Bennati, Marina

[["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.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","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"]]