Bock, Lars V.

[["dc.bibliographiccitation.firstpage","258a"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","104"],["dc.contributor.author","Vaiana, Andrea C."],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Blau, Christian"],["dc.contributor.author","Schroeder, Gunnar F."],["dc.contributor.author","Fischer, Niels"],["dc.contributor.author","Stark, Holger"],["dc.contributor.author","Rodnina, Marina"],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2022-03-01T11:44:56Z"],["dc.date.available","2022-03-01T11:44:56Z"],["dc.date.issued","2013"],["dc.identifier.doi","10.1016/j.bpj.2012.11.1447"],["dc.identifier.pii","S0006349512026938"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103165"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.issn","0006-3495"],["dc.title","Modulation of Intersubunit Interactions during tRNA Translocation through the Ribosome"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","1709"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","13"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2022-05-02T08:02:06Z"],["dc.date.available","2022-05-02T08:02:06Z"],["dc.date.issued","2022"],["dc.description.abstract","Abstract Structure determination by cryo electron microscopy (cryo-EM) provides information on structural heterogeneity and ensembles at atomic resolution. To obtain cryo-EM images of macromolecules, the samples are first rapidly cooled down to cryogenic temperatures. To what extent the structural ensemble is perturbed during cooling is currently unknown. Here, to quantify the effects of cooling, we combined continuum model calculations of the temperature drop, molecular dynamics simulations of a ribosome complex before and during cooling with kinetic models. Our results suggest that three effects markedly contribute to the narrowing of the structural ensembles: thermal contraction, reduced thermal motion within local potential wells, and the equilibration into lower free-energy conformations by overcoming separating free-energy barriers. During cooling, barrier heights below 10 kJ/mol were found to be overcome, which is expected to reduce B-factors in ensembles imaged by cryo-EM. Our approach now enables the quantification of the heterogeneity of room-temperature ensembles from cryo-EM structures."],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft"],["dc.identifier.doi","10.1038/s41467-022-29332-2"],["dc.identifier.pii","29332"],["dc.identifier.pmid","35361752"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/107232"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/503"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-561"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.eissn","2041-1723"],["dc.relation.workinggroup","RG Grubmüller"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Effects of cryo-EM cooling on structural ensembles"],["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","234a"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","110"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Arenz, Stefan"],["dc.contributor.author","Wilson, Daniel N."],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Vaiana, Andrea C."],["dc.date.accessioned","2021-03-05T08:57:59Z"],["dc.date.available","2021-03-05T08:57:59Z"],["dc.date.issued","2016"],["dc.identifier.doi","10.1016/j.bpj.2015.11.1291"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79959"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","ErmBL Translation on the Ribosome in the Presence of Erythromycin is Stalled by Inhibition of Peptide Bond Formation"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","European Biophysics Journal"],["dc.bibliographiccitation.volume","44"],["dc.contributor.author","Fischer, N."],["dc.contributor.author","Neumann, P."],["dc.contributor.author","Bock, L."],["dc.contributor.author","Ficner, Ralf"],["dc.contributor.author","Rodnina, Marina"],["dc.contributor.author","Stark, Holger"],["dc.date.accessioned","2018-11-07T09:55:31Z"],["dc.date.available","2018-11-07T09:55:31Z"],["dc.date.issued","2015"],["dc.format.extent","S46"],["dc.identifier.isi","000380001400013"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/36763"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Springer"],["dc.publisher.place","New york"],["dc.relation.eventlocation","Dresden, GERMANY"],["dc.relation.issn","1432-1017"],["dc.relation.issn","0175-7571"],["dc.title","Breaking the 3 angstrom resolution barrier in single particle cryo-EM"],["dc.type","conference_abstract"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","663a"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","104"],["dc.contributor.author","Blau, Christian"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Schröder, Gunnar F."],["dc.contributor.author","Fischer, Niels"],["dc.contributor.author","Stark, Holger"],["dc.contributor.author","Rodnina, Marina V."],["dc.contributor.author","Vaiana, Andrea C."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2021-03-05T08:57:55Z"],["dc.date.available","2021-03-05T08:57:55Z"],["dc.date.issued","2013"],["dc.identifier.doi","10.1016/j.bpj.2012.11.3662"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79932"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","Rate Estimates from Sampling Sparse Transitions: TRNA Motion Limits Transitions between Ribosomal Translocation Intermediates"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["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","491a"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","106"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Blau, Christian"],["dc.contributor.author","Vaiana, Andrea C."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2021-03-05T08:57:57Z"],["dc.date.available","2021-03-05T08:57:57Z"],["dc.date.issued","2014"],["dc.identifier.doi","10.1016/j.bpj.2013.11.2748"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79943"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","Concerted Interactions between Ribosomal Subunits Allow for Large-Scale Rotations"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","6747"],["dc.bibliographiccitation.issue","14"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","6760"],["dc.bibliographiccitation.volume","43"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Blau, Christian"],["dc.contributor.author","Vaiana, Andrea C."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2018-02-09T08:00:05Z"],["dc.date.available","2018-02-09T08:00:05Z"],["dc.date.issued","2015-08-18"],["dc.description.abstract","During ribosomal translation, the two ribosomal subunits remain associated through intersubunit bridges, despite rapid large-scale intersubunit rotation. The absence of large barriers hindering rotation is a prerequisite for rapid rotation. Here, we investigate how such a flat free-energy landscape is achieved, in particular considering the large shifts the bridges undergo at the periphery. The dynamics and energetics of the intersubunit contact network are studied using molecular dynamics simulations of the prokaryotic ribosome in intermediate states of spontaneous translocation. Based on observed occupancies of intersubunit contacts, residues were grouped into clusters. In addition to the central contact clusters, peripheral clusters were found to maintain strong steady interactions by changing contacts in the course of rotation. The peripheral B1 bridges are stabilized by a changing contact pattern of charged residues that adapts to the rotational state. In contrast, steady strong interactions of the B4 bridge are ensured by the flexible helix H34 following the movement of protein S15. The tRNAs which span the subunits contribute to the intersubunit binding enthalpy to an almost constant degree, despite their different positions in the ribosome. These mechanisms keep the intersubunit interaction strong and steady during rotation, thereby preventing dissociation and enabling rapid rotation."],["dc.identifier.doi","10.1093/nar/gkv649"],["dc.identifier.pmid","26109353"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/12081"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1362-4962"],["dc.title","Dynamic contact network between ribosomal subunits enables rapid large-scale rotation during spontaneous translocation"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","80"],["dc.bibliographiccitation.issue","7631"],["dc.bibliographiccitation.journal","Nature"],["dc.bibliographiccitation.lastpage","85"],["dc.bibliographiccitation.volume","540"],["dc.contributor.author","Fischer, Niels"],["dc.contributor.author","Neumann, Piotr"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Maracci, Cristina"],["dc.contributor.author","Wang, Zhe"],["dc.contributor.author","Paleskava, Alena"],["dc.contributor.author","Konevega, Andrey L."],["dc.contributor.author","Schröder, Gunnar F."],["dc.contributor.author","Grubmüller, Helmut"],["dc.contributor.author","Ficner, Ralf"],["dc.contributor.author","Rodnina, Marina V."],["dc.contributor.author","Stark, Holger"],["dc.date.accessioned","2017-09-07T11:44:31Z"],["dc.date.available","2017-09-07T11:44:31Z"],["dc.date.issued","2016"],["dc.description.abstract","In all domains of life, selenocysteine (Sec) is delivered to the ribosome by selenocysteine-specific tRNA (tRNA(Sec)) with the help of a specialized translation factor, SelB in bacteria. Sec-tRNA(Sec) recodes a UGA stop codon next to a downstream mRNA stem-loop. Here we present the structures of six intermediates on the pathway of UGA recoding in Escherichia coli by single-particle cryo-electron microscopy. The structures explain the specificity of Sec-tRNA(Sec) binding by SelB and show large-scale rearrangements of Sec-tRNA(Sec). Upon initial binding of SelB-Sec-tRNA(Sec) to the ribosome and codon reading, the 30S subunit adopts an open conformation with Sec-tRNA(Sec) covering the sarcin-ricin loop (SRL) on the 50S subunit. Subsequent codon recognition results in a local closure of the decoding site, which moves Sec-tRNA(Sec) away from the SRL and triggers a global closure of the 30S subunit shoulder domain. As a consequence, SelB docks on the SRL, activating the GTPase of SelB. These results reveal how codon recognition triggers GTPase activation in translational GTPases."],["dc.identifier.doi","10.1038/nature20560"],["dc.identifier.gro","3141595"],["dc.identifier.isi","000388916600051"],["dc.identifier.pmid","27842381"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/6"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.eissn","1476-4687"],["dc.relation.issn","0028-0836"],["dc.title","The pathway to GTPase activation of elongation factor SelB 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","160a"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","114"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2021-03-05T08:58:03Z"],["dc.date.available","2021-03-05T08:58:03Z"],["dc.date.issued","2018"],["dc.identifier.doi","10.1016/j.bpj.2017.11.897"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79985"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","Effects of cryo-EM Freezing on the Structural Ensemble"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]