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  • 550 - Earth sciences  (891)
  • Models, Molecular  (132)
  • FLUID MECHANICS AND HEAT TRANSFER
  • 2005-2009  (1,023)
  • 1
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    Crystal structure of opsin in its G-protein-interacting conformation (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-09-27
    Description: Opsin, the ligand-free form of the G-protein-coupled receptor rhodopsin, at low pH adopts a conformationally distinct, active G-protein-binding state known as Ops*. A synthetic peptide derived from the main binding site of the heterotrimeric G protein-the carboxy terminus of the alpha-subunit (GalphaCT)-stabilizes Ops*. Here we present the 3.2 A crystal structure of the bovine Ops*-GalphaCT peptide complex. GalphaCT binds to a site in opsin that is opened by an outward tilt of transmembrane helix (TM) 6, a pairing of TM5 and TM6, and a restructured TM7-helix 8 kink. Contacts along the inner surface of TM5 and TM6 induce an alpha-helical conformation in GalphaCT with a C-terminal reverse turn. Main-chain carbonyl groups in the reverse turn constitute the centre of a hydrogen-bonded network, which links the two receptor regions containing the conserved E(D)RY and NPxxY(x)(5,6)F motifs. On the basis of the Ops*-GalphaCT structure and known conformational changes in Galpha, we discuss signal transfer from the receptor to the G protein nucleotide-binding site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scheerer, Patrick -- Park, Jung Hee -- Hildebrand, Peter W -- Kim, Yong Ju -- Krauss, Norbert -- Choe, Hui-Woog -- Hofmann, Klaus Peter -- Ernst, Oliver P -- England -- Nature. 2008 Sep 25;455(7212):497-502. doi: 10.1038/nature07330.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Medizinische Physik und Biophysik (CC2), Charite - Universitatsmedizin Berlin, Chariteplatz 1, D-10117 Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18818650" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Arginine/chemistry/metabolism ; Binding Sites ; Cattle ; Conserved Sequence ; Crystallization ; Crystallography, X-Ray ; GTP-Binding Protein alpha Subunits/*chemistry/*metabolism ; Models, Biological ; Models, Molecular ; Protein Conformation ; Regeneration ; Retinaldehyde/chemistry/metabolism ; Rhodopsin/chemistry ; Rod Opsins/*chemistry/*metabolism ; Signal Transduction
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-12-25
    Description: Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms. There are now nearly 1,000 completed bacterial and archaeal genomes available, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic 'phylogenomic' efforts to compile a phylogeny-driven 'Genomic Encyclopedia of Bacteria and Archaea' in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3073058/" 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/PMC3073058/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Dongying -- Hugenholtz, Philip -- Mavromatis, Konstantinos -- Pukall, Rudiger -- Dalin, Eileen -- Ivanova, Natalia N -- Kunin, Victor -- Goodwin, Lynne -- Wu, Martin -- Tindall, Brian J -- Hooper, Sean D -- Pati, Amrita -- Lykidis, Athanasios -- Spring, Stefan -- Anderson, Iain J -- D'haeseleer, Patrik -- Zemla, Adam -- Singer, Mitchell -- Lapidus, Alla -- Nolan, Matt -- Copeland, Alex -- Han, Cliff -- Chen, Feng -- Cheng, Jan-Fang -- Lucas, Susan -- Kerfeld, Cheryl -- Lang, Elke -- Gronow, Sabine -- Chain, Patrick -- Bruce, David -- Rubin, Edward M -- Kyrpides, Nikos C -- Klenk, Hans-Peter -- Eisen, Jonathan A -- R01 GM054592-09/GM/NIGMS NIH HHS/ -- R01 GM067012-04/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Dec 24;462(7276):1056-60. doi: 10.1038/nature08656.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉DOE Joint Genome Institute, Walnut Creek, California 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20033048" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/chemistry ; Amino Acid Sequence ; Archaea/*classification/*genetics ; Bacteria/*classification/*genetics ; Bacterial Proteins/chemistry ; Biodiversity ; Databases, Genetic ; Genes, rRNA/genetics ; Genome, Archaeal/*genetics ; Genome, Bacterial/*genetics ; Models, Molecular ; Molecular Sequence Data ; *Phylogeny ; Protein Structure, Tertiary ; Sequence Alignment
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
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    Structure and molecular mechanism of a nucleobase-cation-symport-1 family transporter (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-10-18
    Description: The nucleobase-cation-symport-1 (NCS1) transporters are essential components of salvage pathways for nucleobases and related metabolites. Here, we report the 2.85-angstrom resolution structure of the NCS1 benzyl-hydantoin transporter, Mhp1, from Microbacterium liquefaciens. Mhp1 contains 12 transmembrane helices, 10 of which are arranged in two inverted repeats of five helices. The structures of the outward-facing open and substrate-bound occluded conformations were solved, showing how the outward-facing cavity closes upon binding of substrate. Comparisons with the leucine transporter LeuT(Aa) and the galactose transporter vSGLT reveal that the outward- and inward-facing cavities are symmetrically arranged on opposite sides of the membrane. The reciprocal opening and closing of these cavities is synchronized by the inverted repeat helices 3 and 8, providing the structural basis of the alternating access model for membrane transport.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885439/" 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/PMC2885439/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weyand, Simone -- Shimamura, Tatsuro -- Yajima, Shunsuke -- Suzuki, Shun'ichi -- Mirza, Osman -- Krusong, Kuakarun -- Carpenter, Elisabeth P -- Rutherford, Nicholas G -- Hadden, Jonathan M -- O'Reilly, John -- Ma, Pikyee -- Saidijam, Massoud -- Patching, Simon G -- Hope, Ryan J -- Norbertczak, Halina T -- Roach, Peter C J -- Iwata, So -- Henderson, Peter J F -- Cameron, Alexander D -- 062164/Z/00/Z/Wellcome Trust/United Kingdom -- 079209/Wellcome Trust/United Kingdom -- B17935/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/C51725/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G020043/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Oct 31;322(5902):709-13. doi: 10.1126/science.1164440. Epub 2008 Oct 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Membrane Protein Laboratory, Diamond Light Source Limited, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18927357" target="_blank"〉PubMed〈/a〉
    Keywords: Actinomycetales/*chemistry/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Cations/chemistry/metabolism ; Cell Membrane/chemistry/metabolism ; Crystallography, X-Ray ; Hydantoins/chemistry/metabolism ; Ion Transport ; Models, Molecular ; Molecular Sequence Data ; Nucleobase Transport Proteins/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Sodium/metabolism ; Symporters/*chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-05-16
    Description: The potential impact of pandemic influenza makes effective measures to limit the spread and morbidity of virus infection a public health priority. Antiviral drugs are seen as essential requirements for control of initial influenza outbreaks caused by a new virus, and in pre-pandemic plans there is a heavy reliance on drug stockpiles. The principal target for these drugs is a virus surface glycoprotein, neuraminidase, which facilitates the release of nascent virus and thus the spread of infection. Oseltamivir (Tamiflu) and zanamivir (Relenza) are two currently used neuraminidase inhibitors that were developed using knowledge of the enzyme structure. It has been proposed that the closer such inhibitors resemble the natural substrate, the less likely they are to select drug-resistant mutant viruses that retain viability. However, there have been reports of drug-resistant mutant selection in vitro and from infected humans. We report here the enzymatic properties and crystal structures of neuraminidase mutants from H5N1-infected patients that explain the molecular basis of resistance. Our results show that these mutants are resistant to oseltamivir but still strongly inhibited by zanamivir owing to an altered hydrophobic pocket in the active site of the enzyme required for oseltamivir binding. Together with recent reports of the viability and pathogenesis of H5N1 (ref. 7) and H1N1 (ref. 8) viruses with neuraminidases carrying these mutations, our results indicate that it would be prudent for pandemic stockpiles of oseltamivir to be augmented by additional antiviral drugs, including zanamivir.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Collins, Patrick J -- Haire, Lesley F -- Lin, Yi Pu -- Liu, Junfeng -- Russell, Rupert J -- Walker, Philip A -- Skehel, John J -- Martin, Stephen R -- Hay, Alan J -- Gamblin, Steven J -- MC_U117512711/Medical Research Council/United Kingdom -- MC_U117512723/Medical Research Council/United Kingdom -- MC_U117570592/Medical Research Council/United Kingdom -- MC_U117584222/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- England -- Nature. 2008 Jun 26;453(7199):1258-61. doi: 10.1038/nature06956. Epub 2008 May 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC-National Institute for Medical Research, Mill Hill, London NW7 1AA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18480754" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; *Drug Resistance, Viral ; Enzyme Inhibitors/chemistry/metabolism/pharmacology ; Humans ; Influenza A Virus, H1N1 Subtype/drug effects/enzymology/genetics ; Influenza A Virus, H5N1 Subtype/*drug effects/*enzymology/genetics ; Influenza, Human/virology ; Kinetics ; Models, Molecular ; Molecular Conformation ; Mutation/*genetics ; Neuraminidase/antagonists & inhibitors/*chemistry/*genetics/metabolism ; Oseltamivir/chemistry/metabolism/*pharmacology ; Protein Binding ; Zanamivir/pharmacology
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
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    Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-11-07
    Description: Xeroderma pigmentosum is a monogenic disease characterized by hypersensitivity to ultraviolet light. The cells of xeroderma pigmentosum patients are defective in nucleotide excision repair, limiting their capacity to eliminate ultraviolet-induced DNA damage, and resulting in a strong predisposition to develop skin cancers. The use of rare cutting DNA endonucleases-such as homing endonucleases, also known as meganucleases-constitutes one possible strategy for repairing DNA lesions. Homing endonucleases have emerged as highly specific molecular scalpels that recognize and cleave DNA sites, promoting efficient homologous gene targeting through double-strand-break-induced homologous recombination. Here we describe two engineered heterodimeric derivatives of the homing endonuclease I-CreI, produced by a semi-rational approach. These two molecules-Amel3-Amel4 and Ini3-Ini4-cleave DNA from the human XPC gene (xeroderma pigmentosum group C), in vitro and in vivo. Crystal structures of the I-CreI variants complexed with intact and cleaved XPC target DNA suggest that the mechanism of DNA recognition and cleavage by the engineered homing endonucleases is similar to that of the wild-type I-CreI. Furthermore, these derivatives induced high levels of specific gene targeting in mammalian cells while displaying no obvious genotoxicity. Thus, homing endonucleases can be designed to recognize and cleave the DNA sequences of specific genes, opening up new possibilities for genome engineering and gene therapy in xeroderma pigmentosum patients whose illness can be treated ex vivo.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Redondo, Pilar -- Prieto, Jesus -- Munoz, Ines G -- Alibes, Andreu -- Stricher, Francois -- Serrano, Luis -- Cabaniols, Jean-Pierre -- Daboussi, Fayza -- Arnould, Sylvain -- Perez, Christophe -- Duchateau, Philippe -- Paques, Frederic -- Blanco, Francisco J -- Montoya, Guillermo -- England -- Nature. 2008 Nov 6;456(7218):107-11. doi: 10.1038/nature07343.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Macromolecular Crystallography Group, Spanish National Cancer Research Centre (CNIO), c/Melchor Fdez. Almagro 3, 28029 Madrid, Spain.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18987743" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; CHO Cells ; Cell Line ; Cricetinae ; Cricetulus ; Crystallography, X-Ray ; DNA/chemistry/*genetics/*metabolism ; DNA Repair ; DNA Restriction Enzymes/*chemistry/genetics/*metabolism/toxicity ; DNA-Binding Proteins/*genetics ; Enzyme Stability ; *Genetic Engineering ; Humans ; Models, Molecular ; Phosphorylation ; Protein Multimerization ; Substrate Specificity ; Xeroderma Pigmentosum/*genetics
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
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    Identification of ALK as a major familial neuroblastoma predisposition gene (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-08-30
    Description: Neuroblastoma is a childhood cancer that can be inherited, but the genetic aetiology is largely unknown. Here we show that germline mutations in the anaplastic lymphoma kinase (ALK) gene explain most hereditary neuroblastomas, and that activating mutations can also be somatically acquired. We first identified a significant linkage signal at chromosome bands 2p23-24 using a whole-genome scan in neuroblastoma pedigrees. Resequencing of regional candidate genes identified three separate germline missense mutations in the tyrosine kinase domain of ALK that segregated with the disease in eight separate families. Resequencing in 194 high-risk neuroblastoma samples showed somatically acquired mutations in the tyrosine kinase domain in 12.4% of samples. Nine of the ten mutations map to critical regions of the kinase domain and were predicted, with high probability, to be oncogenic drivers. Mutations resulted in constitutive phosphorylation, and targeted knockdown of ALK messenger RNA resulted in profound inhibition of growth in all cell lines harbouring mutant or amplified ALK, as well as in two out of six wild-type cell lines for ALK. Our results demonstrate that heritable mutations of ALK are the main cause of familial neuroblastoma, and that germline or acquired activation of this cell-surface kinase is a tractable therapeutic target for this lethal paediatric malignancy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2672043/" 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/PMC2672043/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mosse, Yael P -- Laudenslager, Marci -- Longo, Luca -- Cole, Kristina A -- Wood, Andrew -- Attiyeh, Edward F -- Laquaglia, Michael J -- Sennett, Rachel -- Lynch, Jill E -- Perri, Patrizia -- Laureys, Genevieve -- Speleman, Frank -- Kim, Cecilia -- Hou, Cuiping -- Hakonarson, Hakon -- Torkamani, Ali -- Schork, Nicholas J -- Brodeur, Garrett M -- Tonini, Gian P -- Rappaport, Eric -- Devoto, Marcella -- Maris, John M -- K08 CA111733/CA/NCI NIH HHS/ -- K08 CA111733-04/CA/NCI NIH HHS/ -- K08-111733/PHS HHS/ -- R01 CA078545/CA/NCI NIH HHS/ -- R01 CA078545-09/CA/NCI NIH HHS/ -- R01 CA124709/CA/NCI NIH HHS/ -- R01-CA78454/CA/NCI NIH HHS/ -- R01-CA87847/CA/NCI NIH HHS/ -- U10 CA098543/CA/NCI NIH HHS/ -- U10 CA098543-06/CA/NCI NIH HHS/ -- England -- Nature. 2008 Oct 16;455(7215):930-5. doi: 10.1038/nature07261. Epub 2008 Aug 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Department of Pediatrics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18724359" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Cell Line, Tumor ; Child ; Chromosomes, Human, Pair 2/genetics ; Female ; Gene Dosage ; Gene Expression Regulation, Neoplastic ; Genetic Predisposition to Disease/*genetics ; Germ-Line Mutation/genetics ; Humans ; Male ; Models, Molecular ; Molecular Sequence Data ; Mutation/*genetics ; Neuroblastoma/*enzymology/*genetics ; Pedigree ; Phosphorylation ; Protein Structure, Tertiary ; Protein-Tyrosine Kinases/chemistry/deficiency/*genetics ; Receptor Protein-Tyrosine Kinases
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 7
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    Crystal structure of the ligand-free G-protein-coupled receptor opsin (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-06-20
    Description: In the G-protein-coupled receptor (GPCR) rhodopsin, the inactivating ligand 11-cis-retinal is bound in the seven-transmembrane helix (TM) bundle and is cis/trans isomerized by light to form active metarhodopsin II. With metarhodopsin II decay, all-trans-retinal is released, and opsin is reloaded with new 11-cis-retinal. Here we present the crystal structure of ligand-free native opsin from bovine retinal rod cells at 2.9 angstrom (A) resolution. Compared to rhodopsin, opsin shows prominent structural changes in the conserved E(D)RY and NPxxY(x)(5,6)F regions and in TM5-TM7. At the cytoplasmic side, TM6 is tilted outwards by 6-7 A, whereas the helix structure of TM5 is more elongated and close to TM6. These structural changes, some of which were attributed to an active GPCR state, reorganize the empty retinal-binding pocket to disclose two openings that may serve the entry and exit of retinal. The opsin structure sheds new light on ligand binding to GPCRs and on GPCR activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, Jung Hee -- Scheerer, Patrick -- Hofmann, Klaus Peter -- Choe, Hui-Woog -- Ernst, Oliver Peter -- England -- Nature. 2008 Jul 10;454(7201):183-7. doi: 10.1038/nature07063. Epub 2008 Jun 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Medizinische Physik und Biophysik (CC2), Charite-Universitatsmedizin Berlin, Chariteplatz 1, D-10117 Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18563085" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cattle ; Conserved Sequence ; Crystallography, X-Ray ; Ligands ; Models, Molecular ; Protein Conformation ; Protein Folding ; Receptors, G-Protein-Coupled/*chemistry/metabolism ; Retinal Rod Photoreceptor Cells/chemistry/cytology ; Retinaldehyde/chemistry/metabolism ; Rhodopsin/chemistry ; Rod Opsins/*chemistry/metabolism
    Print ISSN: 0028-0836
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  • 8
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    Core signaling pathways in human pancreatic cancers revealed by global genomic analyses (2008)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2008-09-06
    Description: There are currently few therapeutic options for patients with pancreatic cancer, and new insights into the pathogenesis of this lethal disease are urgently needed. Toward this end, we performed a comprehensive genetic analysis of 24 pancreatic cancers. We first determined the sequences of 23,219 transcripts, representing 20,661 protein-coding genes, in these samples. Then, we searched for homozygous deletions and amplifications in the tumor DNA by using microarrays containing probes for approximately 10(6) single-nucleotide polymorphisms. We found that pancreatic cancers contain an average of 63 genetic alterations, the majority of which are point mutations. These alterations defined a core set of 12 cellular signaling pathways and processes that were each genetically altered in 67 to 100% of the tumors. Analysis of these tumors' transcriptomes with next-generation sequencing-by-synthesis technologies provided independent evidence for the importance of these pathways and processes. Our data indicate that genetically altered core pathways and regulatory processes only become evident once the coding regions of the genome are analyzed in depth. Dysregulation of these core pathways and processes through mutation can explain the major features of pancreatic tumorigenesis.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848990/" 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/PMC2848990/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jones, Sian -- Zhang, Xiaosong -- Parsons, D Williams -- Lin, Jimmy Cheng-Ho -- Leary, Rebecca J -- Angenendt, Philipp -- Mankoo, Parminder -- Carter, Hannah -- Kamiyama, Hirohiko -- Jimeno, Antonio -- Hong, Seung-Mo -- Fu, Baojin -- Lin, Ming-Tseh -- Calhoun, Eric S -- Kamiyama, Mihoko -- Walter, Kimberly -- Nikolskaya, Tatiana -- Nikolsky, Yuri -- Hartigan, James -- Smith, Douglas R -- Hidalgo, Manuel -- Leach, Steven D -- Klein, Alison P -- Jaffee, Elizabeth M -- Goggins, Michael -- Maitra, Anirban -- Iacobuzio-Donahue, Christine -- Eshleman, James R -- Kern, Scott E -- Hruban, Ralph H -- Karchin, Rachel -- Papadopoulos, Nickolas -- Parmigiani, Giovanni -- Vogelstein, Bert -- Velculescu, Victor E -- Kinzler, Kenneth W -- CA121113/CA/NCI NIH HHS/ -- CA43460/CA/NCI NIH HHS/ -- CA57345/CA/NCI NIH HHS/ -- CA62924/CA/NCI NIH HHS/ -- P50 CA062924/CA/NCI NIH HHS/ -- P50 CA062924-130011/CA/NCI NIH HHS/ -- P50 CA062924-140011/CA/NCI NIH HHS/ -- P50 CA062924-160017/CA/NCI NIH HHS/ -- R01 CA121113/CA/NCI NIH HHS/ -- R01 CA121113-04/CA/NCI NIH HHS/ -- R37 CA043460/CA/NCI NIH HHS/ -- R37 CA043460-27/CA/NCI NIH HHS/ -- R37 CA057345/CA/NCI NIH HHS/ -- R37 CA057345-17/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Sep 26;321(5897):1801-6. doi: 10.1126/science.1164368. Epub 2008 Sep 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sol Goldman Pancreatic Cancer Research Center, Ludwig Center and Howard Hughes Medical Institute at the Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18772397" target="_blank"〉PubMed〈/a〉
    Keywords: Adenocarcinoma/etiology/*genetics/*metabolism ; Algorithms ; Carcinoma, Pancreatic Ductal/etiology/genetics/metabolism ; Computational Biology ; Gene Amplification ; Gene Expression Profiling ; Genome, Human ; Humans ; Models, Molecular ; *Mutation ; Mutation, Missense ; Oligonucleotide Array Sequence Analysis ; Pancreatic Neoplasms/etiology/*genetics/*metabolism ; Point Mutation ; Polymorphism, Single Nucleotide ; Sequence Deletion ; Signal Transduction/*genetics
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Apolipoprotein L-I promotes trypanosome lysis by forming pores in lysosomal membranes (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-07-16
    Description: Apolipoprotein L-I is the trypanolytic factor of human serum. Here we show that this protein contains a membrane pore-forming domain functionally similar to that of bacterial colicins, flanked by a membrane-addressing domain. In lipid bilayer membranes, apolipoprotein L-I formed anion channels. In Trypanosoma brucei, apolipoprotein L-I was targeted to the lysosomal membrane and triggered depolarization of this membrane, continuous influx of chloride, and subsequent osmotic swelling of the lysosome until the trypanosome lysed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Perez-Morga, David -- Vanhollebeke, Benoit -- Paturiaux-Hanocq, Francoise -- Nolan, Derek P -- Lins, Laurence -- Homble, Fabrice -- Vanhamme, Luc -- Tebabi, Patricia -- Pays, Annette -- Poelvoorde, Philippe -- Jacquet, Alain -- Brasseur, Robert -- Pays, Etienne -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2005 Jul 15;309(5733):469-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Parasitology, IBMM, Universite Libre de Bruxelles, 12, rue des Profs Jeener et Brachet, B6041 Gosselies, Belgium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16020735" target="_blank"〉PubMed〈/a〉
    Keywords: 4,4'-Diisothiocyanostilbene-2,2'-Disulfonic Acid/pharmacology ; Amino Acid Sequence ; Animals ; Anions/metabolism ; Apolipoproteins/*chemistry/genetics/*metabolism/pharmacology ; Cells, Immobilized ; Chlorides/metabolism ; Colicins/chemistry/pharmacology ; Escherichia coli/drug effects/growth & development ; Humans ; Intracellular Membranes/drug effects/*metabolism/ultrastructure ; Ion Channels/metabolism ; Lipid Bilayers/chemistry ; Lipoproteins, HDL/*chemistry/genetics/*metabolism/pharmacology ; Lysosomes/drug effects/*metabolism/ultrastructure ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Permeability ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Proteins/metabolism ; Trypanosoma brucei brucei/drug effects/*metabolism/ultrastructure
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Structural basis for the selectivity of the external thioesterase of the surfactin synthetase (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-08-16
    Description: Non-ribosomal peptide synthetases (NRPS) and polyketide synthases (PKS) found in bacteria, fungi and plants use two different types of thioesterases for the production of highly active biological compounds. Type I thioesterases (TEI) catalyse the release step from the assembly line of the final product where it is transported from one reaction centre to the next as a thioester linked to a 4'-phosphopantetheine (4'-PP) cofactor that is covalently attached to thiolation (T) domains. The second enzyme involved in the synthesis of these secondary metabolites, the type II thioesterase (TEII), is a crucial repair enzyme for the regeneration of functional 4'-PP cofactors of holo-T domains of NRPS and PKS systems. Mispriming of 4'-PP cofactors by acetyl- and short-chain acyl-residues interrupts the biosynthetic system. This repair reaction is very important, because roughly 80% of CoA, the precursor of the 4'-PP cofactor, is acetylated in bacteria. Here we report the three-dimensional structure of a type II thioesterase from Bacillus subtilis free and in complex with a T domain. Comparison with structures of TEI enzymes shows the basis for substrate selectivity and the different modes of interaction of TEII and TEI enzymes with T domains. Furthermore, we show that the TEII enzyme exists in several conformations of which only one is selected on interaction with its native substrate, a modified holo-T domain.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2854587/" 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/PMC2854587/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koglin, Alexander -- Lohr, Frank -- Bernhard, Frank -- Rogov, Vladimir V -- Frueh, Dominique P -- Strieter, Eric R -- Mofid, Mohammad R -- Guntert, Peter -- Wagner, Gerhard -- Walsh, Christopher T -- Marahiel, Mohamed A -- Dotsch, Volker -- P01 GM047467/GM/NIGMS NIH HHS/ -- P01 GM047467-110009/GM/NIGMS NIH HHS/ -- P01 GM047467-12/GM/NIGMS NIH HHS/ -- P01 GM047467-13/GM/NIGMS NIH HHS/ -- P01 GM047467-14/GM/NIGMS NIH HHS/ -- P01 GM047467-15/GM/NIGMS NIH HHS/ -- P01 GM047467-16/GM/NIGMS NIH HHS/ -- P01 GM047467-160010/GM/NIGMS NIH HHS/ -- P01 GM047467-160012/GM/NIGMS NIH HHS/ -- P01 GM047467-17/GM/NIGMS NIH HHS/ -- P01 GM047467-170012/GM/NIGMS NIH HHS/ -- P41 EB002026/EB/NIBIB NIH HHS/ -- P41 EB002026-29/EB/NIBIB NIH HHS/ -- P41 EB002026-30/EB/NIBIB NIH HHS/ -- P41 EB002026-31/EB/NIBIB NIH HHS/ -- P41 EB002026-32/EB/NIBIB NIH HHS/ -- P41 EB002026-33/EB/NIBIB NIH HHS/ -- R01 AI042738/AI/NIAID NIH HHS/ -- R01 AI042738-09/AI/NIAID NIH HHS/ -- R01 GM020011/GM/NIGMS NIH HHS/ -- R01 GM020011-28/GM/NIGMS NIH HHS/ -- R01 GM020011-29/GM/NIGMS NIH HHS/ -- R01 GM020011-30/GM/NIGMS NIH HHS/ -- R01 GM020011-31/GM/NIGMS NIH HHS/ -- R01 GM020011-32/GM/NIGMS NIH HHS/ -- R01 GM020011-37/GM/NIGMS NIH HHS/ -- R01 GM020011-38/GM/NIGMS NIH HHS/ -- R01 GM049338/GM/NIGMS NIH HHS/ -- R01 GM049338-17/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Aug 14;454(7206):907-11. doi: 10.1038/nature07161.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance and Cluster of Excellence Macromolecular Complexes (CEF), J.W.-Goethe University, 60438 Frankfurt am Main, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18704089" target="_blank"〉PubMed〈/a〉
    Keywords: Bacillus subtilis/*enzymology ; Bacterial Proteins/biosynthesis/*chemistry/*metabolism ; Fatty Acid Synthases/*chemistry/*metabolism ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Peptide Synthases/biosynthesis/*chemistry/*metabolism ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Thiolester Hydrolases/*chemistry/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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