Peske, Frank

[["dc.bibliographiccitation.firstpage","5210"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","5222"],["dc.bibliographiccitation.volume","47"],["dc.contributor.author","Korniy, Natalia"],["dc.contributor.author","Goyal, Akanksha"],["dc.contributor.author","Hoffmann, Markus"],["dc.contributor.author","Samatova, Ekaterina"],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Pöhlmann, Stefan"],["dc.contributor.author","Rodnina, Marina V"],["dc.date.accessioned","2020-12-10T18:19:35Z"],["dc.date.available","2020-12-10T18:19:35Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1093/nar/gkz202"],["dc.identifier.eissn","1362-4962"],["dc.identifier.issn","0305-1048"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/16451"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/75304"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.notes.intern","Merged from goescholar"],["dc.rights","CC BY-NC 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by-nc/4.0"],["dc.title","Modulation of HIV-1 Gag/Gag-Pol frameshifting by tRNA abundance"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1183"],["dc.bibliographiccitation.issue","5"],["dc.bibliographiccitation.journal","Journal of Molecular Biology"],["dc.bibliographiccitation.lastpage","1194"],["dc.bibliographiccitation.volume","343"],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Savelsbergh, Andreas"],["dc.contributor.author","Katunin, Vladimir I."],["dc.contributor.author","Rodnina, Marina"],["dc.contributor.author","Wintermeyer, Wolfgang"],["dc.date.accessioned","2017-09-07T11:43:10Z"],["dc.date.available","2017-09-07T11:43:10Z"],["dc.date.issued","2004"],["dc.description.abstract","Translocation, a coordinated movement of two tRNAs together with mRNA on the ribosome, is catalyzed by elongation factor G (EF-G). The reaction is accompanied by conformational rearrangements of the ribosome that are, as yet, not well characterized. Here, we analyze those rearrangements by restricting the conformational flexibility of the ribosome by antibiotics binding to specific sites of the ribosome. Paromomycin (Par), viomycin (Vio), spectinomycin (Spc), and hygromycin B (HygB) inhibited the tRNA-mRNA movement, while the other partial reactions of translocation, including the unlocking rearrangement of the ribosome that precedes tRNA-mRNA movement, were not affected. The functional cycle of EF-G, i.e. binding of EF-G(.)GTP to the ribosome, GTP hydrolysis, Pi release, and dissociation of EF-G(.)GDP from the ribosome, was not affected either, indicating that EF-G turnover is not coupled directly to tRNA-mRNA movement. The inhibition of translocation. by Par and Vio is attributed to the stabilization of tRNA binding in the A site, whereas Spc and HygB had a direct inhibitory effect on tRNA-mRNA movement. Streptomycin (Str) had essentially no effect on translocation, although it caused a large increase in tRNA affinity to the A site. These results suggest that conformational changes in the vicinity of the decoding region at the binding sites of Spc and HygB are important for tRNA-mRNA movement, whereas Str seems to stabilize a conformation of the ribosome that is prone to rapid translocation, thereby compensating the effect on tRNA affinity. (C) 2004 Elsevier Ltd. All rights reserved."],["dc.identifier.doi","10.1016/j.jmb.2004.08.097"],["dc.identifier.gro","3143929"],["dc.identifier.isi","000224838800003"],["dc.identifier.pmid","15491605"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/1497"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Academic Press Ltd Elsevier Science Ltd"],["dc.relation.issn","0022-2836"],["dc.title","Conformational changes of the small ribosomal subunit during elongation factor G-dependent tRNA-mRNA translocation"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","5933"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","12"],["dc.contributor.author","Petrychenko, Valentyn"],["dc.contributor.author","Peng, Bee-Zen"],["dc.contributor.author","de A. P. Schwarzer, Ana C."],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Rodnina, Marina V."],["dc.contributor.author","Fischer, Niels"],["dc.date.accessioned","2021-12-01T09:20:50Z"],["dc.date.available","2021-12-01T09:20:50Z"],["dc.date.issued","2021"],["dc.description.abstract","Abstract GTPases are regulators of cell signaling acting as molecular switches. The translational GTPase EF-G stands out, as it uses GTP hydrolysis to generate force and promote the movement of the ribosome along the mRNA. The key unresolved question is how GTP hydrolysis drives molecular movement. Here, we visualize the GTPase-powered step of ongoing translocation by time-resolved cryo-EM. EF-G in the active GDP–Pi form stabilizes the rotated conformation of ribosomal subunits and induces twisting of the sarcin-ricin loop of the 23 S rRNA. Refolding of the GTPase switch regions upon Pi release initiates a large-scale rigid-body rotation of EF-G pivoting around the sarcin-ricin loop that facilitates back rotation of the ribosomal subunits and forward swiveling of the head domain of the small subunit, ultimately driving tRNA forward movement. The findings demonstrate how a GTPase orchestrates spontaneous thermal fluctuations of a large RNA-protein complex into force-generating molecular movement."],["dc.description.abstract","Abstract GTPases are regulators of cell signaling acting as molecular switches. The translational GTPase EF-G stands out, as it uses GTP hydrolysis to generate force and promote the movement of the ribosome along the mRNA. The key unresolved question is how GTP hydrolysis drives molecular movement. Here, we visualize the GTPase-powered step of ongoing translocation by time-resolved cryo-EM. EF-G in the active GDP–Pi form stabilizes the rotated conformation of ribosomal subunits and induces twisting of the sarcin-ricin loop of the 23 S rRNA. Refolding of the GTPase switch regions upon Pi release initiates a large-scale rigid-body rotation of EF-G pivoting around the sarcin-ricin loop that facilitates back rotation of the ribosomal subunits and forward swiveling of the head domain of the small subunit, ultimately driving tRNA forward movement. The findings demonstrate how a GTPase orchestrates spontaneous thermal fluctuations of a large RNA-protein complex into force-generating molecular movement."],["dc.identifier.doi","10.1038/s41467-021-26133-x"],["dc.identifier.pii","26133"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/94282"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-478"],["dc.relation.eissn","2041-1723"],["dc.title","Structural mechanism of GTPase-powered ribosome-tRNA movement"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","265"],["dc.bibliographiccitation.issue","5"],["dc.bibliographiccitation.journal","Trends in Biochemical Sciences"],["dc.bibliographiccitation.lastpage","274"],["dc.bibliographiccitation.volume","40"],["dc.contributor.author","Caliskan, Neva"],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Rodnina, Marina V."],["dc.date.accessioned","2017-09-07T11:44:25Z"],["dc.date.available","2017-09-07T11:44:25Z"],["dc.date.issued","2015"],["dc.description.abstract","Programmed -1 ribosomal frameshifting (-1PRF) is an mRNA recoding event commonly utilized by viruses and bacteria to increase the information content of their genomes. Recent results have implicated -1PRF in quality control of mRNA and DNA stability in eukaryotes. Biophysical experiments demonstrated that the ribosome changes the reading frame while attempting to move over a slippery sequence of the mRNA - when a roadblockformed by a folded downstream segment in the mRNA stalls the ribosome in a metastable conformational state. The efficiency of -1PRF is modulated not only by cis-regulatory elements in the mRNA but also by transacting factors such as proteins, miRNAs, and antibiotics. These recent results suggest a molecular mechanism and new important cellular roles for -1PRF."],["dc.identifier.doi","10.1016/j.tibs.2015.03.006"],["dc.identifier.gro","3141911"],["dc.identifier.isi","000354143900005"],["dc.identifier.pmid","25850333"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2444"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10 / Funder: Max Planck Society; Deutsche Forschungsgemeinschaft"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","0968-0004"],["dc.title","Changed in translation: mRNA recoding by-1 programmed ribosomal frameshifting"],["dc.type","review"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","7442"],["dc.bibliographiccitation.firstpage","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.lastpage","11"],["dc.bibliographiccitation.volume","6"],["dc.contributor.author","Adio, Sarah"],["dc.contributor.author","Senyushkina, Tamara"],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Fischer, Niels"],["dc.contributor.author","Wintermeyer, Wolfgang"],["dc.contributor.author","Rodnina, Marina V."],["dc.date.accessioned","2017-09-07T11:44:23Z"],["dc.date.available","2017-09-07T11:44:23Z"],["dc.date.issued","2015"],["dc.description.abstract","The coupled translocation of transfer RNA and messenger RNA through the ribosome entails large-scale structural rearrangements, including step-wise movements of the tRNAs. Recent structural work has visualized intermediates of translocation induced by elongation factor G (EF-G) with tRNAs trapped in chimeric states with respect to 30S and 50S ribosomal subunits. The functional role of the chimeric states is not known. Here we follow the formation of translocation intermediates by single-molecule fluorescence resonance energy transfer. Using EF-G mutants, a non-hydrolysable GTP analogue, and fusidic acid, we interfere with either translocation or EF-G release from the ribosome and identify several rapidly interconverting chimeric tRNA states on the reaction pathway. EF-G engagement prevents backward transitions early in translocation and increases the fraction of ribosomes that rapidly fluctuate between hybrid, chimeric and posttranslocation states. Thus, the engagement of EF-G alters the energetics of translocation towards a flat energy landscape, thereby promoting forward tRNA movement."],["dc.identifier.doi","10.1038/ncomms8442"],["dc.identifier.gro","3141892"],["dc.identifier.isi","000357176700008"],["dc.identifier.pmid","26072700"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2234"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","2041-1723"],["dc.title","Fluctuations between multiple EF-G-induced chimeric tRNA states during translocation on the ribosome"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","559"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Molecular Biology"],["dc.bibliographiccitation.lastpage","568"],["dc.bibliographiccitation.volume","35"],["dc.contributor.author","Rodnina, Marina"],["dc.contributor.author","Semenkov, Yuri P."],["dc.contributor.author","Savelsbergh, Andreas"],["dc.contributor.author","Katunin, Vladimir I."],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Wilden, Berthold"],["dc.contributor.author","Wintermeyer, Wolfgang"],["dc.date.accessioned","2017-09-07T11:46:05Z"],["dc.date.available","2017-09-07T11:46:05Z"],["dc.date.issued","2001"],["dc.description.abstract","During the translocation step of the elongation cycle of peptide synthesis two tRNAs together with the mRNA move synchronously and rapidly on the ribosome. Translocation is catalyzed by the elongation factor G (EF-G) and requires GTP hydrolysis. The fundamental biochemical features of the process were worked out in the 1970-80s, to a large part by A.S. Spirin and his colleagues. Recent results from pre-steady-state kinetic analysis and cryoelectron microscopy suggest that translocation is a multistep dynamic process that entails large-scale structural rearrangements of both ribosome and EF-G. Kinetic and thermodynamic data, together with the structural information on the conformational changes in the ribosome and EF-G, provide a detailed mechanistic model of translocation and suggest a mechanism of translocation catalysis by EF-G."],["dc.identifier.doi","10.1023/A:1010523026531"],["dc.identifier.gro","3144276"],["dc.identifier.isi","000170715300012"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/1882"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Consultants Bureau"],["dc.relation.issn","0026-8933"],["dc.title","Mechanism of tRNA translocation on the ribosome"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","361a"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","116"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Caliskan, Neva"],["dc.contributor.author","Korniy, Natalia"],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Rodnina, Marina V."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2022-03-01T11:45:00Z"],["dc.date.available","2022-03-01T11:45:00Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1016/j.bpj.2018.11.1966"],["dc.identifier.pii","S0006349518332314"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103186"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.issn","0006-3495"],["dc.title","Thermodynamic Control of Ribosomal Frameshifting"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1073"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","The EMBO journal"],["dc.bibliographiccitation.lastpage","1085"],["dc.bibliographiccitation.volume","33"],["dc.contributor.author","Holtkamp, Wolf"],["dc.contributor.author","Cunha, Carlos E. da"],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Konevega, Andrey L."],["dc.contributor.author","Wintermeyer, Wolfgang"],["dc.contributor.author","Rodnina, Marina V."],["dc.date.accessioned","2018-01-26T06:04:53Z"],["dc.date.available","2018-01-26T06:04:53Z"],["dc.date.issued","2014"],["dc.description.abstract","Elongation factor G (EF-G) promotes the movement of two tRNAs and the mRNA through the ribosome in each cycle of peptide elongation. During translocation, the tRNAs transiently occupy intermediate positions on both small (30S) and large (50S) ribosomal subunits. How EF-G and GTP hydrolysis control these movements is still unclear. We used fluorescence labels that specifically monitor movements on either 30S or 50S subunits in combination with EF-G mutants and translocation-specific antibiotics to investigate timing and energetics of translocation. We show that EF-G-GTP facilitates synchronous movements of peptidyl-tRNA on the two subunits into an early post-translocation state, which resembles a chimeric state identified by structural studies. EF-G binding without GTP hydrolysis promotes only partial tRNA movement on the 50S subunit. However, rapid 30S translocation and the concomitant completion of 50S translocation require GTP hydrolysis and a functional domain 4 of EF-G. Our results reveal two distinct modes for utilizing the energy of EF-G binding and GTP hydrolysis and suggest that coupling of GTP hydrolysis to translocation is mediated through rearrangements of the 30S subunit."],["dc.identifier.doi","10.1002/embj.201387465"],["dc.identifier.pmid","24614227"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/11834"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1460-2075"],["dc.title","GTP hydrolysis by EF-G synchronizes tRNA movement on small and large ribosomal subunits"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1197"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","RNA Biology"],["dc.bibliographiccitation.lastpage","1203"],["dc.bibliographiccitation.volume","13"],["dc.contributor.author","Belardinelli, Riccardo"],["dc.contributor.author","Sharma, Heena"],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Wintermeyer, Wolfgang"],["dc.contributor.author","Rodnina, Marina"],["dc.date.accessioned","2017-09-07T11:54:04Z"],["dc.date.available","2017-09-07T11:54:04Z"],["dc.date.issued","2016"],["dc.description.abstract","In each round of translation elongation, tRNAs and mRNA move within the ribosome by one codon at a time. tRNA–mRNA translocation is promoted by elongation factor G (EF-G) at the cost of GTP hydrolysis. The key questions for understanding translocation are how and when the tRNAs move and how EF-G coordinates motions of the ribosomal subunits with tRNA movement. Here we present 2 recent papers which describe the choreography of movements over the whole trajectory of translocation. We present the view that EF-G accelerates translocation by promoting the steps that lead to GTPase-dependent ribosome unlocking. EF-G facilitates the formation of the rotated state of the ribosome and uncouples the backward motions of the ribosomal subunits, forming an open conformation in which the tRNAs can rapidly move. Ribosome dynamics are important not only in translocation, but also in recoding events, such as frameshifting and bypassing, and mediate sensitivity to antibiotics."],["dc.identifier.doi","10.1080/15476286.2016.1240140"],["dc.identifier.gro","3145096"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2795"],["dc.language.iso","en"],["dc.notes.intern","Crossref Import"],["dc.notes.status","final"],["dc.relation.issn","1547-6286"],["dc.subject","EF-G; mRNA; molecular machines; protein synthesis; ribosome; tRNA; translation; translation elongation; translocation"],["dc.title","Translocation as continuous movement through the ribosome"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.peerReviewed","no"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1619"],["dc.bibliographiccitation.issue","7"],["dc.bibliographiccitation.journal","Cell"],["dc.bibliographiccitation.lastpage","1631"],["dc.bibliographiccitation.volume","157"],["dc.contributor.author","Caliskan, Neva"],["dc.contributor.author","Katunin, Vladimir I."],["dc.contributor.author","Belardinelli, Riccardo"],["dc.contributor.author","Peske, Frank"],["dc.contributor.author","Rodnina, Marina V."],["dc.date.accessioned","2017-09-07T11:46:12Z"],["dc.date.available","2017-09-07T11:46:12Z"],["dc.date.issued","2014"],["dc.description.abstract","Programmed -1 ribosomal frameshifting (-1PRF) is an mRNA recoding event utilized by cells to enhance the information content of the genome and to regulate gene expression. The mechanism of -1PRF and its timing during translation elongation are unclear. Here, we identified the steps that govern -1PRF by following the stepwise movement of the ribosome through the frameshifting site of a model mRNA derived from the IBV 1a/1b gene in a reconstituted in vitro translation system from Escherichia coli. Frameshifting occurs at a late stage of translocation when the two tRNAs are bound to adjacent slippery sequence codons of the mRNA. The downstream pseudoknot in the mRNA impairs the closing movement of the 30S subunit head, the dissociation of EF-G, and the release of tRNA from the ribosome. The slippage of the ribosome into the -1 frame accelerates the completion of translocation, thereby further favoring translation in the new reading frame."],["dc.identifier.doi","10.1016/j.cell.2014.04.041"],["dc.identifier.gro","3142104"],["dc.identifier.isi","000340941900016"],["dc.identifier.pmid","24949973"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/4589"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10 / Funder: Deutsche Forschungsgemeinschaft [RO 2004/9-1, SFB860]"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.eissn","1097-4172"],["dc.relation.issn","0092-8674"],["dc.title","Programmed-1 Frameshifting by Kinetic Partitioning during Impeded Translocation"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]