de Groot, Bert L.

[["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","299"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Journal of Biomolecular NMR"],["dc.bibliographiccitation.lastpage","307"],["dc.bibliographiccitation.volume","63"],["dc.contributor.author","Gapsys, Vytautas"],["dc.contributor.author","Narayanan, Raghavendran L."],["dc.contributor.author","Xiang, ShengQi"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Zweckstetter, Markus"],["dc.date.accessioned","2018-11-07T09:49:30Z"],["dc.date.available","2018-11-07T09:49:30Z"],["dc.date.issued","2015"],["dc.description.abstract","Intrinsically disordered proteins (IDPs) are best described by ensembles of conformations and a variety of approaches have been developed to determine IDP ensembles. Because of the large number of conformations, however, cross-validation of the determined ensembles by independent experimental data is crucial. The (1)J(C alpha H alpha) coupling constant is particularly suited for cross-validation, because it has a large magnitude and mostly depends on the often less accessible dihedral angle psi. Here, we reinvestigated the connection between (1)J(C alpha H alpha) values and protein backbone dihedral angles. We show that accurate amino-acid specific random coil values of the (1)J(C alpha H alpha) coupling constant, in combination with a reparameterized empirical Karplus-type equation, allow for reliable cross-validation of molecular ensembles of IDPs."],["dc.description.sponsorship","DFG [ZW71/8-1]"],["dc.identifier.doi","10.1007/s10858-015-9990-z"],["dc.identifier.isi","000365088800008"],["dc.identifier.pmid","26433382"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/35521"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Springer"],["dc.relation.issn","1573-5001"],["dc.relation.issn","0925-2738"],["dc.title","Improved validation of IDP ensembles by one-bond C alpha-H alpha scalar couplings"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1396"],["dc.bibliographiccitation.issue","7"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.lastpage","1405"],["dc.bibliographiccitation.volume","112"],["dc.contributor.author","Machtens, Jan-Philipp"],["dc.contributor.author","Briones, Rodolfo"],["dc.contributor.author","Alleva, Claudia"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Fahlke, Christoph"],["dc.date.accessioned","2021-03-05T08:58:02Z"],["dc.date.available","2021-03-05T08:58:02Z"],["dc.date.issued","2017"],["dc.identifier.doi","10.1016/j.bpj.2017.02.016"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79978"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","Gating Charge Calculations by Computational Electrophysiology Simulations"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","e1000480"],["dc.bibliographiccitation.issue","8"],["dc.bibliographiccitation.journal","PLoS Computational Biology"],["dc.bibliographiccitation.volume","5"],["dc.contributor.author","Hub, Jochen S."],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.editor","Nussinov, Ruth"],["dc.date.accessioned","2021-03-05T08:59:11Z"],["dc.date.available","2021-03-05T08:59:11Z"],["dc.date.issued","2009"],["dc.identifier.doi","10.1371/journal.pcbi.1000480"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80388"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","1553-7358"],["dc.title","Detection of Functional Modes in Protein Dynamics"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","10246"],["dc.bibliographiccitation.issue","35"],["dc.bibliographiccitation.journal","Physical Chemistry, Chemical Physics"],["dc.bibliographiccitation.volume","12"],["dc.contributor.author","Aponte-Santamaría, Camilo"],["dc.contributor.author","Hub, Jochen S."],["dc.contributor.author","de Groot, Bert L."],["dc.date.accessioned","2021-03-05T08:58:34Z"],["dc.date.available","2021-03-05T08:58:34Z"],["dc.date.issued","2010"],["dc.identifier.doi","10.1039/c004384m"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80185"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","1463-9084"],["dc.relation.issn","1463-9076"],["dc.title","Dynamics and energetics of solute permeation through the Plasmodium falciparum aquaglyceroporin"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","9a"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","110"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Koepfer, David"],["dc.contributor.author","Song, Chen"],["dc.contributor.author","Gruene, Tim"],["dc.contributor.author","Sheldrick, George M."],["dc.contributor.author","Zachariae, Ulrich"],["dc.date.accessioned","2020-12-10T14:22:41Z"],["dc.date.available","2020-12-10T14:22:41Z"],["dc.date.issued","2016"],["dc.format.extent","9A"],["dc.identifier.doi","10.1016/j.bpj.2015.11.101"],["dc.identifier.isi","000375093500050"],["dc.identifier.issn","0006-3495"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/71695"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Cell Press"],["dc.publisher.place","Cambridge"],["dc.relation.conference","60th Annual Meeting of the Biophysical-Society"],["dc.relation.eventlocation","Los Angeles, CA"],["dc.relation.issn","1542-0086"],["dc.relation.issn","0006-3495"],["dc.title","The Molecular Dynamics of Ion Channel Permeation, Selectivity and Gating"],["dc.type","conference_abstract"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","acs.jcim.2c00044"],["dc.bibliographiccitation.journal","Journal of Chemical Information and Modeling"],["dc.contributor.author","Kutzner, Carsten"],["dc.contributor.author","Kniep, Christian"],["dc.contributor.author","Cherian, Austin"],["dc.contributor.author","Nordstrom, Ludvig"],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Gapsys, Vytautas"],["dc.date.accessioned","2022-04-01T10:01:40Z"],["dc.date.available","2022-04-01T10:01:40Z"],["dc.date.issued","2022"],["dc.identifier.doi","10.1021/acs.jcim.2c00044"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/105722"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-530"],["dc.relation.eissn","1549-960X"],["dc.relation.issn","1549-9596"],["dc.title","GROMACS in the Cloud: A Global Supercomputer to Speed Up Alchemical Drug Design"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","81"],["dc.bibliographiccitation.journal","Archives of Biochemistry and Biophysics"],["dc.bibliographiccitation.lastpage","91"],["dc.bibliographiccitation.volume","628"],["dc.contributor.author","Ban, David"],["dc.contributor.author","Smith, Colin A."],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Lee, Donghan"],["dc.date.accessioned","2018-01-17T11:31:26Z"],["dc.date.available","2018-01-17T11:31:26Z"],["dc.date.issued","2017"],["dc.description.abstract","Protein function can be modulated or dictated by the amplitude and timescale of biomolecular motion, therefore it is imperative to study protein dynamics. Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful technique capable of studying timescales of motion that range from those faster than molecular reorientation on the picosecond timescale to those that occur in real-time. Across this entire regime, NMR observables can report on the amplitude of atomic motion, and the kinetics of atomic motion can be ascertained with a wide variety of experimental techniques from real-time to milliseconds and several nanoseconds to picoseconds. Still a four orders of magnitude window between several nanoseconds and tens of microseconds has remained elusive. Here, we highlight new relaxation dispersion NMR techniques that serve to cover this \"hidden-time\" window up to hundreds of nanoseconds that achieve atomic resolution while studying the molecule under physiological conditions."],["dc.identifier.doi","10.1016/j.abb.2017.05.016"],["dc.identifier.pmid","28576576"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/11679"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1096-0384"],["dc.title","Recent advances in measuring the kinetics of biomolecules by NMR relaxation dispersion spectroscopy"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","215"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Structure"],["dc.bibliographiccitation.lastpage","222.e3"],["dc.bibliographiccitation.volume","28"],["dc.contributor.author","de Maré, Sofia W."],["dc.contributor.author","Venskutonytė, Raminta"],["dc.contributor.author","Eltschkner, Sandra"],["dc.contributor.author","de Groot, Bert L."],["dc.contributor.author","Lindkvist-Petersson, Karin"],["dc.date.accessioned","2021-03-05T08:58:12Z"],["dc.date.available","2021-03-05T08:58:12Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1016/j.str.2019.11.011"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80041"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0969-2126"],["dc.title","Structural Basis for Glycerol Efflux and Selectivity of Human Aquaporin 7"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","eLife"],["dc.bibliographiccitation.volume","8"],["dc.contributor.author","Gapsys, Vytautas"],["dc.contributor.author","de Groot, Bert L."],["dc.date.accessioned","2021-03-05T08:59:19Z"],["dc.date.available","2021-03-05T08:59:19Z"],["dc.date.issued","2019"],["dc.description.abstract","A recent molecular dynamics investigation into the stability of hemoglobin concluded that the unliganded protein is only stable in the T state when a solvent box is used in the simulations that is ten times larger than what is usually employed (El Hage et al., 2018). Here, we express three main concerns about that study. In addition, we find that with an order of magnitude more statistics, the reported box size dependence is not reproducible. Overall, no significant effects on the kinetics or thermodynamics of conformational transitions were observed."],["dc.identifier.doi","10.7554/eLife.44718"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80424"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","2050-084X"],["dc.title","Comment on 'Valid molecular dynamics simulations of human hemoglobin require a surprisingly large box size'"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]