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  • 1
    Publication Date: 2008-01-04
    Description: The 'RNA world' hypothesis holds that during evolution the structural and enzymatic functions initially served by RNA were assumed by proteins, leading to the latter's domination of biological catalysis. This progression can still be seen in modern biology, where ribozymes, such as the ribosome and RNase P, have evolved into protein-dependent RNA catalysts ('RNPzymes'). Similarly, group I introns use RNA-catalysed splicing reactions, but many function as RNPzymes bound to proteins that stabilize their catalytically active RNA structure. One such protein, the Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (TyrRS; CYT-18), is bifunctional and both aminoacylates mitochondrial tRNA(Tyr) and promotes the splicing of mitochondrial group I introns. Here we determine a 4.5-A co-crystal structure of the Twort orf142-I2 group I intron ribozyme bound to splicing-active, carboxy-terminally truncated CYT-18. The structure shows that the group I intron binds across the two subunits of the homodimeric protein with a newly evolved RNA-binding surface distinct from that which binds tRNA(Tyr). This RNA binding surface provides an extended scaffold for the phosphodiester backbone of the conserved catalytic core of the intron RNA, allowing the protein to promote the splicing of a wide variety of group I introns. The group I intron-binding surface includes three small insertions and additional structural adaptations relative to non-splicing bacterial TyrRSs, indicating a multistep adaptation for splicing function. The co-crystal structure provides insight into how CYT-18 promotes group I intron splicing, how it evolved to have this function, and how proteins could have incrementally replaced RNA structures during the transition from an RNA world to an RNP world.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Paukstelis, Paul J -- Chen, Jui-Hui -- Chase, Elaine -- Lambowitz, Alan M -- Golden, Barbara L -- England -- Nature. 2008 Jan 3;451(7174):94-7. doi: 10.1038/nature06413.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, and Section of Molecular Genetics and Microbiology, School of Biological Sciences, University of Texas at Austin, Austin, Texas 78712, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18172503" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Introns/*genetics ; Models, Molecular ; Molecular Conformation ; Neurospora crassa/*enzymology ; Protein Binding ; RNA/genetics/metabolism ; *RNA Splicing ; RNA, Catalytic/chemistry/genetics/metabolism ; RNA-Binding Proteins/*chemistry/*metabolism ; Staphylococcus Phages/enzymology/genetics ; Tyrosine-tRNA Ligase/*chemistry/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2010-10-29
    Description: The plant SLAC1 anion channel controls turgor pressure in the aperture-defining guard cells of plant stomata, thereby regulating the exchange of water vapour and photosynthetic gases in response to environmental signals such as drought or high levels of carbon dioxide. Here we determine the crystal structure of a bacterial homologue (Haemophilus influenzae) of SLAC1 at 1.20 A resolution, and use structure-inspired mutagenesis to analyse the conductance properties of SLAC1 channels. SLAC1 is a symmetrical trimer composed from quasi-symmetrical subunits, each having ten transmembrane helices arranged from helical hairpin pairs to form a central five-helix transmembrane pore that is gated by an extremely conserved phenylalanine residue. Conformational features indicate a mechanism for control of gating by kinase activation, and electrostatic features of the pore coupled with electrophysiological characteristics indicate that selectivity among different anions is largely a function of the energetic cost of ion dehydration.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548404/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548404/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Yu-Hang -- Hu, Lei -- Punta, Marco -- Bruni, Renato -- Hillerich, Brandan -- Kloss, Brian -- Rost, Burkhard -- Love, James -- Siegelbaum, Steven A -- Hendrickson, Wayne A -- R01 GM034102/GM/NIGMS NIH HHS/ -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54 GM095315/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Oct 28;467(7319):1074-80. doi: 10.1038/nature09487.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20981093" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Arabidopsis/genetics/metabolism ; Arabidopsis Proteins/*chemistry ; Bacterial Proteins/*chemistry/genetics/metabolism ; Crystallography, X-Ray ; Electric Conductivity ; Haemophilus influenzae/*chemistry/genetics ; Ion Channel Gating ; Membrane Proteins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Oocytes/metabolism ; Phenylalanine/chemistry/metabolism ; Plant Stomata/*metabolism ; Static Electricity ; *Structural Homology, Protein ; Substrate Specificity ; Xenopus laevis
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2014-05-13
    Description: Sulphur is an essential element for life and is ubiquitous in living systems. Yet how the sulphur atom is incorporated into many sulphur-containing secondary metabolites is poorly understood. For bond formation between carbon and sulphur in primary metabolites, the major ionic sulphur sources are the persulphide and thiocarboxylate groups on sulphur-carrier (donor) proteins. Each group is post-translationally generated through the action of a specific activating enzyme. In all reported bacterial cases, the gene encoding the enzyme that catalyses the carbon-sulphur bond formation reaction and that encoding the cognate sulphur-carrier protein exist in the same gene cluster. To study the production of the 2-thiosugar moiety in BE-7585A, an antibiotic from Amycolatopsis orientalis, we identified a putative 2-thioglucose synthase, BexX, whose protein sequence and mode of action seem similar to those of ThiG, the enzyme that catalyses thiazole formation in thiamine biosynthesis. However, no gene encoding a sulphur-carrier protein could be located in the BE-7585A cluster. Subsequent genome sequencing uncovered a few genes encoding sulphur-carrier proteins that are probably involved in the biosynthesis of primary metabolites but only one activating enzyme gene in the A. orientalis genome. Further experiments showed that this activating enzyme can adenylate each of these sulphur-carrier proteins and probably also catalyses the subsequent thiolation, through its rhodanese domain. A proper combination of these sulphur-delivery systems is effective for BexX-catalysed 2-thioglucose production. The ability of BexX to selectively distinguish sulphur-carrier proteins is given a structural basis using X-ray crystallography. This study is, to our knowledge, the first complete characterization of thiosugar formation in nature and also demonstrates the receptor promiscuity of the A. orientalis sulphur-delivery system. Our results also show that co-opting the sulphur-delivery machinery of primary metabolism for the biosynthesis of sulphur-containing natural products is probably a general strategy found in nature.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4082789/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4082789/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sasaki, Eita -- Zhang, Xuan -- Sun, He G -- Lu, Mei-yeh Jade -- Liu, Tsung-lin -- Ou, Albert -- Li, Jeng-yi -- Chen, Yu-hsiang -- Ealick, Steven E -- Liu, Hung-wen -- DK67081/DK/NIDDK NIH HHS/ -- GM035906/GM/NIGMS NIH HHS/ -- GM103403/GM/NIGMS NIH HHS/ -- GM103485/GM/NIGMS NIH HHS/ -- P41 GM103403/GM/NIGMS NIH HHS/ -- P41 GM103485/GM/NIGMS NIH HHS/ -- R01 DK067081/DK/NIDDK NIH HHS/ -- R01 GM035906/GM/NIGMS NIH HHS/ -- England -- Nature. 2014 Jun 19;510(7505):427-31. doi: 10.1038/nature13256. Epub 2014 May 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA. ; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA. ; Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, USA. ; 1] Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan [2] Genomics Research Center, Academia Sinica, Taipei 115, Taiwan. ; 1] Genomics Research Center, Academia Sinica, Taipei 115, Taiwan [2] Institute of Bioinformatics and Biosignal Transduction, National Cheng-Kung University, Tainan 701, Taiwan. ; Genomics Research Center, Academia Sinica, Taipei 115, Taiwan. ; Biodiversity Research Center, Academia Sinica, Taipei 115, Taiwan. ; 1] Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA [2] Division of Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, Texas 78712, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24814342" target="_blank"〉PubMed〈/a〉
    Keywords: Actinomycetales/*enzymology/*genetics/metabolism ; Carrier Proteins/chemistry/*metabolism ; Catalytic Domain ; Genome, Bacterial/genetics ; Ligases/*chemistry/genetics/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Tertiary ; Sulfur/*metabolism ; Thiosugars/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2013-08-13
    Description: KRAS and BRAF activating mutations drive tumorigenesis through constitutive activation of the MAPK pathway. As these tumours represent an area of high unmet medical need, multiple allosteric MEK inhibitors, which inhibit MAPK signalling in both genotypes, are being tested in clinical trials. Impressive single-agent activity in BRAF-mutant melanoma has been observed; however, efficacy has been far less robust in KRAS-mutant disease. Here we show that, owing to distinct mechanisms regulating MEK activation in KRAS- versus BRAF-driven tumours, different mechanisms of inhibition are required for optimal antitumour activity in each genotype. Structural and functional analysis illustrates that MEK inhibitors with superior efficacy in KRAS-driven tumours (GDC-0623 and G-573, the former currently in phase I clinical trials) form a strong hydrogen-bond interaction with S212 in MEK that is critical for blocking MEK feedback phosphorylation by wild-type RAF. Conversely, potent inhibition of active, phosphorylated MEK is required for strong inhibition of the MAPK pathway in BRAF-mutant tumours, resulting in superior efficacy in this genotype with GDC-0973 (also known as cobimetinib), a MEK inhibitor currently in phase III clinical trials. Our study highlights that differences in the activation state of MEK in KRAS-mutant tumours versus BRAF-mutant tumours can be exploited through the design of inhibitors that uniquely target these distinct activation states of MEK. These inhibitors are currently being evaluated in clinical trials to determine whether improvements in therapeutic index within KRAS versus BRAF preclinical models translate to improved clinical responses in patients.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hatzivassiliou, Georgia -- Haling, Jacob R -- Chen, Huifen -- Song, Kyung -- Price, Steve -- Heald, Robert -- Hewitt, Joanne F M -- Zak, Mark -- Peck, Ariana -- Orr, Christine -- Merchant, Mark -- Hoeflich, Klaus P -- Chan, Jocelyn -- Luoh, Shiuh-Ming -- Anderson, Daniel J -- Ludlam, Mary J C -- Wiesmann, Christian -- Ultsch, Mark -- Friedman, Lori S -- Malek, Shiva -- Belvin, Marcia -- England -- Nature. 2013 Sep 12;501(7466):232-6. doi: 10.1038/nature12441. Epub 2013 Aug 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Translational Oncology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA. hatzivassiliou.georgia@gene.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23934108" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation/drug effects ; Azetidines/pharmacology ; Cell Survival/drug effects ; Clinical Trials as Topic ; Crystallography, X-Ray ; Enzyme Activation/drug effects ; Feedback, Physiological/drug effects ; Genes, ras/*genetics ; HCT116 Cells ; Humans ; MAP Kinase Signaling System/drug effects ; Mitogen-Activated Protein Kinase Kinases/*antagonists & ; inhibitors/chemistry/metabolism ; Models, Molecular ; Neoplasms/*enzymology/*genetics/pathology ; Oncogene Protein p21(ras)/*genetics ; Phosphorylation/drug effects ; Phosphoserine/metabolism ; Piperidines/pharmacology ; Protein Kinase Inhibitors/*pharmacology ; Proto-Oncogene Proteins B-raf/genetics/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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