Bennati, Marina

[["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","2170"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Chem. Sci."],["dc.bibliographiccitation.lastpage","2178"],["dc.bibliographiccitation.volume","7"],["dc.contributor.author","Kasanmascheff, Müge"],["dc.contributor.author","Lee, Wankyu"],["dc.contributor.author","Nick, Thomas U."],["dc.contributor.author","Stubbe, JoAnne"],["dc.contributor.author","Bennati, Marina"],["dc.date.accessioned","2017-01-16T10:08:55Z"],["dc.date.accessioned","2021-10-27T13:12:30Z"],["dc.date.available","2017-01-16T10:08:55Z"],["dc.date.available","2021-10-27T13:12:30Z"],["dc.date.issued","2016"],["dc.description.abstract","Ribonucleotide reductases (RNRs) catalyze the conversion of ribonucleotides to deoxyribonucleotides in all living organisms. The catalytic cycle of E. coli RNR involves a long-range proton-coupled electron transfer (PCET) from a tyrosyl radical (Y122c) in subunit b2 to a cysteine (C439) in the active site of subunit a2, which subsequently initiates nucleotide reduction. This oxidation occurs over 35 °A and involves a specific pathway of redox active amino acids (Y1224[W48?]4Y356 in b2 to Y7314Y7304C439 in a2). The mechanisms of the PCET steps at the interface of the a2b2 complex remain puzzling due to a lack of structural information for this region. Recently, DFT calculations on the 3-aminotyrosyl radical (NH2Y731c)-a2 trapped by incubation of NH2Y731-a2/b2/CDP(substrate)/ATP(allosteric effector) suggested that R411-a2, a residue close to the a2b2 interface, interacts with NH2Y731c and accounts in part for its perturbed EPR parameters. To examine its role, we further modified NH2Y731-a2 with a R411A substitution. NH2Y731c/ R411A generated upon incubation of NH2Y731/R411A-a2/b2/CDP/ATP was investigated using multifrequency (34, 94 and 263 GHz) EPR, 34 GHz pulsed electron–electron double resonance (PELDOR) and electron–nuclear double resonance (ENDOR) spectroscopies. The data indicate a large conformational change in NH2Y731c/R411A relative to the NH2Y731c single mutant. Particularly, the inter-spin distance from NH2Y731c/R411A in one ab pair to Y122c in a second ab pair decreases by 3 °A in the presence of the R411A mutation. This is the first experimental evidence for the flexibility of pathway residue Y731-a2 in an a2b2 complex and suggests a role for R411 in the stacked Y731/Y730 conformation involved in collinear PCET. Furthermore, NH2Y731c/R411A serves as a probe of the PCET process across the subunit interface."],["dc.identifier.doi","10.1039/C5SC03460D"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/14149"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/91697"],["dc.language.iso","en"],["dc.notes.intern","Migrated from goescholar"],["dc.relation.issn","2041-6539"],["dc.relation.issn","2041-6520"],["dc.relation.orgunit","Fakultät für Chemie"],["dc.rights","Goescholar"],["dc.rights.access","openAccess"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.subject","E. coli ribonucleotide; RNRs"],["dc.title","Radical transfer in E. coli ribonucleotide reductase: a NH2Y731/R411A-α mutant unmasks a new conformation of the pathway residue 731"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3172"],["dc.bibliographiccitation.issue","5"],["dc.bibliographiccitation.journal","Chemical Science"],["dc.bibliographiccitation.lastpage","3180"],["dc.bibliographiccitation.volume","7"],["dc.contributor.author","Halbmair, Karin"],["dc.contributor.author","Seikowski, Jan"],["dc.contributor.author","Tkach, Igor"],["dc.contributor.author","Höbartner, Claudia"],["dc.contributor.author","Sezer, Deniz"],["dc.contributor.author","Bennati, Marina"],["dc.date.accessioned","2016-07-05T10:41:32Z"],["dc.date.accessioned","2021-10-27T13:12:28Z"],["dc.date.available","2016-07-05T10:41:32Z"],["dc.date.available","2021-10-27T13:12:28Z"],["dc.date.issued","2016"],["dc.description.abstract","Structural information at atomic resolution of biomolecular assemblies, such as RNA and RNA protein complexes, is fundamental to comprehend biological function. Modern spectroscopic methods offer exceptional opportunities in this direction. Here we present the capability of pulse EPR to report highresolution long-range distances in RNAs by means of a recently developed spin labeled nucleotide, which carries the TEMPO group directly attached to the nucleobase and preserves Watson–Crick base-pairing. In a representative RNA duplex with spin-label separations up to 28 base pairs (z8 nm) we demonstrate that the label allows for a model-free conversion of inter-spin distances into base-pair separation (Dbp) if broadband pulse excitation at Q band frequencies (34 GHz) is applied. The observed distance distribution increases from 0.2 nm for Dbp ¼ 10 to only 0.5 nm for Dbp ¼ 28, consistent with only small deviations from the “ideal” A-form RNA structure. Molecular dynamics (MD) simulations conducted at 20 C show restricted conformational freedom of the label. MD-generated structural deviations from an “ideal” A-RNA geometry help disentangle the contributions of local flexibility of the label and its neighboring nucleobases and global deformations of the RNA double helix to the experimental distance distributions. The study demonstrates that our simple but strategic spin labeling procedure can access detailed structural information on RNAs at atomic resolution over distances that match the size of macromolecular RNA complexes."],["dc.description.sponsorship","DFG Collaborative Research Centre (CRC) [803]; Max Planck Society"],["dc.identifier.doi","10.1039/C5SC04631A"],["dc.identifier.isi","000374859300027"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/13415"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/91693"],["dc.language.iso","en"],["dc.notes.intern","Migrated from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Royal Soc Chemistry"],["dc.relation.issn","2041-6539"],["dc.relation.issn","2041-6520"],["dc.relation.orgunit","Fakultät für Chemie"],["dc.rights","CC BY-NC 3.0"],["dc.rights.access","openAccess"],["dc.rights.uri","https://creativecommons.org/licenses/by-nc/3.0"],["dc.subject","long-range distances; RNA; EPR spectroscopy"],["dc.title","High-resolution measurement of long-range distances in RNA: pulse EPR spectroscopy with TEMPO-labeled nucleotides"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","S1090780721001804"],["dc.bibliographiccitation.firstpage","107091"],["dc.bibliographiccitation.journal","Journal of Magnetic Resonance"],["dc.bibliographiccitation.volume","333"],["dc.contributor.author","Kehl, Annemarie"],["dc.contributor.author","Hiller, Markus"],["dc.contributor.author","Hecker, Fabian"],["dc.contributor.author","Tkach, Igor"],["dc.contributor.author","Dechert, Sebastian"],["dc.contributor.author","Bennati, Marina"],["dc.contributor.author","Meyer, Andreas"],["dc.date.accessioned","2021-12-01T09:24:13Z"],["dc.date.available","2021-12-01T09:24:13Z"],["dc.date.issued","2021"],["dc.description.abstract","Pulsed 19F ENDOR spectroscopy provides a selective method for measuring angstrom to nanometer distances in structural biology. Here, the performance of 19F ENDOR at fields of 3.4 T and 9.4 T is compared using model compounds containing one to three 19F atoms. CF3 groups are included in two compounds, for which the possible occurrence of uniaxial rotation might affect the distance distribution. At 9.4 T, pronounced asymmetric features are observed in many of the presented 19F ENDOR spectra. Data analysis by spectral simulations shows that these features arise from the chemical shift anisotropy (CSA) of the 19F nuclei. This asymmetry is also observed at 3.4 T, albeit to a much smaller extent, confirming the physical origin of the effect. The CSA parameters are well consistent with DFT predicted values and can be extracted from simulation of the experimental data in favourable cases, thereby providing additional information about the geometrical and electronic structure of the spin system. The feasibility of resolving the CSA at 9.4 T provides important information for the interpretation of line broadening in ENDOR spectra also at lower fields, which is relevant for developing methods to extract distance distributions from 19F ENDOR spectra."],["dc.identifier.doi","10.1016/j.jmr.2021.107091"],["dc.identifier.pii","S1090780721001804"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/94884"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-478"],["dc.relation","SFB 1456: Mathematik des Experiments: Die Herausforderung indirekter Messungen in den Naturwissenschaften"],["dc.relation","SFB 1456 | Cluster A | A01: Geometric and Bayesian statistics to reconstruct protein radical structures from ENDOR spectroscopy"],["dc.relation.issn","1090-7807"],["dc.rights","CC BY-NC-ND 4.0"],["dc.title","Resolution of chemical shift anisotropy in 19F ENDOR spectroscopy at 263 GHz/9.4 T"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","Applied Magnetic Resonance"],["dc.contributor.author","Hiller, M."],["dc.contributor.author","Tkach, I."],["dc.contributor.author","Wiechers, H."],["dc.contributor.author","Eltzner, Benjamin"],["dc.contributor.author","Huckemann, Stephan F."],["dc.contributor.author","Pokern, Y."],["dc.contributor.author","Bennati, Marina"],["dc.date.accessioned","2021-09-03T12:57:30Z"],["dc.date.available","2021-09-03T12:57:30Z"],["dc.date.issued","2021-08-26"],["dc.description.abstract","H ENDOR spectra of tyrosyl radicals (Y∙) have been the subject of numerous EPR spectroscopic studies due to their importance in biology. Nevertheless, assignment of all internal 1H hyperfine couplings has been challenging because of substantial spectral overlap. Recently, using 263 GHz ENDOR in conjunction with statistical analysis, we could identify the signature of the Hβ2 coupling in the essential Y122 radical of Escherichia coli ribonucleotide reductase, and modeled it with a distribution of radical conformations. Here, we demonstrate that this analysis can be extended to the full-width 1H ENDOR spectra that contain the larger Hβ1 coupling. The Hβ2 and Hβ1 couplings are related to each other through the ring dihedral and report on the amino acid conformation. The 263 GHz ENDOR data, acquired in batches instead of averaging, and data processing by a new “drift model” allow reconstructing the ENDOR spectra with statistically meaningful confidence intervals and separating them from baseline distortions. Spectral simulations using a distribution of ring dihedral angles confirm the presence of a conformational distribution, consistent with the previous analysis of the Hβ2 coupling. The analysis was corroborated by 94 GHz 2H ENDOR of deuterated Y∙122. These studies provide a starting point to investigate low populated states of tyrosyl radicals in greater detail."],["dc.identifier.doi","10.1007/s00723-021-01411-5"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/89260"],["dc.language.iso","en"],["dc.relation","SFB 1456 | Cluster A | A01: Geometric and Bayesian statistics to reconstruct protein radical structures from ENDOR spectroscopy"],["dc.relation","SFB 1456 | Cluster A: Data with Geometric Nonlinearities"],["dc.relation","SFB 1456: Mathematik des Experiments: Die Herausforderung indirekter Messungen in den Naturwissenschaften"],["dc.relation.issn","0937-9347"],["dc.relation.issn","1613-7507"],["dc.relation.orgunit","Max-Planck-Institut für biophysikalische Chemie"],["dc.relation.orgunit","Fakultät für Chemie"],["dc.relation.orgunit","Institut für Mathematische Stochastik"],["dc.rights","CC BY 4.0"],["dc.title","Distribution of H$^\\beta$ Hyperfine Couplings in a Tyrosyl Radical Revealed by 263 GHz ENDOR Spectroscopy"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3433"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Physical Chemistry Chemical Physics"],["dc.bibliographiccitation.lastpage","3437"],["dc.bibliographiccitation.volume","15"],["dc.contributor.author","Tkach, Igor"],["dc.contributor.author","Pornsuwan, Soraya"],["dc.contributor.author","Höbartner, Claudia"],["dc.contributor.author","Wachowius, Falk"],["dc.contributor.author","Sigurdsson, Snorri Th."],["dc.contributor.author","Baranova, Tatiana Y."],["dc.contributor.author","Diederichsen, Ulf"],["dc.contributor.author","Sicoli, Giuseppe"],["dc.contributor.author","Bennati, Marina"],["dc.date.accessioned","2018-11-07T09:30:21Z"],["dc.date.available","2018-11-07T09:30:21Z"],["dc.date.issued","2013"],["dc.description.abstract","Pulsed electron-electron double resonance (PELDOR, also known as DEER) has become a method of choice to measure distances in biomolecules. In this work we show how the performance of the method can be improved at high EPR frequencies (94 GHz) using variable dual frequency irradiation in a dual mode cavity in order to obtain enhanced resolution toward orientation selection. Dipolar evolution traces of a representative RNA duplex and an alpha-helical peptide were analysed in terms of possible bi-radical structures by considering the inherent ambiguity of symmetry-related solutions."],["dc.identifier.doi","10.1039/c3cp44415e"],["dc.identifier.isi","000314846600006"],["dc.identifier.pmid","23381580"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/10192"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/31286"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Royal Soc Chemistry"],["dc.relation.issn","1463-9076"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.title","Orientation selection in distance measurements between nitroxide spin labels at 94 GHz EPR with variable dual frequency irradiation"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","7681"],["dc.bibliographiccitation.issue","17"],["dc.bibliographiccitation.journal","Physical Chemistry Chemical Physics"],["dc.bibliographiccitation.lastpage","7685"],["dc.bibliographiccitation.volume","16"],["dc.contributor.author","Rizzato, Roberto"],["dc.contributor.author","Bennati, Marina"],["dc.date.accessioned","2018-11-07T09:46:18Z"],["dc.date.available","2018-11-07T09:46:18Z"],["dc.date.issued","2014"],["dc.description.abstract","Electron-nuclear double resonance (ENDOR) is a method of choice to detect magnetic nuclei in the coordination sphere of paramagnetic molecules, but its sensitivity substantially suffers from saturation effects. Recently we introduced a new pulsed ENDOR experiment based on electron-nuclear cross polarisation (CP) transfer. Here we analyse the time evolution of the spin polarization in CP-ENDOR and show that CP combined with inherent fast relaxation leads to enhanced sensitivity as compared to Davies ENDOR."],["dc.description.sponsorship","DFG [SPP1601]; Max Planck Society"],["dc.identifier.doi","10.1039/c3cp55395g"],["dc.identifier.isi","000334200400005"],["dc.identifier.pmid","24647689"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/11431"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/34841"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Royal Soc Chemistry"],["dc.relation.issn","1463-9084"],["dc.relation.issn","1463-9076"],["dc.rights.access","openAccess"],["dc.title","Enhanced sensitivity of electron-nuclear double resonance (ENDOR) by cross polarisation and relaxation"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","373"],["dc.bibliographiccitation.issue","58"],["dc.bibliographiccitation.journal","Angewandte Chemie. International Edition"],["dc.bibliographiccitation.lastpage","379"],["dc.bibliographiccitation.volume","59"],["dc.contributor.author","Meyer, Andreas"],["dc.contributor.author","Dechert, Sebastian"],["dc.contributor.author","Dey, Surjendu"],["dc.contributor.author","Höbartner, Claudia"],["dc.contributor.author","Bennati, Marina"],["dc.date.accessioned","2019-12-09T11:04:02Z"],["dc.date.accessioned","2021-10-27T13:12:49Z"],["dc.date.available","2019-12-09T11:04:02Z"],["dc.date.available","2021-10-27T13:12:49Z"],["dc.date.issued","2019"],["dc.description.abstract","Spectroscopic and biophysical methods for structural determination at atomic resolution are fundamental in studies of biological function. Here we introduce an approach to measure molecular distances in bio-macromolecules using 19 F nuclear spins and nitroxide radicals in combination with high-frequency (94 GHz/3.4 T) electron-nuclear double resonance (ENDOR). The small size and large gyromagnetic ratio of the 19 F label enables to access distances up to about 1.5 nm with an accuracy of 0.1-1 Å. The experiment is not limited by the size of the bio-macromolecule. Performance is illustrated on synthesized fluorinated model compounds as well as spin-labelled RNA duplexes. The results demonstrate that our simple but strategic spin-labelling procedure combined with state-of-the-art spectroscopy accesses a distance range crucial to elucidate active sites of nucleic acids or proteins in the solution state."],["dc.identifier.doi","10.1002/anie.201908584"],["dc.identifier.isbn","31539187"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/16871"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/91724"],["dc.language.iso","en"],["dc.notes.intern","Migrated from goescholar"],["dc.relation.eissn","1521-3773"],["dc.relation.issn","1521-3773"],["dc.relation.orgunit","Fakultät für Chemie"],["dc.rights","CC BY-NC 4.0"],["dc.rights.access","openAccess"],["dc.rights.uri","https://creativecommons.org/licenses/by-nc/4.0"],["dc.subject","RNA; fluorine; high field ENDOR; spin labelling; structural biology"],["dc.subject.ddc","540"],["dc.title","Measurement of Angstrom to Nanometer Molecular Distances with 19 F Nuclear Spins by EPR/ENDOR Spectroscopy"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","e2023615118"],["dc.bibliographiccitation.issue","27"],["dc.bibliographiccitation.journal","Proceedings of the National Academy of Sciences"],["dc.bibliographiccitation.volume","118"],["dc.contributor.author","Pokern, Yvo"],["dc.contributor.author","Eltzner, Benjamin"],["dc.contributor.author","Huckemann, Stephan F."],["dc.contributor.author","Beeken, Clemens"],["dc.contributor.author","Stubbe, JoAnne"],["dc.contributor.author","Tkach, Igor"],["dc.contributor.author","Bennati, Marina"],["dc.contributor.author","Hiller, Markus"],["dc.date.accessioned","2021-08-12T07:45:08Z"],["dc.date.available","2021-08-12T07:45:08Z"],["dc.date.issued","2021"],["dc.description.abstract","Electron–nuclear double resonance (ENDOR) measures the hyperfine interaction of magnetic nuclei with paramagnetic centers and is hence a powerful tool for spectroscopic investigations extending from biophysics to material science. Progress in microwave technology and the recent availability of commercial electron paramagnetic resonance (EPR) spectrometers up to an electron Larmor frequency of 263 GHz now open the opportunity for a more quantitative spectral analysis. Using representative spectra of a prototype amino acid radical in a biologically relevant enzyme, the Y 122 • in Escherichia coli ribonucleotide reductase, we developed a statistical model for ENDOR data and conducted statistical inference on the spectra including uncertainty estimation and hypothesis testing. Our approach in conjunction with 1 H/ 2 H isotopic labeling of Y 122 • in the protein unambiguously established new unexpected spectral contributions. Density functional theory (DFT) calculations and ENDOR spectral simulations indicated that these features result from the beta-methylene hyperfine coupling and are caused by a distribution of molecular conformations, likely important for the biological function of this essential radical. The results demonstrate that model-based statistical analysis in combination with state-of-the-art spectroscopy accesses information hitherto beyond standard approaches."],["dc.identifier.doi","10.1073/pnas.2023615118"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/88376"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-448"],["dc.relation","SFB 1456 | Cluster A | A01: Geometric and Bayesian statistics to reconstruct protein radical structures from ENDOR spectroscopy"],["dc.relation","SFB 1456 | Cluster A: Data with Geometric Nonlinearities"],["dc.relation","SFB 1456: Mathematik des Experiments: Die Herausforderung indirekter Messungen in den Naturwissenschaften"],["dc.relation.eissn","1091-6490"],["dc.relation.issn","0027-8424"],["dc.rights","CC BY 4.0"],["dc.title","Statistical analysis of ENDOR spectra"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]