the serine/arginine-rich splicing factor 1 from a fully disordered state to a partially rigidified arch-like structure. Nuclear magnetic resonance spectroscopy in combination with molecular dynamics simulations revealed that the conformational switch is restricted to RS repeats, critically depends on the phosphate charge state and strongly decreases the conformational entropy of RS domains. The dynamic switch also occurs in the 100 kDa SR-related protein hPrp28, for which phosphorylation at the RS repeat is required for spliceosome assembly. Thus, a phosphorylation-induced dynamic switch is common to the class of serine/arginine-rich proteins and provides a molecular basis for the functional redundancy of serine/arginine-rich proteins and the profound influence of RS domain phosphorylation on protein-protein and protein-RNA interactions."],["dc.identifier.doi","10.1016/j.str.2013.09.014"],["dc.identifier.gro","3142236"],["dc.identifier.isi","000328914900010"],["dc.identifier.pmid","24183573"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/6043"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.eissn","1878-4186"],["dc.relation.issn","0969-2126"],["dc.title","Phosphorylation Drives a Dynamic Switch in Serine/Arginine-Rich Proteins"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]