Vaiana, Andrea C.

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[["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"]]

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[["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"]]

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[["dc.bibliographiccitation.journal","eLife"],["dc.bibliographiccitation.volume","8"],["dc.contributor.author","Igaev, Maxim"],["dc.contributor.author","Kutzner, Carsten"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Vaiana, Andrea C."],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2021-03-05T08:59:19Z"],["dc.date.available","2021-03-05T08:59:19Z"],["dc.date.issued","2019"],["dc.description.abstract","We present a correlation-driven molecular dynamics (CDMD) method for automated refinement of atomistic models into cryo-electron microscopy (cryo-EM) maps at resolutions ranging from near-atomic to subnanometer. It utilizes a chemically accurate force field and thermodynamic sampling to improve the real-space correlation between the modeled structure and the cryo-EM map. Our framework employs a gradual increase in resolution and map-model agreement as well as simulated annealing, and allows fully automated refinement without manual intervention or any additional rotamer- and backbone-specific restraints. Using multiple challenging systems covering a wide range of map resolutions, system sizes, starting model geometries and distances from the target state, we assess the quality of generated models in terms of both model accuracy and potential of overfitting. To provide an objective comparison, we apply several well-established methods across all examples and demonstrate that CDMD performs best in most cases."],["dc.identifier.doi","10.7554/eLife.43542"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/80423"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.eissn","2050-084X"],["dc.title","Automated cryo-EM structure refinement using correlation-driven molecular dynamics"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

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[["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Blau, Christian"],["dc.contributor.author","Schröder, Gunnar F."],["dc.contributor.author","Davydov, Iakov I."],["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","2017-09-07T11:46:53Z"],["dc.date.available","2017-09-07T11:46:53Z"],["dc.date.issued","2014"],["dc.identifier.doi","10.1016/j.bpj.2013.11.2758"],["dc.identifier.eissn","1542-0086"],["dc.identifier.gro","3142197"],["dc.identifier.isi","000337000402731"],["dc.identifier.issn","0006-3495"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/5610"],["dc.language.iso","en"],["dc.notes","http://pubman.mpdl.mpg.de/pubman/faces/viewItemFullPage.jsp?itemId=escidoc:2049946:2"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Cell Press"],["dc.publisher.place","Cambridge"],["dc.relation.conference","58th Annual Meeting of the Biophysical-Society"],["dc.relation.eventend","2014-02-19"],["dc.relation.eventlocation","San Francisco, CA"],["dc.relation.eventstart","2014-02-15"],["dc.relation.ispartof","Biophysical Journal, 106(Supplement 1), 493a-493a."],["dc.title","Rapid and Stable Transfer RNA Translocation through the Ribosome Ensured by Specific Contact Mechanisms"],["dc.type","conference_abstract"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","240a"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Biophysical Journal"],["dc.bibliographiccitation.volume","106"],["dc.contributor.author","Vaiana, Andrea C."],["dc.contributor.author","Kutzner, Carsten"],["dc.contributor.author","Bock, Lars V."],["dc.contributor.author","Blau, Christian"],["dc.contributor.author","Grubmüller, Helmut"],["dc.date.accessioned","2021-03-05T08:57:56Z"],["dc.date.available","2021-03-05T08:57:56Z"],["dc.date.issued","2014"],["dc.identifier.doi","10.1016/j.bpj.2013.11.1405"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/79939"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-393"],["dc.relation.issn","0006-3495"],["dc.title","Refining Crystal Structures Against Cryo-EM Data using Molecular Dynamics Simulations to Obtain a Complete Atomistic Pathway of Transfer RNA Translocation"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]