Neumann, Piotr D.

[["dc.bibliographiccitation.artnumber","5715"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Nature Communications"],["dc.bibliographiccitation.volume","12"],["dc.contributor.author","Gomkale, Ridhima"],["dc.contributor.author","Linden, Andreas"],["dc.contributor.author","Neumann, Piotr"],["dc.contributor.author","Schendzielorz, Alexander Benjamin"],["dc.contributor.author","Stoldt, Stefan"],["dc.contributor.author","Dybkov, Olexandr"],["dc.contributor.author","Kilisch, Markus"],["dc.contributor.author","Schulz, Christian"],["dc.contributor.author","Cruz-Zaragoza, Luis Daniel"],["dc.contributor.author","Schwappach, Blanche"],["dc.contributor.author","Rehling, Peter"],["dc.date.accessioned","2021-10-01T09:57:33Z"],["dc.date.available","2021-10-01T09:57:33Z"],["dc.date.issued","2021"],["dc.description.abstract","Abstract Nuclear-encoded mitochondrial proteins destined for the matrix have to be transported across two membranes. The TOM and TIM23 complexes facilitate the transport of precursor proteins with N-terminal targeting signals into the matrix. During transport, precursors are recognized by the TIM23 complex in the inner membrane for handover from the TOM complex. However, we have little knowledge on the organization of the TOM-TIM23 transition zone and on how precursor transfer between the translocases occurs. Here, we have designed a precursor protein that is stalled during matrix transport in a TOM-TIM23-spanning manner and enables purification of the translocation intermediate. Combining chemical cross-linking with mass spectrometric analyses and structural modeling allows us to map the molecular environment of the intermembrane space interface of TOM and TIM23 as well as the import motor interactions with amino acid resolution. Our analyses provide a framework for understanding presequence handover and translocation during matrix protein transport."],["dc.description.sponsorship","Open-Access-Publikationsfonds 2021"],["dc.identifier.doi","10.1038/s41467-021-26016-1"],["dc.identifier.pii","26016"],["dc.identifier.pmid","34588454"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/89863"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/348"],["dc.identifier.url","https://sfb1190.med.uni-goettingen.de/production/literature/publications/157"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-469"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation","SFB 1190: Transportmaschinen und Kontaktstellen zellulärer Kompartimente"],["dc.relation","SFB 1190 | P01: Untersuchung der Unterschiede in der Zusammensetzung, Funktion und Position von individuellen MICOS Komplexen in einzelnen Säugerzellen"],["dc.relation","SFB 1190 | P04: Der GET-Rezeptor als ein Eingangstor zum ER und sein Zusammenspiel mit GET bodies"],["dc.relation","SFB 1190 | P13: Protein Transport über den mitochondrialen Carrier Transportweg"],["dc.relation","SFB 1190 | Z02: Massenspektrometrie-basierte Proteomanalyse"],["dc.relation.eissn","2041-1723"],["dc.relation.workinggroup","RG Ficner (Molecular Structural Biology)"],["dc.relation.workinggroup","RG Jakobs (Structure and Dynamics of Mitochondria)"],["dc.relation.workinggroup","RG Rehling (Mitochondrial Protein Biogenesis)"],["dc.relation.workinggroup","RG Schwappach (Membrane Protein Biogenesis)"],["dc.relation.workinggroup","RG Urlaub (Bioanalytische Massenspektrometrie)"],["dc.rights","CC BY 4.0"],["dc.title","Mapping protein interactions in the active TOM-TIM23 supercomplex"],["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","1502"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Biomolecules"],["dc.bibliographiccitation.volume","11"],["dc.contributor.author","Montino, Alice"],["dc.contributor.author","Balakrishnan, Karthi"],["dc.contributor.author","Dippel, Stefan"],["dc.contributor.author","Trebels, Björn"],["dc.contributor.author","Neumann, Piotr"],["dc.contributor.author","Wimmer, Ernst A."],["dc.date.accessioned","2021-12-01T09:22:46Z"],["dc.date.available","2021-12-01T09:22:46Z"],["dc.date.issued","2021"],["dc.description.abstract","Olfaction is crucial for insects to find food sources, mates, and oviposition sites. One of the initial steps in olfaction is facilitated by odorant-binding proteins (OBPs) that translocate hydrophobic odorants through the aqueous olfactory sensilla lymph to the odorant receptor complexes embedded in the dendritic membrane of olfactory sensory neurons. The Tribolium castaneum (Coleoptera, Tenebrionidae) OBPs encoded by the gene pair TcasOBP9A and TcasOBP9B represent the closest homologs to the well-studied Drosophila melanogaster OBP Lush (DmelOBP76a), which mediates pheromone reception. By an electroantennographic analysis, we can show that these two OBPs are not pheromone-specific but rather enhance the detection of a broad spectrum of organic volatiles. Both OBPs are expressed in the antenna but in a mutually exclusive pattern, despite their homology and gene pair character by chromosomal location. A phylogenetic analysis indicates that this gene pair arose at the base of the Cucujiformia, which dates the gene duplication event to about 200 Mio years ago. Therefore, this gene pair is not the result of a recent gene duplication event and the high sequence conservation in spite of their expression in different sensilla is potentially the result of a common function as co-OBPs."],["dc.description.abstract","Olfaction is crucial for insects to find food sources, mates, and oviposition sites. One of the initial steps in olfaction is facilitated by odorant-binding proteins (OBPs) that translocate hydrophobic odorants through the aqueous olfactory sensilla lymph to the odorant receptor complexes embedded in the dendritic membrane of olfactory sensory neurons. The Tribolium castaneum (Coleoptera, Tenebrionidae) OBPs encoded by the gene pair TcasOBP9A and TcasOBP9B represent the closest homologs to the well-studied Drosophila melanogaster OBP Lush (DmelOBP76a), which mediates pheromone reception. By an electroantennographic analysis, we can show that these two OBPs are not pheromone-specific but rather enhance the detection of a broad spectrum of organic volatiles. Both OBPs are expressed in the antenna but in a mutually exclusive pattern, despite their homology and gene pair character by chromosomal location. A phylogenetic analysis indicates that this gene pair arose at the base of the Cucujiformia, which dates the gene duplication event to about 200 Mio years ago. Therefore, this gene pair is not the result of a recent gene duplication event and the high sequence conservation in spite of their expression in different sensilla is potentially the result of a common function as co-OBPs."],["dc.description.sponsorship","Open-Access-Publikationsfonds 2021"],["dc.identifier.doi","10.3390/biom11101502"],["dc.identifier.pii","biom11101502"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/94479"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-478"],["dc.relation.eissn","2218-273X"],["dc.relation.orgunit","Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0/"],["dc.title","Mutually Exclusive Expression of Closely Related Odorant-Binding Proteins 9A and 9B in the Antenna of the Red Flour Beetle Tribolium castaneum"],["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","R780"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","CRITICAL CARE"],["dc.bibliographiccitation.lastpage","R789"],["dc.bibliographiccitation.volume","9"],["dc.contributor.author","Wrigge, Hermann"],["dc.contributor.author","Zinserling, Jörg"],["dc.contributor.author","Neumann, P."],["dc.contributor.author","Muders, T."],["dc.contributor.author","Magnusson, A."],["dc.contributor.author","Putensen, Christian"],["dc.contributor.author","Hedenstierna, G."],["dc.date.accessioned","2018-11-07T10:53:47Z"],["dc.date.available","2018-11-07T10:53:47Z"],["dc.date.issued","2005"],["dc.description.abstract","Introduction Experimental and clinical studies have shown a reduction in intrapulmonary shunt with spontaneous breathing during airway pressure release ventilation (APRV) in acute lung injury. This reduction was related to reduced atelectasis and increased aeration. We hypothesized that spontaneous breathing will result in better ventilation and aeration of dependent lung areas and in less cyclic collapse during the tidal breath. Methods In this randomized controlled experimental trial, 22 pigs with oleic-acid-induced lung injury were randomly assigned to receive APRV with or without spontaneous breathing at comparable airway pressures. Four hours after randomization, dynamic computed tomography scans of the lung were obtained in an apical slice and in a juxtadiaphragmatic transverse slice. Analyses of regional attenuation were performed separately in nondependent and dependent halves of the lungs on end-expiratory scans and end-inspiratory scans. Tidal changes were assessed as differences between inspiration and expiration of the mechanical breaths. Results Whereas no differences were observed in the apical slices, spontaneous breathing resulted in improved tidal ventilation of dependent lung regions ( P < 0.05) and less cyclic collapse ( P < 0.05) in the juxtadiaphragmatic slices. In addition, with spontaneous breathing, the end-expiratory aeration increased and nonaerated tissue decreased in dependent lung regions close to the diaphragm ( P < 0.05 for the interaction ventilator mode and lung region). Conclusion Spontaneous breathing during APRV redistributes ventilation and aeration to dependent, usually well-perfused, lung regions close to the diaphragm, and may thereby contribute to improved arterial oxygenation. Spontaneous breathing also counters cyclic collapse, which is a risk factor for ventilation-associated lung injury."],["dc.identifier.doi","10.1186/cc3908"],["dc.identifier.isi","000235514400028"],["dc.identifier.pmid","16356227"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?goescholar/1260"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/49419"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","1466-609X"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.title","Spontaneous breathing with airway pressure release ventilation favors ventilation in dependent lung regions and counters cyclic alveolar collapse in oleic-acid-induced lung injury: a randomized controlled computed tomography trial"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","643"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","The Journal of Cell Biology"],["dc.bibliographiccitation.lastpage","656"],["dc.bibliographiccitation.volume","195"],["dc.contributor.author","Schulz, Christian"],["dc.contributor.author","Lytovchenko, Oleksandr"],["dc.contributor.author","Melin, Jonathan"],["dc.contributor.author","Chacinska, Agnieszka"],["dc.contributor.author","Guiard, Bernard"],["dc.contributor.author","Neumann, Piotr"],["dc.contributor.author","Ficner, Ralf"],["dc.contributor.author","Jahn, Olaf"],["dc.contributor.author","Schmidt, Bernhard"],["dc.contributor.author","Rehling, Peter"],["dc.date.accessioned","2017-09-07T11:43:19Z"],["dc.date.available","2017-09-07T11:43:19Z"],["dc.date.issued","2011"],["dc.description.abstract","N-terminal targeting signals (presequences) direct proteins across the TOM complex in the outer mitochondrial membrane and the TIM23 complex in the inner mitochondrial membrane. Presequences provide directionality to the transport process and regulate the transport machineries during translocation. However, surprisingly little is known about how presequence receptors interact with the signals and what role these interactions play during preprotein transport. Here, we identify signal-binding sites of presequence receptors through photo-affinity labeling. Using engineered presequence probes, photo cross-linking sites on mitochondrial proteins were mapped mass spectrometrically, thereby defining a presequence-binding domain of Tim50, a core subunit of the TIM23 complex that is essential for mitochondrial protein import. Our results establish Tim50 as the primary presequence receptor at the inner membrane and show that targeting signals and Tim50 regulate the Tim23 channel in an antagonistic manner."],["dc.identifier.doi","10.1083/jcb.201105098"],["dc.identifier.gro","3142630"],["dc.identifier.isi","000297206400012"],["dc.identifier.pmid","22065641"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/8033"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/55"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Rockefeller Univ Press"],["dc.relation.issn","0021-9525"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.title","Tim50's presequence receptor domain is essential for signal driven transport across the TIM23 complex"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","e1007141"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","PLOS Genetics"],["dc.bibliographiccitation.volume","14"],["dc.contributor.author","Kolog Gulko, Miriam"],["dc.contributor.author","Heinrich, Gabriele"],["dc.contributor.author","Gross, Carina"],["dc.contributor.author","Popova, Blagovesta"],["dc.contributor.author","Valerius, Oliver"],["dc.contributor.author","Neumann, Piotr"],["dc.contributor.author","Ficner, Ralf"],["dc.contributor.author","Braus, Gerhard H."],["dc.creator.editor","Brakhage, Axel A."],["dc.date.accessioned","2018-04-23T11:47:09Z"],["dc.date.available","2018-04-23T11:47:09Z"],["dc.date.issued","2018"],["dc.description.abstract","The transition from vegetative growth to multicellular development represents an evolutionary hallmark linked to an oxidative stress signal and controlled protein degradation. We identified the Sem1 proteasome subunit, which connects stress response and cellular differentiation. The sem1 gene encodes the fungal counterpart of the human Sem1 proteasome lid subunit and is essential for fungal cell differentiation and development. A sem1 deletion strain of the filamentous fungus Aspergillus nidulans is able to grow vegetatively and expresses an elevated degree of 20S proteasomes with multiplied ATP-independent catalytic activity compared to wildtype. Oxidative stress induces increased transcription of the genes sem1 and rpn11 for the proteasomal deubiquitinating enzyme. Sem1 is required for stabilization of the Rpn11 deubiquitinating enzyme, incorporation of the ubiquitin receptor Rpn10 into the 19S regulatory particle and efficient 26S proteasome assembly. Sem1 maintains high cellular NADH levels, controls mitochondria integrity during stress and developmental transition."],["dc.identifier.doi","10.1371/journal.pgen.1007141"],["dc.identifier.gro","3142187"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/15668"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/13306"],["dc.language.iso","en"],["dc.notes.intern","lifescience updates Crossref Import"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","final"],["dc.relation.issn","1553-7404"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0/"],["dc.title","Sem1 links proteasome stability and specificity to multicellular development"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.peerReviewed","no"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","496"],["dc.bibliographiccitation.issue","4"],["dc.bibliographiccitation.journal","Acta Crystallographica Section D Structural Biology"],["dc.bibliographiccitation.lastpage","509"],["dc.bibliographiccitation.volume","77"],["dc.contributor.affiliation","Hamann, Florian; 1Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077Göttingen, Germany"],["dc.contributor.affiliation","Zimmerningkat, Lars C.; 1Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077Göttingen, Germany"],["dc.contributor.affiliation","Becker, Robert A.; 3Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany"],["dc.contributor.affiliation","Garbers, Tim B.; 1Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077Göttingen, Germany"],["dc.contributor.affiliation","Neumann, Piotr; 1Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Göttingen Center for Molecular Biosciences (GZMB), Georg-August-University Göttingen, Justus-von-Liebig-Weg 11, 37077Göttingen, Germany"],["dc.contributor.affiliation","Hub, Jochen S.; 3Theoretical Physics and Center for Biophysics, Saarland University, Saarbrücken, Germany"],["dc.contributor.author","Hamann, Florian"],["dc.contributor.author","Zimmerningkat, Lars C."],["dc.contributor.author","Becker, Robert A."],["dc.contributor.author","Garbers, Tim B."],["dc.contributor.author","Neumann, Piotr"],["dc.contributor.author","Hub, Jochen S."],["dc.contributor.author","Ficner, Ralf"],["dc.date.accessioned","2021-06-01T09:41:58Z"],["dc.date.available","2021-06-01T09:41:58Z"],["dc.date.issued","2021"],["dc.date.updated","2022-02-09T13:20:58Z"],["dc.description.abstract","Noncoding intron sequences present in precursor mRNAs need to be removed prior to translation, and they are excised via the spliceosome, a multimegadalton molecular machine composed of numerous protein and RNA components. The DEAH-box ATPase Prp2 plays a crucial role during pre-mRNA splicing as it ensures the catalytic activation of the spliceosome. Despite high structural similarity to other spliceosomal DEAH-box helicases, Prp2 does not seem to function as an RNA helicase, but rather as an RNA-dependent ribonucleoprotein particle-modifying ATPase. Recent crystal structures of the spliceosomal DEAH-box ATPases Prp43 and Prp22, as well as of the related RNA helicase MLE, in complex with RNA have contributed to a better understanding of how RNA binding and processivity might be achieved in this helicase family. In order to shed light onto the divergent manner of function of Prp2, an N-terminally truncated construct of Chaetomium thermophilum Prp2 was crystallized in the presence of ADP-BeF 3 − and a poly-U 12 RNA. The refined structure revealed a virtually identical conformation of the helicase core compared with the ADP-BeF 3 − - and RNA-bound structure of Prp43, and only a minor shift of the C-terminal domains. However, Prp2 and Prp43 differ in the hook-loop and a loop of the helix-bundle domain, which interacts with the hook-loop and evokes a different RNA conformation immediately after the 3′ stack. On replacing these loop residues in Prp43 by the Prp2 sequence, the unwinding activity of Prp43 was abolished. Furthermore, a putative exit tunnel for the γ-phosphate after ATP hydrolysis could be identified in one of the Prp2 structures."],["dc.identifier.doi","10.1107/S2059798321001194"],["dc.identifier.pmid","33825710"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/85096"],["dc.identifier.url","https://mbexc.uni-goettingen.de/literature/publications/249"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-425"],["dc.publisher","International Union of Crystallography"],["dc.relation","EXC 2067: Multiscale Bioimaging"],["dc.relation.issn","2059-7983"],["dc.relation.workinggroup","RG Ficner (Molecular Structural Biology)"],["dc.rights","This is an open access article under the terms of the Creative Commons Attribution License, which permits use,\r\n distribution and reproduction in any medium, provided the original work is properly cited."],["dc.title","The structure of Prp2 bound to RNA and ADP-BeF 3 − reveals structural features important for RNA unwinding by DEAH-box ATPases"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","e1001750"],["dc.bibliographiccitation.firstpage","1"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","PLoS Biology"],["dc.bibliographiccitation.lastpage","15"],["dc.bibliographiccitation.volume","11"],["dc.contributor.author","Ahmed, Yasar Luqman"],["dc.contributor.author","Gerke, Jennifer"],["dc.contributor.author","Park, Hee-Soo"],["dc.contributor.author","Bayram, Ozgür"],["dc.contributor.author","Neumann, Piotr"],["dc.contributor.author","Ni, Min"],["dc.contributor.author","Dickmanns, Achim"],["dc.contributor.author","Kim, Sun Chang"],["dc.contributor.author","Yu, Jae-Hyuk"],["dc.contributor.author","Braus, Gerhard H."],["dc.contributor.author","Ficner, Ralf"],["dc.date.accessioned","2017-09-07T11:47:00Z"],["dc.date.available","2017-09-07T11:47:00Z"],["dc.date.issued","2013"],["dc.description.abstract","Morphological development of fungi and their combined production of secondary metabolites are both acting in defence and protection. These processes are mainly coordinated by velvet regulators, which contain a yet functionally and structurally uncharacterized velvet domain. Here we demonstrate that the velvet domain of VosA is a novel DNA-binding motif that specifically recognizes an 11-nucleotide consensus sequence consisting of two motifs in the promoters of key developmental regulatory genes. The crystal structure analysis of the VosA velvet domain revealed an unforeseen structural similarity with the Rel homology domain (RHD) of the mammalian transcription factor NF-B. Based on this structural similarity several conserved amino acid residues present in all velvet domains have been identified and shown to be essential for the DNA binding ability of VosA. The velvet domain is also involved in dimer formation as seen in the solved crystal structures of the VosA homodimer and the VosA-VelB heterodimer. These findings suggest that defence mechanisms of both fungi and animals might be governed by structurally related DNA-binding transcription factors."],["dc.description.sponsorship","Open-Access-Publikationsfonds 2013"],["dc.description.sponsorship","Open-Access-Publikationsfonds 2014"],["dc.identifier.doi","10.1371/journal.pbio.1001750"],["dc.identifier.gro","3142241"],["dc.identifier.isi","000329367200028"],["dc.identifier.pmid","24391470"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/9579"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/6098"],["dc.language.iso","en"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.relation.issn","1545-7885"],["dc.rights","CC BY 2.5"],["dc.rights.uri","https://creativecommons.org/licenses/by/2.5"],["dc.title","The Velvet Family of Fungal Regulators Contains a DNA-Binding Domain Structurally Similar to NF-κB"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","e12784"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","PLoS ONE"],["dc.bibliographiccitation.volume","5"],["dc.contributor.author","Khoshnevis, Sohail"],["dc.contributor.author","Neumann, Piotr"],["dc.contributor.author","Ficner, Ralf"],["dc.date.accessioned","2017-09-07T11:45:19Z"],["dc.date.available","2017-09-07T11:45:19Z"],["dc.date.issued","2010"],["dc.description.abstract","Background: The multi-subunit eukaryotic initiation factor3 (eIF3) plays a central role in the initiation step of protein synthesis in eukaryotes. One of its large subunits, eIF3b, serves as a scaffold within eIF3 as it interacts with several other subunits. It harbors an RNA Recognition Motif (RRM), which is shown to be a non-canonical RRM in human as it is not capable to interact with oligonucleotides, but rather interacts with eIF3j, a sub-stoichiometric subunit of eIF3. Principal Finding: We have analyzed the high-resolution crystal structure of the eIF3b RRM domain from yeast. It exhibits the same fold as its human ortholog, with similar charge distribution on the surface interacting with the eIF3j in human. Thermodynamic analysis of the interaction between yeast eIF3b-RRM and eIF3j revealed the same range of enthalpy change and dissociation constant as for the human proteins, providing another line of evidence for the same mode of interaction between eIF3b and eIF3j in both organisms. However, analysis of the surface charge distribution of the putative RNA-binding beta-sheet suggested that in contrast to its human ortholog, it potentially could bind oligonucleotides. Three-dimensional positioning of the so called \"RNP1\" motif in this domain is similar to other canonical RRMs, suggesting that this domain might indeed be a canonical RRM, conferring oligonucleotide binding capability to eIF3 in yeast. Interaction studies with yeast total RNA extract confirmed the proposed RNA binding activity of yeast eIF3b-RRM. Conclusion: We showed that yeast eIF3b-RRM interacts with eIF3j in a manner similar to its human ortholog. However, it shows similarities in the oligonucleotide binding surface to canonical RRMs and interacts with yeast total RNA. The proposed RNA binding activity of eIF3b-RRM may help eIF3 to either bind to the ribosome or recruit the mRNA to the 43S pre-initiation complex."],["dc.identifier.doi","10.1371/journal.pone.0012784"],["dc.identifier.gro","3142861"],["dc.identifier.isi","000281864100019"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/7272"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/311"],["dc.notes.intern","WoS Import 2017-03-10 / Funder: State of Lower Saxony"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Public Library Science"],["dc.relation.issn","1932-6203"],["dc.rights","CC BY 2.5"],["dc.rights.uri","https://creativecommons.org/licenses/by/2.5"],["dc.title","Crystal Structure of the RNA Recognition Motif of Yeast Translation Initiation Factor eIF3bw Reveals Differences to Human eIF3b"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","6673"],["dc.bibliographiccitation.issue","10"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","6685"],["dc.bibliographiccitation.volume","42"],["dc.contributor.author","Neumann, Piotr"],["dc.contributor.author","Lakomek, Kristina"],["dc.contributor.author","Naumann, Peter-Thomas"],["dc.contributor.author","Erwin, Whitney M."],["dc.contributor.author","Lauhon, Charles T."],["dc.contributor.author","Ficner, Ralf"],["dc.date.accessioned","2017-09-07T11:46:54Z"],["dc.date.available","2017-09-07T11:46:54Z"],["dc.date.issued","2014"],["dc.description.abstract","In prokaryotes and archaea transfer ribonucleic acid (tRNA) stability as well as cellular UV protection relies on the post-transcriptional modification of uracil at position 8 (U8) of tRNAs by the 4-thiouridine synthetase ThiI. Here, we report three crystal structures of ThiI from Thermotoga maritima in complex with a truncated tRNA. The RNA is mainly bound by the N-terminal ferredoxin-like domain (NFLD) and the THUMP domain of one subunit within the ThiI homodimer thereby positioning the U8 close to the catalytic center in the pyrophosphatase domain of the other subunit. The recognition of the 3'-CCA end by the THUMP domain yields a molecular ruler defining the specificity for U8 thiolation. This first structure of a THUMP/NFLD-RNA complex might serve as paradigm for the RNA recognition by THUMP domains of other proteins. The ternary ThiI-RNA-ATP complex shows no significant structural changes due to adenosine triphosphate (ATP) binding, but two different states of active site loops are observed independent of the nucleotide loading state. Thereby conformational changes of the active site are coupled with conformational changes of the bound RNA. The ThiI-RNA complex structures indicate that full-length tRNA has to adopt a non-canonical conformation upon binding to ThiI."],["dc.description.sponsorship","Open-Access-Publikationsfonds 2014"],["dc.identifier.doi","10.1093/nar/gku249"],["dc.identifier.gro","3142207"],["dc.identifier.isi","000338768100052"],["dc.identifier.pmid","24705700"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/10117"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/5721"],["dc.notes.intern","WoS Import 2017-03-10 / Funder: German Research Foundation (DFG); Gottingen University"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Oxford Univ Press"],["dc.relation.eissn","1362-4962"],["dc.relation.issn","0305-1048"],["dc.rights","CC BY 3.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/3.0"],["dc.title","Crystal structure of a 4-thiouridine synthetase-RNA complex reveals specificity of tRNA U8 modification"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","10845"],["dc.bibliographiccitation.issue","18"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","10860"],["dc.bibliographiccitation.volume","45"],["dc.contributor.author","Gonzalez, Grecia M."],["dc.contributor.author","Durica-Mitic, Svetlana"],["dc.contributor.author","Hardwick, Steven W."],["dc.contributor.author","Moncrieffe, Martin C."],["dc.contributor.author","Resch, Marcus"],["dc.contributor.author","Neumann, Piotr"],["dc.contributor.author","Ficner, Ralf"],["dc.contributor.author","Görke, Boris"],["dc.contributor.author","Luisi, Ben F."],["dc.date.accessioned","2018-04-23T11:47:10Z"],["dc.date.available","2018-04-23T11:47:10Z"],["dc.date.issued","2017"],["dc.description.abstract","In phylogenetically diverse bacteria, the conserved protein RapZ plays a central role in RNA-mediated regulation of amino-sugar metabolism. RapZ contributes to the control of glucosamine phosphate biogenesis by selectively presenting the regulatory small RNA GlmZ to the essential ribonuclease RNase E for inactivation. Here, we report the crystal structures of full length Escherichia coli RapZ at 3.40 Å and 3.25 Å, and its isolated C-terminal domain at 1.17 Å resolution. The structural data confirm that the N-terminal domain of RapZ possesses a kinase fold, whereas the C-terminal domain bears closest homology to a subdomain of 6-phosphofructokinase, an important enzyme in the glycolytic pathway. RapZ self-associates into a domain swapped dimer of dimers, and in vivo data support the importance of quaternary structure in RNA-mediated regulation of target gene expression. Based on biochemical, structural and genetic data, we suggest a mechanism for binding and presentation by RapZ of GlmZ and the closely related decoy sRNA, GlmY. We discuss a scenario for the molecular evolution of RapZ through re-purpose of enzyme components from central metabolism."],["dc.identifier.doi","10.1093/nar/gkx732"],["dc.identifier.gro","3142189"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/14812"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/13308"],["dc.language.iso","en"],["dc.notes.intern","lifescience updates Crossref Import"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","final"],["dc.relation.issn","0305-1048"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dc.type.peerReviewed","no"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]