Rodnina, Marina V.

[["dc.bibliographiccitation.firstpage","341"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Molecular Cell"],["dc.bibliographiccitation.lastpage","351"],["dc.bibliographiccitation.volume","61"],["dc.contributor.author","Buhr, Florian"],["dc.contributor.author","Jha, Sujata"],["dc.contributor.author","Thommen, Michael"],["dc.contributor.author","Mittelstaet, Joerg"],["dc.contributor.author","Kutz, Felicitas"],["dc.contributor.author","Schwalbe, Harald"],["dc.contributor.author","Rodnina, Marina V."],["dc.contributor.author","Komar, Anton A."],["dc.date.accessioned","2017-09-07T11:54:38Z"],["dc.date.available","2017-09-07T11:54:38Z"],["dc.date.issued","2016"],["dc.description.abstract","In all genomes, most amino acids are encoded by more than one codon. Synonymous codons can modulate protein production and folding, but the mechanism connecting codon usage to protein homeostasis is not known. Here we show that synonymous codon variants in the gene encoding gamma-B crystallin, a mammalian eye-lens protein, modulate the rates of translation and cotranslational folding of protein domains monitored in real time by Forster resonance energy transfer and fluorescence-intensity changes. Gamma-B crystallins produced from mRNAs with changed codon bias have the same amino acid sequence but attain different conformations, as indicated by altered in vivo stability and in vitro protease resistance. 2D NMR spectroscopic data suggest that structural differences are associated with different cysteine oxidation states of the purified proteins, providing a link between translation, folding, and the structures of isolated proteins. Thus, synonymous codons provide a secondary code for protein folding in the cell."],["dc.identifier.doi","10.1016/j.molcel.2016.01.008"],["dc.identifier.gro","3141730"],["dc.identifier.isi","000372325800004"],["dc.identifier.pmid","26849192"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/435"],["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","1097-4164"],["dc.relation.issn","1097-2765"],["dc.title","Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","305"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","European Journal of Biochemistry"],["dc.bibliographiccitation.lastpage","310"],["dc.bibliographiccitation.volume","225"],["dc.contributor.author","Rodnina, Marina"],["dc.contributor.author","SEREBRYANIK, A. I."],["dc.contributor.author","Ovcharenko, G. V."],["dc.contributor.author","Elskaya, A. V."],["dc.date.accessioned","2017-09-07T11:51:25Z"],["dc.date.available","2017-09-07T11:51:25Z"],["dc.date.issued","1994"],["dc.description.abstract","80 S ribosomes from a number of higher eukaryotic organisms are able to hydrolyse ATP and GTP without the addition of soluble protein factors. ATPase seems to be an intrinsic activity of the ribosome, as indicated by the findings that ATPase activity is not diminished upon dissociation of ribosomes and reassociation of subunits, by washing with 0.66 M (KCl + NH4Cl) or 0.6 M LiCl treatment and ethanol precipitation; 1.5 M LiCl treatment removes only 40% ATPase activity. 80 S ribosomes are able to bind a variety of NTPs, NDPs and NTP analogues, with a preference for ATP. Effective inhibitors of the ribosomal ATPase are ammonium metavanadate and alcaloid emetine. The ATPase activity is present on both ribosomal subunits, which may reflect the existence of two catalytical sites for ATP on the 80 S ribosome. Ribosomal ATPase is stimulated by the occupancy of the A site, in particular with charged tRNA. The ATPase inhibitor adenylylimidodiphosphate almost completely prevents elongation-factor(EF)-1-dependent binding of Phe-tRNA(Phe) to the A site. The hydrolysis of ATP, therefore, is likely to be involved in the mechanism of tRNA binding to the A site of the 80 S ribosome. As far as wide substrate specificity and possible participation in tRNA interaction with the ribosome are concerned, the ribosomal ATPase seems to be similar to EF-3 found in fungi. A synergism in ATPase activities of yeast EF-3 and rabbit liver ribosomes at high ATP concentration and certain ribosome/EF-3 ratios have been observed. Rabbit liver ribosomes seem to stimulate the ATPase activity of yeast EF-3 similar to the mechanism in yeast ribosomes, though less efficiently."],["dc.identifier.doi","10.1111/j.1432-1033.1994.00305.x"],["dc.identifier.gro","3144718"],["dc.identifier.isi","A1994PJ53200033"],["dc.identifier.pmid","7925450"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2373"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Springer"],["dc.relation.issn","0014-2956"],["dc.title","ATPASE STRONGLY BOUND TO HIGHER EUKARYOTIC RIBOSOMES"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","871121"],["dc.bibliographiccitation.journal","Frontiers in Molecular Biosciences"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Mercier, Evan"],["dc.contributor.author","Wang, Xiaolin"],["dc.contributor.author","Bögeholz, Lena A. K."],["dc.contributor.author","Wintermeyer, Wolfgang"],["dc.contributor.author","Rodnina, Marina V."],["dc.date.accessioned","2022-06-01T09:39:51Z"],["dc.date.available","2022-06-01T09:39:51Z"],["dc.date.issued","2022"],["dc.description.abstract","Nascent polypeptides emerging from the ribosome during translation are rapidly scanned and processed by ribosome-associated protein biogenesis factors (RPBs). RPBs cleave the N-terminal formyl and methionine groups, assist cotranslational protein folding, and sort the proteins according to their cellular destination. Ribosomes translating inner-membrane proteins are recognized and targeted to the translocon with the help of the signal recognition particle, SRP, and SRP receptor, FtsY. The growing nascent peptide is then inserted into the phospholipid bilayer at the translocon, an inner-membrane protein complex consisting of SecY, SecE, and SecG. Folding of membrane proteins requires that transmembrane helices (TMs) attain their correct topology, the soluble domains are inserted at the correct (cytoplasmic or periplasmic) side of the membrane, and – for polytopic membrane proteins – the TMs find their interaction partner TMs in the phospholipid bilayer. This review describes the recent progress in understanding how growing nascent peptides are processed and how inner-membrane proteins are targeted to the translocon and find their correct orientation at the membrane, with the focus on biophysical approaches revealing the dynamics of the process. We describe how spontaneous fluctuations of the translocon allow diffusion of TMs into the phospholipid bilayer and argue that the ribosome orchestrates cotranslational targeting not only by providing the binding platform for the RPBs or the translocon, but also by helping the nascent chains to find their correct orientation in the membrane. Finally, we present the auxiliary role of YidC as a chaperone for inner-membrane proteins. We show how biophysical approaches provide new insights into the dynamics of membrane protein biogenesis and raise new questions as to how translation modulates protein folding."],["dc.description.sponsorship"," Deutsche Forschungsgemeinschaft"],["dc.description.sponsorship"," European Research Council"],["dc.identifier.doi","10.3389/fmolb.2022.871121"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/108581"],["dc.notes.intern","DOI-Import GROB-572"],["dc.relation.eissn","2296-889X"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0/"],["dc.title","Cotranslational Biogenesis of Membrane Proteins in Bacteria"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["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.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","380"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Analytical Biochemistry"],["dc.bibliographiccitation.lastpage","381"],["dc.bibliographiccitation.volume","219"],["dc.contributor.author","Rodnina, Marina V."],["dc.contributor.author","Semenkov, Y.P."],["dc.contributor.author","Wintermeyer, W."],["dc.date.accessioned","2022-03-01T11:46:52Z"],["dc.date.available","2022-03-01T11:46:52Z"],["dc.date.issued","1994"],["dc.identifier.doi","10.1006/abio.1994.1282"],["dc.identifier.pii","S0003269784712826"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/103826"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-531"],["dc.relation.issn","0003-2697"],["dc.title","Purification of fMET-tRNAfMET by Fast Protein Liquid Chromatography"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","4977"],["dc.bibliographiccitation.issue","17"],["dc.bibliographiccitation.journal","Biochemistry"],["dc.bibliographiccitation.lastpage","4984"],["dc.bibliographiccitation.volume","46"],["dc.contributor.author","Schuemmer, Tobias"],["dc.contributor.author","Gromadski, Kirill B."],["dc.contributor.author","Rodnina, Marina"],["dc.date.accessioned","2017-09-07T11:49:49Z"],["dc.date.available","2017-09-07T11:49:49Z"],["dc.date.issued","2007"],["dc.description.abstract","Elongation factor Tu (EF-Tu) belongs to the family of GTP-binding proteins and requires elongation factor Ts (EF-Ts) for nucleotide exchange. Crystal structures suggested that one of the salient features in the EF-Tu center dot EF-Ts complex is a conformation change in the switch II region of EF-Tu that is initiated by intrusion of Phe81 of EF-Ts between His84 and His118 of EF-Tu and may result in a destabilization of Mg2+ coordination and guanine nucleotide release. In the present paper, the contribution of His84 to nucleotide release was studied by pre-steady-state kinetic analysis of nucleotide exchange in mutant EF-Tu in which His84 was replaced by Ala. Both intrinsic and EF-Ts-catalyzed nucleotide release was affected by the mutation, resulting in a 10-fold faster spontaneous GDP release and a 4-fold faster EF-Ts-catalyzed release of GTP and GDP. Removal of Mg2+ from the EF-Tu center dot EF-Ts complex increased the rate constant of GDP release 2-fold, suggesting a small contribution to nucleotide exchange. Together with published data on the effects of mutations interfering with other putative interactions between EF-Tu and EF-Ts, the results suggest that each of the contacts in the EF-Tu center dot EF-Ts complex alone contributes moderately to nucleotide destabilization, but together they act synergistically to bring about the overall 60000-fold acceleration of nucleotide exchange in EF-Tu by EF-Ts."],["dc.identifier.doi","10.1021/bi602486c"],["dc.identifier.gro","3143504"],["dc.identifier.isi","000245899900004"],["dc.identifier.pmid","17397188"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/1026"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Amer Chemical Soc"],["dc.relation.issn","0006-2960"],["dc.title","Mechanism of EF-Ts-catalyzed guanine nucleotide exchange in EF-Tu: Contribution of interactions mediated by helix B of EF-Tu"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","15408"],["dc.bibliographiccitation.issue","44"],["dc.bibliographiccitation.journal","Biochemistry"],["dc.bibliographiccitation.lastpage","15413"],["dc.bibliographiccitation.volume","37"],["dc.contributor.author","Jagath, J. R."],["dc.contributor.author","Rodnina, Marina"],["dc.contributor.author","Lentzen, G."],["dc.contributor.author","Wintermeyer, Wolfgang"],["dc.date.accessioned","2017-09-07T11:48:05Z"],["dc.date.available","2017-09-07T11:48:05Z"],["dc.date.issued","1998"],["dc.description.abstract","The bacterial signal recognition particle (SRP) is an RNA-protein complex. In Escherichia coli, the particle consists of a 114 nt RNA, a 4.5S RNA, and a 48 kDa GTP-binding protein, Ffh. GDP-GTP exchange on, and GTP hydrolysis by, Ffh are thought to regulate SRP function in membrane targeting of translating ribosomes. In the present paper, we report the equilibrium and kinetic constants of guanine nucleotide binding to Ffh in different functional complexes. The association and dissociation rate constants of GTP/GDP binding to Ffh were measured using a fluorescent analogue of GTP/GDP, mant-GTP/GDP. For both nucleotides, association and dissociation rate constants were about 10(6) M-1 s(-1) and 10 s(-1) respectively. The equilibrium constants of nonmodified GTP and GDP binding to Ffh alone and in SRP, and in the complex with the ribosomes were measured by competition with mant-GDP. In all cases, the same 1-2 mu M affinity for GTP and GDP was observed. Binding of both GTP and GDP to Ffh was independent of Mg2+ ions. The data suggest that, at conditions in vivo, (i) there will be rapid spontaneous GDP-GTP exchange, and (ii) the GTP-bound form of Ffh, or of SRP, will be predominant."],["dc.identifier.doi","10.1021/bi981523a"],["dc.identifier.gro","3144511"],["dc.identifier.isi","000076887400019"],["dc.identifier.pmid","9799502"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2143"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Amer Chemical Soc"],["dc.relation.issn","0006-2960"],["dc.title","Interaction of guanine nucleotides with the signal recognition particle from Escherichia coli"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","390"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Molecular Microbiology"],["dc.bibliographiccitation.lastpage","401"],["dc.bibliographiccitation.volume","69"],["dc.contributor.author","Lancaster, Lorna E."],["dc.contributor.author","Savelsbergh, Andreas"],["dc.contributor.author","Kleanthous, Colin"],["dc.contributor.author","Wintermeyer, Wolfgang"],["dc.contributor.author","Rodnina, Marina V."],["dc.date.accessioned","2018-01-29T15:14:13Z"],["dc.date.available","2018-01-29T15:14:13Z"],["dc.date.issued","2008"],["dc.description.abstract","The cytotoxin colicin E3 targets the 30S subunit of bacterial ribosomes and specifically cleaves 16S rRNA at the decoding centre, thereby inhibiting translation. Although the cleavage site is well known, it is not clear which step of translation is inhibited. We studied the effects of colicin E3 cleavage on ribosome functions by analysing individual steps of protein synthesis. We find that the cleavage affects predominantly the elongation step. The inhibitory effect of colicin E3 cleavage originates from the accumulation of sequential impaired decoding events, each of which results in low occupancy of the A site and, consequently, decreasing yield of elongating peptide. The accumulation leads to an almost complete halt of translation after reading of a few codons. The cleavage of 16S rRNA does not impair monitoring of codon-anticodon complexes or GTPase activation during elongation-factor Tu-dependent binding of aminoacyl-tRNA, but decreases the stability of the codon-recognition complex and slows down aminoacyl-tRNA accommodation in the A site. The tRNA-mRNA translocation is faster on colicin E3-cleaved than on intact ribosomes and is less sensitive to inhibition by the antibiotic viomycin."],["dc.identifier.doi","10.1111/j.1365-2958.2008.06283.x"],["dc.identifier.pmid","18485067"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/11894"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.relation.eissn","1365-2958"],["dc.title","Colicin E3 cleavage of 16S rRNA impairs decoding and accelerates tRNA translocation on Escherichia coli ribosomes"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","7237"],["dc.bibliographiccitation.issue","13"],["dc.bibliographiccitation.journal","Proceedings of the National Academy of Sciences"],["dc.bibliographiccitation.lastpage","7239"],["dc.bibliographiccitation.volume","95"],["dc.contributor.author","Rodnina, Marina"],["dc.contributor.author","Wintermeyer, Wolfgang"],["dc.date.accessioned","2017-09-07T11:48:09Z"],["dc.date.available","2017-09-07T11:48:09Z"],["dc.date.issued","1998"],["dc.identifier.doi","10.1073/pnas.95.13.7237"],["dc.identifier.gro","3144541"],["dc.identifier.isi","000074436400001"],["dc.identifier.pmid","9636131"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/2176"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Natl Acad Sciences"],["dc.relation.issn","0027-8424"],["dc.title","Form follows function: Structure of an elongation factor G-ribosome complex"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","letter_note"],["dspace.entity.type","Publication"]]