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  • Models, Molecular  (762)
  • Reproducibility of Results  (484)
  • History, 21st Century  (459)
  • Nature Publishing Group (NPG)  (1,678)
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  • 1
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    Human genome at ten: Life is complicated (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-04-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Check Hayden, Erika -- England -- Nature. 2010 Apr 1;464(7289):664-7. doi: 10.1038/464664a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360709" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Data Mining ; Gene Expression Regulation ; Genes/genetics ; Genome, Human/*genetics ; Genomics/history/trends ; History, 20th Century ; History, 21st Century ; Human Genome Project/history ; Humans ; *Models, Biological ; Molecular Biology/*history ; Neoplasms/genetics/therapy ; RNA, Untranslated/genetics/metabolism ; Sea Urchins/embryology/genetics ; Systems Biology/*trends ; Tumor Suppressor Protein p53/chemistry/genetics/metabolism ; *Uncertainty
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 2
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    IPCC flooded by criticism (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-02-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schiermeier, Quirin -- England -- Nature. 2010 Feb 4;463(7281):596-7. doi: 10.1038/463596a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20130621" target="_blank"〉PubMed〈/a〉
    Keywords: *Conflict of Interest ; Ecology/ethics/organization & administration/*standards ; Ethics, Professional ; *Global Warming/statistics & numerical data ; Ice Cover ; Reproducibility of Results ; Research Design ; Risk Assessment ; United Nations/ethics/*organization & administration/standards
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
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    The structural basis for autonomous dimerization of the pre-T-cell antigen receptor (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-10-15
    Description: The pre-T-cell antigen receptor (pre-TCR), expressed by immature thymocytes, has a pivotal role in early T-cell development, including TCR beta-selection, survival and proliferation of CD4(-)CD8(-) double-negative thymocytes, and subsequent alphabeta T-cell lineage differentiation. Whereas alphabetaTCR ligation by the peptide-loaded major histocompatibility complex initiates T-cell signalling, pre-TCR-induced signalling occurs by means of a ligand-independent dimerization event. The pre-TCR comprises an invariant alpha-chain (pre-Talpha) that pairs with any TCR beta-chain (TCRbeta) following successful TCR beta-gene rearrangement. Here we provide the basis of pre-Talpha-TCRbeta assembly and pre-TCR dimerization. The pre-Talpha chain comprised a single immunoglobulin-like domain that is structurally distinct from the constant (C) domain of the TCR alpha-chain; nevertheless, the mode of association between pre-Talpha and TCRbeta mirrored that mediated by the Calpha-Cbeta domains of the alphabetaTCR. The pre-TCR had a propensity to dimerize in solution, and the molecular envelope of the pre-TCR dimer correlated well with the observed head-to-tail pre-TCR dimer. This mode of pre-TCR dimerization enabled the pre-Talpha domain to interact with the variable (V) beta domain through residues that are highly conserved across the Vbeta and joining (J) beta gene families, thus mimicking the interactions at the core of the alphabetaTCR's Valpha-Vbeta interface. Disruption of this pre-Talpha-Vbeta dimer interface abrogated pre-TCR dimerization in solution and impaired pre-TCR expression on the cell surface. Accordingly, we provide a mechanism of pre-TCR self-association that allows the pre-Talpha chain to simultaneously 'sample' the correct folding of both the V and C domains of any TCR beta-chain, regardless of its ultimate specificity, which represents a critical checkpoint in T-cell development. This unusual dual-chaperone-like sensing function of pre-Talpha represents a unique mechanism in nature whereby developmental quality control regulates the expression and signalling of an integral membrane receptor complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pang, Siew Siew -- Berry, Richard -- Chen, Zhenjun -- Kjer-Nielsen, Lars -- Perugini, Matthew A -- King, Glenn F -- Wang, Christina -- Chew, Sock Hui -- La Gruta, Nicole L -- Williams, Neal K -- Beddoe, Travis -- Tiganis, Tony -- Cowieson, Nathan P -- Godfrey, Dale I -- Purcell, Anthony W -- Wilce, Matthew C J -- McCluskey, James -- Rossjohn, Jamie -- England -- Nature. 2010 Oct 14;467(7317):844-8. doi: 10.1038/nature09448.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Protein Crystallography Unit, Department of Biochemistry and Molecular Biology, School of Biomedical Sciences, Monash University, Clayton, Victoria 3800, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20944746" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Gene Rearrangement, T-Lymphocyte/genetics ; Humans ; Models, Molecular ; Mutation ; Protein Folding ; *Protein Multimerization ; Protein Structure, Tertiary ; Receptors, Antigen, T-Cell/*chemistry/genetics/*metabolism ; Receptors, Antigen, T-Cell, alpha-beta/chemistry/metabolism ; Signal Transduction ; Solutions ; T-Lymphocytes/cytology/immunology/metabolism
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  • 4
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    Organic-walled microfossils in 3.2-billion-year-old shallow-marine siliciclastic deposits (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-02-09
    Description: Although the notion of an early origin and diversification of life on Earth during the Archaean eon has received increasing support in geochemical, sedimentological and palaeontological evidence, ambiguities and controversies persist regarding the biogenicity and syngeneity of the record older than Late Archaean. Non-biological processes are known to produce morphologies similar to some microfossils, and hydrothermal fluids have the potential to produce abiotic organic compounds with depleted carbon isotope values, making it difficult to establish unambiguous traces of life. Here we report the discovery of a population of large (up to about 300 mum in diameter) carbonaceous spheroidal microstructures in Mesoarchaean shales and siltstones of the Moodies Group, South Africa, the Earth's oldest siliciclastic alluvial to tidal-estuarine deposits. These microstructures are interpreted as organic-walled microfossils on the basis of petrographic and geochemical evidence for their endogenicity and syngeneity, their carbonaceous composition, cellular morphology and ultrastructure, occurrence in populations, taphonomic features of soft wall deformation, and the geological context plausible for life, as well as a lack of abiotic explanation falsifying a biological origin. These are the oldest and largest Archaean organic-walled spheroidal microfossils reported so far. Our observations suggest that relatively large microorganisms cohabited with earlier reported benthic microbial mats in the photic zone of marginal marine siliciclastic environments 3.2 billion years ago.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Javaux, Emmanuelle J -- Marshall, Craig P -- Bekker, Andrey -- England -- Nature. 2010 Feb 18;463(7283):934-8. doi: 10.1038/nature08793. Epub 2010 Feb 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geology, University of Liege, 17 allee du 6 Aout B18, Liege 4000, Belgium. ej.javaux@ulg.ac.be〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20139963" target="_blank"〉PubMed〈/a〉
    Keywords: Acids ; Bacteria/chemistry/cytology/isolation & purification/metabolism ; Carbon/analysis/chemistry ; Carbon Isotopes ; *Ecosystem ; Eukaryotic Cells/chemistry/cytology ; *Fossils ; Geologic Sediments/*microbiology ; History, Ancient ; Oceans and Seas ; Organic Chemicals/*analysis/chemistry ; *Phylogeny ; Reproducibility of Results ; Seawater/*microbiology ; South Africa ; Spectrum Analysis, Raman ; Sunlight
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  • 5
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    Which way for genetic-test regulation? Assign regulation appropriate to the level of risk (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-08-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Javitt, Gail -- England -- Nature. 2010 Aug 12;466(7308):817-8. doi: 10.1038/466817a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Berman Institute of Bioethics, Johns Hopkins University, USA. gjavitt1@jhu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20703288" target="_blank"〉PubMed〈/a〉
    Keywords: *Consumer Advocacy ; Genetic Counseling/*legislation & jurisprudence/standards ; Genetic Predisposition to Disease/*genetics ; Genetic Testing/*legislation & jurisprudence/*standards ; *Government Regulation ; Humans ; Marketing ; Reproducibility of Results ; United States ; United States Food and Drug Administration/legislation & jurisprudence
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  • 6
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    Active site remodelling accompanies thioester bond formation in the SUMO E1 (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-02-19
    Description: E1 enzymes activate ubiquitin (Ub) and ubiquitin-like (Ubl) proteins in two steps by carboxy-terminal adenylation and thioester bond formation to a conserved catalytic cysteine in the E1 Cys domain. The structural basis for these intermediates remains unknown. Here we report crystal structures for human SUMO E1 in complex with SUMO adenylate and tetrahedral intermediate analogues at 2.45 and 2.6 A, respectively. These structures show that side chain contacts to ATP.Mg are released after adenylation to facilitate a 130 degree rotation of the Cys domain during thioester bond formation that is accompanied by remodelling of key structural elements including the helix that contains the E1 catalytic cysteine, the crossover and re-entry loops, and refolding of two helices that are required for adenylation. These changes displace side chains required for adenylation with side chains required for thioester bond formation. Mutational and biochemical analyses indicate these mechanisms are conserved in other E1s.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2866016/" 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/PMC2866016/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Olsen, Shaun K -- Capili, Allan D -- Lu, Xuequan -- Tan, Derek S -- Lima, Christopher D -- F32 GM075695/GM/NIGMS NIH HHS/ -- F32 GM075695-03/GM/NIGMS NIH HHS/ -- R01 AI068038/AI/NIAID NIH HHS/ -- R01 AI068038-02/AI/NIAID NIH HHS/ -- R01 AI068038-03/AI/NIAID NIH HHS/ -- R01 GM065872/GM/NIGMS NIH HHS/ -- R01 GM065872-09/GM/NIGMS NIH HHS/ -- RR-15301/RR/NCRR NIH HHS/ -- England -- Nature. 2010 Feb 18;463(7283):906-12. doi: 10.1038/nature08765.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology, Sloan-Kettering Institute, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20164921" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; *Biocatalysis ; Catalytic Domain/*physiology ; Conserved Sequence ; Crystallography, X-Ray ; Cysteine/chemistry/metabolism ; Humans ; Magnesium/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; SUMO-1 Protein/*chemistry/*metabolism ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins/metabolism ; Small Ubiquitin-Related Modifier Proteins/metabolism ; Sulfides/*metabolism ; Ubiquitin/metabolism ; Ubiquitin-Activating Enzymes/*chemistry/*metabolism ; Ubiquitins/metabolism
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  • 7
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    A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-05-21
    Description: Type II topoisomerases are required for the management of DNA tangles and supercoils, and are targets of clinical antibiotics and anti-cancer agents. These enzymes catalyse the ATP-dependent passage of one DNA duplex (the transport or T-segment) through a transient, double-stranded break in another (the gate or G-segment), navigating DNA through the protein using a set of dissociable internal interfaces, or 'gates'. For more than 20 years, it has been established that a pair of dimer-related tyrosines, together with divalent cations, catalyse G-segment cleavage. Recent efforts have proposed that strand scission relies on a 'two-metal mechanism', a ubiquitous biochemical strategy that supports vital cellular processes ranging from DNA synthesis to RNA self-splicing. Here we present the structure of the DNA-binding and cleavage core of Saccharomyces cerevisiae topoisomerase II covalently linked to DNA through its active-site tyrosine at 2.5A resolution, revealing for the first time the organization of a cleavage-competent type II topoisomerase configuration. Unexpectedly, metal-soaking experiments indicate that cleavage is catalysed by a novel variation of the classic two-metal approach. Comparative analyses extend this scheme to explain how distantly-related type IA topoisomerases cleave single-stranded DNA, unifying the cleavage mechanisms for these two essential enzyme families. The structure also highlights a hitherto undiscovered allosteric relay that actuates a molecular 'trapdoor' to prevent subunit dissociation during cleavage. This connection illustrates how an indispensable chromosome-disentangling machine auto-regulates DNA breakage to prevent the aberrant formation of mutagenic and cytotoxic genomic lesions.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2882514/" 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/PMC2882514/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schmidt, Bryan H -- Burgin, Alex B -- Deweese, Joseph E -- Osheroff, Neil -- Berger, James M -- CA077373/CA/NCI NIH HHS/ -- GM033944/GM/NIGMS NIH HHS/ -- GM053960/GM/NIGMS NIH HHS/ -- GM08295/GM/NIGMS NIH HHS/ -- R01 CA077373/CA/NCI NIH HHS/ -- R01 CA077373-11S1/CA/NCI NIH HHS/ -- R01 CA077373-12/CA/NCI NIH HHS/ -- R01 GM033944/GM/NIGMS NIH HHS/ -- T32 CA009592/CA/NCI NIH HHS/ -- T32CA09592/CA/NCI NIH HHS/ -- England -- Nature. 2010 Jun 3;465(7298):641-4. doi: 10.1038/nature08974.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20485342" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Base Sequence ; Catalytic Domain ; Crystallography, X-Ray ; DNA/*chemistry/genetics/*metabolism ; DNA Topoisomerases, Type I/*chemistry/*metabolism ; DNA Topoisomerases, Type II/*chemistry/*metabolism ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Saccharomyces cerevisiae/*enzymology ; Tyrosine
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  • 8
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    Germany rising (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-10-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Sep 30;467(7315):499-500. doi: 10.1038/467499b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20881967" target="_blank"〉PubMed〈/a〉
    Keywords: European Union ; Financing, Organized/economics ; Germany ; History, 20th Century ; History, 21st Century ; Internationality ; Politics ; Research Support as Topic/economics/history ; Science/economics/history/*standards/*trends
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  • 9
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    The killing fields (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-09-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Sep 23;467(7314):368. doi: 10.1038/467368a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20864950" target="_blank"〉PubMed〈/a〉
    Keywords: Agriculture/*methods ; Animals ; Cattle ; Disease Reservoirs/microbiology/*statistics & numerical data/*veterinary ; *Federal Government ; Great Britain/epidemiology ; *Mustelidae/microbiology ; Reproducibility of Results ; Tuberculosis Vaccines ; Tuberculosis, Bovine/epidemiology/*prevention & control/transmission ; Vaccination/veterinary
    Print ISSN: 0028-0836
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  • 10
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    Coupled chaperone action in folding and assembly of hexadecameric Rubisco (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-01-16
    Description: Form I Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase), a complex of eight large (RbcL) and eight small (RbcS) subunits, catalyses the fixation of atmospheric CO(2) in photosynthesis. The limited catalytic efficiency of Rubisco has sparked extensive efforts to re-engineer the enzyme with the goal of enhancing agricultural productivity. To facilitate such efforts we analysed the formation of cyanobacterial form I Rubisco by in vitro reconstitution and cryo-electron microscopy. We show that RbcL subunit folding by the GroEL/GroES chaperonin is tightly coupled with assembly mediated by the chaperone RbcX(2). RbcL monomers remain partially unstable and retain high affinity for GroEL until captured by RbcX(2). As revealed by the structure of a RbcL(8)-(RbcX(2))(8) assembly intermediate, RbcX(2) acts as a molecular staple in stabilizing the RbcL subunits as dimers and facilitates RbcL(8) core assembly. Finally, addition of RbcS results in RbcX(2) release and holoenzyme formation. Specific assembly chaperones may be required more generally in the formation of complex oligomeric structures when folding is closely coupled to assembly.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Cuimin -- Young, Anna L -- Starling-Windhof, Amanda -- Bracher, Andreas -- Saschenbrecker, Sandra -- Rao, Bharathi Vasudeva -- Rao, Karnam Vasudeva -- Berninghausen, Otto -- Mielke, Thorsten -- Hartl, F Ulrich -- Beckmann, Roland -- Hayer-Hartl, Manajit -- England -- Nature. 2010 Jan 14;463(7278):197-202. doi: 10.1038/nature08651.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075914" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry/metabolism ; Chaperonin 10/metabolism ; Chaperonin 60/metabolism ; Cryoelectron Microscopy ; Holoenzymes/chemistry/metabolism ; Models, Molecular ; Molecular Chaperones/chemistry/*metabolism ; Protein Binding ; *Protein Folding ; *Protein Multimerization ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Ribulose-Bisphosphate Carboxylase/*chemistry/*metabolism/ultrastructure ; Synechococcus/*chemistry/metabolism
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    The folding cooperativity of a protein is controlled by its chain topology (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-05-25
    Description: The three-dimensional structures of proteins often show a modular architecture comprised of discrete structural regions or domains. Cooperative communication between these regions is important for catalysis, regulation and efficient folding; lack of coupling has been implicated in the formation of fibrils and other misfolding pathologies. How different structural regions of a protein communicate and contribute to a protein's overall energetics and folding, however, is still poorly understood. Here we use a single-molecule optical tweezers approach to induce the selective unfolding of particular regions of T4 lysozyme and monitor the effect on other regions not directly acted on by force. We investigate how the topological organization of a protein (the order of structural elements along the sequence) affects the coupling and folding cooperativity between its domains. To probe the status of the regions not directly subjected to force, we determine the free energy changes during mechanical unfolding using Crooks' fluctuation theorem. We pull on topological variants (circular permutants) and find that the topological organization of the polypeptide chain critically determines the folding cooperativity between domains and thus what parts of the folding/unfolding landscape are explored. We speculate that proteins may have evolved to select certain topologies that increase coupling between regions to avoid areas of the landscape that lead to kinetic trapping and misfolding.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911970/" 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/PMC2911970/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shank, Elizabeth A -- Cecconi, Ciro -- Dill, Jesse W -- Marqusee, Susan -- Bustamante, Carlos -- GM 32543/GM/NIGMS NIH HHS/ -- GM 50945/GM/NIGMS NIH HHS/ -- R01 GM050945/GM/NIGMS NIH HHS/ -- R01 GM050945-17/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jun 3;465(7298):637-40. doi: 10.1038/nature09021. Epub 2010 May 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular & Cell Biology, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20495548" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; Bacteriophage T4/*enzymology ; Models, Molecular ; Mutant Proteins/chemistry/genetics/metabolism ; Optical Tweezers ; Probability ; Protein Denaturation ; *Protein Folding ; Protein Structure, Tertiary ; Viral Proteins/*chemistry/genetics/*metabolism
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  • 12
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    Safeguarding the integrity of protein archive (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-01-30
    Description: 〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4456675/" 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/PMC4456675/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berman, Helen M -- Kleywegt, Gerard J -- Nakamura, Haruki -- Markley, John L -- Burley, Stephen K -- P41 LM005799/LM/NLM NIH HHS/ -- England -- Nature. 2010 Jan 28;463(7280):425. doi: 10.1038/463425c.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20110969" target="_blank"〉PubMed〈/a〉
    Keywords: Databases, Protein/*ethics/*standards ; Ethics, Research ; Reproducibility of Results ; Scientific Misconduct
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    Jasmonate perception by inositol-phosphate-potentiated COI1-JAZ co-receptor (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-10-12
    Description: Jasmonates are a family of plant hormones that regulate plant growth, development and responses to stress. The F-box protein CORONATINE INSENSITIVE 1 (COI1) mediates jasmonate signalling by promoting hormone-dependent ubiquitylation and degradation of transcriptional repressor JAZ proteins. Despite its importance, the mechanism of jasmonate perception remains unclear. Here we present structural and pharmacological data to show that the true Arabidopsis jasmonate receptor is a complex of both COI1 and JAZ. COI1 contains an open pocket that recognizes the bioactive hormone (3R,7S)-jasmonoyl-l-isoleucine (JA-Ile) with high specificity. High-affinity hormone binding requires a bipartite JAZ degron sequence consisting of a conserved alpha-helix for COI1 docking and a loop region to trap the hormone in its binding pocket. In addition, we identify a third critical component of the jasmonate co-receptor complex, inositol pentakisphosphate, which interacts with both COI1 and JAZ adjacent to the ligand. Our results unravel the mechanism of jasmonate perception and highlight the ability of F-box proteins to evolve as multi-component signalling hubs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988090/" 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/PMC2988090/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sheard, Laura B -- Tan, Xu -- Mao, Haibin -- Withers, John -- Ben-Nissan, Gili -- Hinds, Thomas R -- Kobayashi, Yuichi -- Hsu, Fong-Fu -- Sharon, Michal -- Browse, John -- He, Sheng Yang -- Rizo, Josep -- Howe, Gregg A -- Zheng, Ning -- P30 DK056341/DK/NIDDK NIH HHS/ -- P30 DK056341-10/DK/NIDDK NIH HHS/ -- R01 AI068718/AI/NIAID NIH HHS/ -- R01 AI068718-04/AI/NIAID NIH HHS/ -- R01 CA107134/CA/NCI NIH HHS/ -- R01 CA107134-07/CA/NCI NIH HHS/ -- R01 GM057795/GM/NIGMS NIH HHS/ -- R01 GM057795-12/GM/NIGMS NIH HHS/ -- R01AI068718/AI/NIAID NIH HHS/ -- R01GM57795/GM/NIGMS NIH HHS/ -- T32 GM07270/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Nov 18;468(7322):400-5. doi: 10.1038/nature09430. Epub 2010 Oct 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, Box 357280, University of Washington, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20927106" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acids/chemistry/metabolism ; Arabidopsis/chemistry/metabolism ; Arabidopsis Proteins/*chemistry/*metabolism ; Binding Sites ; Crystallography, X-Ray ; Cyclopentanes/chemistry/*metabolism ; F-Box Proteins/chemistry/metabolism ; Indenes/chemistry/metabolism ; Inositol Phosphates/*metabolism ; Isoleucine/analogs & derivatives/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Oxylipins/chemistry/*metabolism ; Peptide Fragments/chemistry/metabolism ; Plant Growth Regulators/chemistry/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Repressor Proteins/*chemistry/*metabolism ; Signal Transduction
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    Questioning the timeline of H1N1 flu vaccination contracts (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-07-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cohen, Deborah -- Carter, Philip -- England -- Nature. 2010 Jul 15;466(7304):315. doi: 10.1038/466315a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20631779" target="_blank"〉PubMed〈/a〉
    Keywords: *Conflict of Interest ; *Drug Industry ; Humans ; *Influenza A Virus, H1N1 Subtype ; Influenza Vaccines/*supply & distribution ; Influenza, Human/*epidemiology/prevention & control/virology ; Reproducibility of Results ; Time Factors ; *Vaccination ; *World Health Organization
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    Microbe gets toxic response (2010)
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    Publication Date: 2010-12-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Katsnelson, Alla -- England -- Nature. 2010 Dec 9;468(7325):741. doi: 10.1038/468741a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21150963" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Arsenic/*metabolism ; Bacteria/cytology/growth & development/*metabolism ; California ; DNA, Bacterial/chemistry/metabolism ; Exobiology ; Life ; Phosphates/metabolism ; Phosphorus/metabolism ; RNA, Bacterial/chemistry/metabolism ; Reproducibility of Results
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    Coherently wired light-harvesting in photosynthetic marine algae at ambient temperature (2010)
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    Publication Date: 2010-02-05
    Description: Photosynthesis makes use of sunlight to convert carbon dioxide into useful biomass and is vital for life on Earth. Crucial components for the photosynthetic process are antenna proteins, which absorb light and transmit the resultant excitation energy between molecules to a reaction centre. The efficiency of these electronic energy transfers has inspired much work on antenna proteins isolated from photosynthetic organisms to uncover the basic mechanisms at play. Intriguingly, recent work has documented that light-absorbing molecules in some photosynthetic proteins capture and transfer energy according to quantum-mechanical probability laws instead of classical laws at temperatures up to 180 K. This contrasts with the long-held view that long-range quantum coherence between molecules cannot be sustained in complex biological systems, even at low temperatures. Here we present two-dimensional photon echo spectroscopy measurements on two evolutionarily related light-harvesting proteins isolated from marine cryptophyte algae, which reveal exceptionally long-lasting excitation oscillations with distinct correlations and anti-correlations even at ambient temperature. These observations provide compelling evidence for quantum-coherent sharing of electronic excitation across the 5-nm-wide proteins under biologically relevant conditions, suggesting that distant molecules within the photosynthetic proteins are 'wired' together by quantum coherence for more efficient light-harvesting in cryptophyte marine algae.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Collini, Elisabetta -- Wong, Cathy Y -- Wilk, Krystyna E -- Curmi, Paul M G -- Brumer, Paul -- Scholes, Gregory D -- England -- Nature. 2010 Feb 4;463(7281):644-7. doi: 10.1038/nature08811.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Institute for Optical Sciences and Centre for Quantum Information and Quantum Control, University of Toronto, 80 St George Street, Toronto, Ontario, M5S 3H6 Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20130647" target="_blank"〉PubMed〈/a〉
    Keywords: Algal Proteins/chemistry/metabolism ; Cryptophyta/*metabolism/*radiation effects ; *Light ; Light-Harvesting Protein Complexes/chemistry/metabolism ; Models, Molecular ; Photons ; Photosynthesis/physiology/*radiation effects ; Protein Conformation ; Quantum Theory ; *Temperature
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    Structural basis for the suppression of skin cancers by DNA polymerase eta (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-06-26
    Description: DNA polymerase eta (Poleta) is unique among eukaryotic polymerases in its proficient ability for error-free replication through ultraviolet-induced cyclobutane pyrimidine dimers, and inactivation of Poleta (also known as POLH) in humans causes the variant form of xeroderma pigmentosum (XPV). We present the crystal structures of Saccharomyces cerevisiae Poleta (also known as RAD30) in ternary complex with a cis-syn thymine-thymine (T-T) dimer and with undamaged DNA. The structures reveal that the ability of Poleta to replicate efficiently through the ultraviolet-induced lesion derives from a simple and yet elegant mechanism, wherein the two Ts of the T-T dimer are accommodated in an active site cleft that is much more open than in other polymerases. We also show by structural, biochemical and genetic analysis that the two Ts are maintained in a stable configuration in the active site via interactions with Gln 55, Arg 73 and Met 74. Together, these features define the basis for Poleta's action on ultraviolet-damaged DNA that is crucial in suppressing the mutagenic and carcinogenic consequences of sun exposure, thereby reducing the incidence of skin cancers in humans.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030469/" 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/PMC3030469/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Silverstein, Timothy D -- Johnson, Robert E -- Jain, Rinku -- Prakash, Louise -- Prakash, Satya -- Aggarwal, Aneel K -- P30 EB009998/EB/NIBIB NIH HHS/ -- R01 CA107650/CA/NCI NIH HHS/ -- R01 CA107650-39/CA/NCI NIH HHS/ -- R01 ES017767/ES/NIEHS NIH HHS/ -- R01 ES017767-01/ES/NIEHS NIH HHS/ -- England -- Nature. 2010 Jun 24;465(7301):1039-43. doi: 10.1038/nature09104.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural and Chemical Biology, Mount Sinai School of Medicine, Box 1677, 1425 Madison Avenue, New York, New York 10029, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20577207" target="_blank"〉PubMed〈/a〉
    Keywords: Biocatalysis ; Catalytic Domain ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; DNA Damage ; DNA-Directed DNA Polymerase/*chemistry/genetics/*metabolism ; Humans ; Kinetics ; Models, Molecular ; Mutation, Missense ; Nucleic Acid Conformation ; Protein Structure, Tertiary ; Pyrimidine Dimers/chemistry/metabolism ; Saccharomyces cerevisiae/*enzymology/genetics ; Skin Neoplasms/*enzymology/genetics ; Structure-Activity Relationship ; Xeroderma Pigmentosum/enzymology/genetics
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    Timeline: Lindau and the zeitgeist (2010)
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    Publication Date: 2010-10-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simmons, John Galbraith -- England -- Nature. 2010 Oct 14;467(7317):S14-5. doi: 10.1038/467S14a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20944614" target="_blank"〉PubMed〈/a〉
    Keywords: Age Factors ; Blogging ; Congresses as Topic/*history/*trends ; Conservation of Natural Resources/trends ; Germany ; History, 20th Century ; History, 21st Century ; *Nobel Prize ; Nuclear Warfare ; *Research Personnel/history/trends ; Science/*history/*trends
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    Science in court (2010)
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    Publication Date: 2010-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Mar 18;464(7287):325. doi: 10.1038/464325a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20237517" target="_blank"〉PubMed〈/a〉
    Keywords: Education, Graduate/trends ; Forensic Sciences/economics/education/organization & administration/*trends ; Reproducibility of Results ; Research/economics/organization & administration/trends ; United States ; United States Government Agencies/economics/organization & administration/trends
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    Francis Collins: One year at the helm (2010)
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    Publication Date: 2010-08-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wadman, Meredith -- England -- Nature. 2010 Aug 12;466(7308):808-10. doi: 10.1038/466808a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20703281" target="_blank"〉PubMed〈/a〉
    Keywords: American Recovery and Reinvestment Act/economics ; Biomedical Research/economics/organization & administration/trends ; Budgets/trends ; Comparative Effectiveness Research ; History, 20th Century ; History, 21st Century ; Human Genome Project/history ; Humans ; National Institutes of Health (U.S.)/*economics/*organization & ; administration/trends ; Religion and Science ; Translational Medical Research ; United States
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    Obituary: Stephen Henry Schneider (1945-2010) (2010)
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    Publication Date: 2010-08-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mastrandrea, Michael D -- England -- Nature. 2010 Aug 19;466(7309):933. doi: 10.1038/466933a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Intergovernmental Panel on Climate Change Working Group II, Stanford University, Stanford, California 94305, USA. mikemas@stanford.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20725032" target="_blank"〉PubMed〈/a〉
    Keywords: Aerosols ; Climate Change/*history ; History, 20th Century ; History, 21st Century ; Policy Making ; United States
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    Increasing springtime ozone mixing ratios in the free troposphere over western North America (2010)
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    Publication Date: 2010-01-22
    Description: In the lowermost layer of the atmosphere-the troposphere-ozone is an important source of the hydroxyl radical, an oxidant that breaks down most pollutants and some greenhouse gases. High concentrations of tropospheric ozone are toxic, however, and have a detrimental effect on human health and ecosystem productivity. Moreover, tropospheric ozone itself acts as an effective greenhouse gas. Much of the present tropospheric ozone burden is a consequence of anthropogenic emissions of ozone precursors resulting in widespread increases in ozone concentrations since the late 1800s. At present, east Asia has the fastest-growing ozone precursor emissions. Much of the springtime east Asian pollution is exported eastwards towards western North America. Despite evidence that the exported Asian pollution produces ozone, no previous study has found a significant increase in free tropospheric ozone concentrations above the western USA since measurements began in the late 1970s. Here we compile springtime ozone measurements from many different platforms across western North America. We show a strong increase in springtime ozone mixing ratios during 1995-2008 and we have some additional evidence that a similar rate of increase in ozone mixing ratio has occurred since 1984. We find that the rate of increase in ozone mixing ratio is greatest when measurements are more heavily influenced by direct transport from Asia. Our result agrees with previous modelling studies, which indicate that global ozone concentrations should be increasing during the early part of the twenty-first century as a result of increasing precursor emissions, especially at northern mid-latitudes, with western North America being particularly sensitive to rising Asian emissions. We suggest that the observed increase in springtime background ozone mixing ratio may hinder the USA's compliance with its ozone air quality standard.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cooper, O R -- Parrish, D D -- Stohl, A -- Trainer, M -- Nedelec, P -- Thouret, V -- Cammas, J P -- Oltmans, S J -- Johnson, B J -- Tarasick, D -- Leblanc, T -- McDermid, I S -- Jaffe, D -- Gao, R -- Stith, J -- Ryerson, T -- Aikin, K -- Campos, T -- Weinheimer, A -- Avery, M A -- England -- Nature. 2010 Jan 21;463(7279):344-8. doi: 10.1038/nature08708.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, USA. owen.r.cooper@noaa.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20090751" target="_blank"〉PubMed〈/a〉
    Keywords: Air Pollutants/analysis/chemistry ; Asia ; Atmosphere/*chemistry ; Ecosystem ; Greenhouse Effect ; History, 20th Century ; History, 21st Century ; North America ; Ozone/*analysis/chemical synthesis/chemistry ; Sample Size ; Seasons
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    Origins and functional impact of copy number variation in the human genome (2009)
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    Publication Date: 2009-10-09
    Description: Structural variations of DNA greater than 1 kilobase in size account for most bases that vary among human genomes, but are still relatively under-ascertained. Here we use tiling oligonucleotide microarrays, comprising 42 million probes, to generate a comprehensive map of 11,700 copy number variations (CNVs) greater than 443 base pairs, of which most (8,599) have been validated independently. For 4,978 of these CNVs, we generated reference genotypes from 450 individuals of European, African or East Asian ancestry. The predominant mutational mechanisms differ among CNV size classes. Retrotransposition has duplicated and inserted some coding and non-coding DNA segments randomly around the genome. Furthermore, by correlation with known trait-associated single nucleotide polymorphisms (SNPs), we identified 30 loci with CNVs that are candidates for influencing disease susceptibility. Despite this, having assessed the completeness of our map and the patterns of linkage disequilibrium between CNVs and SNPs, we conclude that, for complex traits, the heritability void left by genome-wide association studies will not be accounted for by common CNVs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3330748/" 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/PMC3330748/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Conrad, Donald F -- Pinto, Dalila -- Redon, Richard -- Feuk, Lars -- Gokcumen, Omer -- Zhang, Yujun -- Aerts, Jan -- Andrews, T Daniel -- Barnes, Chris -- Campbell, Peter -- Fitzgerald, Tomas -- Hu, Min -- Ihm, Chun Hwa -- Kristiansson, Kati -- Macarthur, Daniel G -- Macdonald, Jeffrey R -- Onyiah, Ifejinelo -- Pang, Andy Wing Chun -- Robson, Sam -- Stirrups, Kathy -- Valsesia, Armand -- Walter, Klaudia -- Wei, John -- Wellcome Trust Case Control Consortium -- Tyler-Smith, Chris -- Carter, Nigel P -- Lee, Charles -- Scherer, Stephen W -- Hurles, Matthew E -- 077006/Z/05/Z/Wellcome Trust/United Kingdom -- 077008/Wellcome Trust/United Kingdom -- 077009/Wellcome Trust/United Kingdom -- 077014/Wellcome Trust/United Kingdom -- 088340/Wellcome Trust/United Kingdom -- GM081533/GM/NIGMS NIH HHS/ -- HG004221/HG/NHGRI NIH HHS/ -- Canadian Institutes of Health Research/Canada -- England -- Nature. 2010 Apr 1;464(7289):704-12. doi: 10.1038/nature08516. Epub 2009 Oct 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19812545" target="_blank"〉PubMed〈/a〉
    Keywords: Continental Population Groups/genetics ; DNA Copy Number Variations/*genetics ; Gene Duplication ; Genetic Predisposition to Disease/*genetics ; Genome, Human/*genetics ; Genome-Wide Association Study ; Genotype ; Haplotypes/genetics ; Humans ; Mutagenesis/*genetics ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results
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    A redox switch in angiotensinogen modulates angiotensin release (2010)
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    Publication Date: 2010-10-12
    Description: Blood pressure is critically controlled by angiotensins, which are vasopressor peptides specifically released by the enzyme renin from the tail of angiotensinogen-a non-inhibitory member of the serpin family of protease inhibitors. Although angiotensinogen has long been regarded as a passive substrate, the crystal structures solved here to 2.1 A resolution show that the angiotensin cleavage site is inaccessibly buried in its amino-terminal tail. The conformational rearrangement that makes this site accessible for proteolysis is revealed in our 4.4 A structure of the complex of human angiotensinogen with renin. The co-ordinated changes involved are seen to be critically linked by a conserved but labile disulphide bridge. Here we show that the reduced unbridged form of angiotensinogen is present in the circulation in a near 40:60 ratio with the oxidized sulphydryl-bridged form, which preferentially interacts with receptor-bound renin. We propose that this redox-responsive transition of angiotensinogen to a form that will more effectively release angiotensin at a cellular level contributes to the modulation of blood pressure. Specifically, we demonstrate the oxidative switch of angiotensinogen to its more active sulphydryl-bridged form in the maternal circulation in pre-eclampsia-the hypertensive crisis of pregnancy that threatens the health and survival of both mother and child.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3024006/" 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/PMC3024006/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Aiwu -- Carrell, Robin W -- Murphy, Michael P -- Wei, Zhenquan -- Yan, Yahui -- Stanley, Peter L D -- Stein, Penelope E -- Broughton Pipkin, Fiona -- Read, Randy J -- 082961/Wellcome Trust/United Kingdom -- BS/05/002/18361/British Heart Foundation/United Kingdom -- MC_U105663142/Medical Research Council/United Kingdom -- PG/08/041/24818/British Heart Foundation/United Kingdom -- PG/09/072/27945/British Heart Foundation/United Kingdom -- British Heart Foundation/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Nov 4;468(7320):108-11. doi: 10.1038/nature09505. Epub 2010 Oct 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK. awz20@cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20927107" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Angiotensinogen/blood/*chemistry/*metabolism ; Angiotensins/chemistry/*metabolism/secretion ; Blood Pressure ; Crystallography, X-Ray ; Disulfides/chemistry/metabolism ; Female ; Humans ; Kinetics ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidative Stress ; Pre-Eclampsia/blood/metabolism ; Pregnancy ; Protein Conformation ; *Protein Processing, Post-Translational ; Renin/chemistry/metabolism
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    Crystal structures of the CusA efflux pump suggest methionine-mediated metal transport (2010)
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    Publication Date: 2010-09-25
    Description: Gram-negative bacteria, such as Escherichia coli, frequently use tripartite efflux complexes in the resistance-nodulation-cell division (RND) family to expel various toxic compounds from the cell. The efflux system CusCBA is responsible for extruding biocidal Cu(I) and Ag(I) ions. No previous structural information was available for the heavy-metal efflux (HME) subfamily of the RND efflux pumps. Here we describe the crystal structures of the inner-membrane transporter CusA in the absence and presence of bound Cu(I) or Ag(I). These CusA structures provide new structural information about the HME subfamily of RND efflux pumps. The structures suggest that the metal-binding sites, formed by a three-methionine cluster, are located within the cleft region of the periplasmic domain. This cleft is closed in the apo-CusA form but open in the CusA-Cu(I) and CusA-Ag(I) structures, which directly suggests a plausible pathway for ion export. Binding of Cu(I) and Ag(I) triggers significant conformational changes in both the periplasmic and transmembrane domains. The crystal structure indicates that CusA has, in addition to the three-methionine metal-binding site, four methionine pairs-three located in the transmembrane region and one in the periplasmic domain. Genetic analysis and transport assays suggest that CusA is capable of actively picking up metal ions from the cytosol, using these methionine pairs or clusters to bind and export metal ions. These structures suggest a stepwise shuttle mechanism for transport between these sites.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2946090/" 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/PMC2946090/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Long, Feng -- Su, Chih-Chia -- Zimmermann, Michael T -- Boyken, Scott E -- Rajashankar, Kanagalaghatta R -- Jernigan, Robert L -- Yu, Edward W -- GM 072014/GM/NIGMS NIH HHS/ -- GM 074027/GM/NIGMS NIH HHS/ -- GM 081680/GM/NIGMS NIH HHS/ -- GM 086431/GM/NIGMS NIH HHS/ -- R01 GM072014/GM/NIGMS NIH HHS/ -- R01 GM074027/GM/NIGMS NIH HHS/ -- R01 GM074027-05/GM/NIGMS NIH HHS/ -- R01 GM086431/GM/NIGMS NIH HHS/ -- R01 GM086431-01A2/GM/NIGMS NIH HHS/ -- RR-15301/RR/NCRR NIH HHS/ -- England -- Nature. 2010 Sep 23;467(7314):484-8. doi: 10.1038/nature09395.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular, Cellular and Developmental Biology Interdepartmental Graduate Program, Iowa State University, Iowa 50011, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20865003" target="_blank"〉PubMed〈/a〉
    Keywords: Apoproteins/chemistry/metabolism ; Binding Sites ; Cell Membrane/metabolism ; Copper/chemistry/*metabolism ; Crystallography, X-Ray ; Cytosol/metabolism ; Escherichia coli/*chemistry ; Escherichia coli Proteins/*chemistry/*metabolism ; Ion Transport ; Membrane Transport Proteins/*chemistry/*metabolism ; Methionine/*metabolism ; Models, Biological ; Models, Molecular ; Periplasm/metabolism ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Silver/chemistry/*metabolism ; Structure-Activity Relationship
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    Structural basis of semaphorin-plexin signalling (2010)
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    Publication Date: 2010-09-30
    Description: Cell-cell signalling of semaphorin ligands through interaction with plexin receptors is important for the homeostasis and morphogenesis of many tissues and is widely studied for its role in neural connectivity, cancer, cell migration and immune responses. SEMA4D and Sema6A exemplify two diverse vertebrate, membrane-spanning semaphorin classes (4 and 6) that are capable of direct signalling through members of the two largest plexin classes, B and A, respectively. In the absence of any structural information on the plexin ectodomain or its interaction with semaphorins the extracellular specificity and mechanism controlling plexin signalling has remained unresolved. Here we present crystal structures of cognate complexes of the semaphorin-binding regions of plexins B1 and A2 with semaphorin ectodomains (human PLXNB1(1-2)-SEMA4D(ecto) and murine PlxnA2(1-4)-Sema6A(ecto)), plus unliganded structures of PlxnA2(1-4) and Sema6A(ecto). These structures, together with biophysical and cellular assays of wild-type and mutant proteins, reveal that semaphorin dimers independently bind two plexin molecules and that signalling is critically dependent on the avidity of the resulting bivalent 2:2 complex (monomeric semaphorin binds plexin but fails to trigger signalling). In combination, our data favour a cell-cell signalling mechanism involving semaphorin-stabilized plexin dimerization, possibly followed by clustering, which is consistent with previous functional data. Furthermore, the shared generic architecture of the complexes, formed through conserved contacts of the amino-terminal seven-bladed beta-propeller (sema) domains of both semaphorin and plexin, suggests that a common mode of interaction triggers all semaphorin-plexin based signalling, while distinct insertions within or between blades of the sema domains determine binding specificity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587840/" 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/PMC3587840/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Janssen, Bert J C -- Robinson, Ross A -- Perez-Branguli, Francesc -- Bell, Christian H -- Mitchell, Kevin J -- Siebold, Christian -- Jones, E Yvonne -- 082301/Wellcome Trust/United Kingdom -- 083111/Wellcome Trust/United Kingdom -- 10976/Cancer Research UK/United Kingdom -- A10976/Cancer Research UK/United Kingdom -- A3964/Cancer Research UK/United Kingdom -- A5261/Cancer Research UK/United Kingdom -- G0700232/Medical Research Council/United Kingdom -- G0700232(82098)/Medical Research Council/United Kingdom -- G0900084/Medical Research Council/United Kingdom -- G9900061/Medical Research Council/United Kingdom -- G9900061(69203)/Medical Research Council/United Kingdom -- Cancer Research UK/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Oct 28;467(7319):1118-22. doi: 10.1038/nature09468. Epub 2010 Sep 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20877282" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antigens, CD/chemistry/genetics/metabolism ; Binding Sites ; Cell Adhesion Molecules/*chemistry/genetics/*metabolism ; Cell Communication ; Crystallography, X-Ray ; Humans ; Ligands ; Mice ; Mice, Inbred C57BL ; Models, Molecular ; NIH 3T3 Cells ; Nerve Tissue Proteins/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Receptors, Cell Surface/chemistry/genetics/metabolism ; Semaphorins/*chemistry/genetics/*metabolism ; *Signal Transduction ; Structure-Activity Relationship
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    Migrastatin analogues target fascin to block tumour metastasis (2010)
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    Publication Date: 2010-04-16
    Description: Tumour metastasis is the primary cause of death of cancer patients. Development of new therapeutics preventing tumour metastasis is urgently needed. Migrastatin is a natural product secreted by Streptomyces, and synthesized migrastatin analogues such as macroketone are potent inhibitors of metastatic tumour cell migration, invasion and metastasis. Here we show that these migrastatin analogues target the actin-bundling protein fascin to inhibit its activity. X-ray crystal structural studies reveal that migrastatin analogues bind to one of the actin-binding sites on fascin. Our data demonstrate that actin cytoskeletal proteins such as fascin can be explored as new molecular targets for cancer treatment, in a similar manner to the microtubule protein tubulin.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2857318/" 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/PMC2857318/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Lin -- Yang, Shengyu -- Jakoncic, Jean -- Zhang, J Jillian -- Huang, Xin-Yun -- CA136837/CA/NCI NIH HHS/ -- R01 CA136837/CA/NCI NIH HHS/ -- R01 CA136837-01A1/CA/NCI NIH HHS/ -- England -- Nature. 2010 Apr 15;464(7291):1062-6. doi: 10.1038/nature08978.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, Cornell University Weill Medical College, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20393565" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/metabolism ; Animals ; Antineoplastic Agents/chemistry/metabolism/pharmacology/therapeutic use ; Binding Sites/drug effects ; Breast Neoplasms/drug therapy/pathology ; Carrier Proteins/*antagonists & inhibitors/chemistry/genetics/metabolism ; Cell Line, Tumor ; Cell Movement/drug effects ; Crystallography, X-Ray ; Drug Resistance, Neoplasm/genetics ; Female ; Humans ; Lung Neoplasms/prevention & control/secondary ; Macrolides/*chemistry/metabolism/*pharmacology/therapeutic use ; Mice ; Mice, Inbred BALB C ; Mice, Inbred NOD ; Mice, SCID ; Microfilament Proteins/*antagonists & inhibitors/chemistry/genetics/metabolism ; Models, Molecular ; Mutation/genetics ; Neoplasm Invasiveness/pathology/prevention & control ; Neoplasm Metastasis/drug therapy/pathology/*prevention & control ; Piperidones/*chemistry/metabolism/*pharmacology/therapeutic use ; Protein Conformation
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    Neurotransmitter/sodium symporter orthologue LeuT has a single high-affinity substrate site (2010)
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    Publication Date: 2010-12-24
    Description: Neurotransmitter/sodium symporters (NSSs) couple the uptake of neurotransmitter with one or more sodium ions, removing neurotransmitter from the synaptic cleft. NSSs are essential to the function of chemical synapses, are associated with multiple neurological diseases and disorders, and are the targets of therapeutic and illicit drugs. LeuT, a prokaryotic orthologue of the NSS family, is a model transporter for understanding the relationships between molecular mechanism and atomic structure in a broad range of sodium-dependent and sodium-independent secondary transporters. At present there is a controversy over whether there are one or two high-affinity substrate binding sites in LeuT. The first-reported crystal structure of LeuT, together with subsequent functional and structural studies, provided direct evidence for a single, high-affinity, centrally located substrate-binding site, defined as the S1 site. Recent binding, flux and molecular simulation studies, however, have been interpreted in terms of a model where there are two high-affinity binding sites: the central, S1, site and a second, the S2 site, located within the extracellular vestibule. Furthermore, it was proposed that the S1 and S2 sites are allosterically coupled such that occupancy of the S2 site is required for the cytoplasmic release of substrate from the S1 site. Here we address this controversy by performing direct measurement of substrate binding to wild-type LeuT and to S2 site mutants using isothermal titration calorimetry, equilibrium dialysis and scintillation proximity assays. In addition, we perform uptake experiments to determine whether the proposed allosteric coupling between the putative S2 site and the S1 site manifests itself in the kinetics of substrate flux. We conclude that LeuT harbours a single, centrally located, high-affinity substrate-binding site and that transport is well described by a simple, single-substrate kinetic mechanism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3079577/" 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/PMC3079577/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Piscitelli, Chayne L -- Krishnamurthy, Harini -- Gouaux, Eric -- R37 MH070039/MH/NIMH NIH HHS/ -- R37 MH070039-07/MH/NIMH NIH HHS/ -- R37 MH070039-08/MH/NIMH NIH HHS/ -- T32 DK007680/DK/NIDDK NIH HHS/ -- T32 DK007680-17/DK/NIDDK NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Dec 23;468(7327):1129-32. doi: 10.1038/nature09581.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21179170" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Humans ; Ionophores/pharmacology ; Kinetics ; Leucine/genetics ; Models, Molecular ; Mutation ; Plasma Membrane Neurotransmitter Transport ; Proteins/*chemistry/genetics/*metabolism ; Protein Transport/drug effects ; Valinomycin/pharmacology
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    Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy (2010)
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    Publication Date: 2010-07-16
    Description: The translocation step of protein synthesis entails large-scale rearrangements of the ribosome-transfer RNA (tRNA) complex. Here we have followed tRNA movement through the ribosome during translocation by time-resolved single-particle electron cryomicroscopy (cryo-EM). Unbiased computational sorting of cryo-EM images yielded 50 distinct three-dimensional reconstructions, showing the tRNAs in classical, hybrid and various novel intermediate states that provide trajectories and kinetic information about tRNA movement through the ribosome. The structures indicate how tRNA movement is coupled with global and local conformational changes of the ribosome, in particular of the head and body of the small ribosomal subunit, and show that dynamic interactions between tRNAs and ribosomal residues confine the path of the tRNAs through the ribosome. The temperature dependence of ribosome dynamics reveals a surprisingly flat energy landscape of conformational variations at physiological temperature. The ribosome functions as a Brownian machine that couples spontaneous conformational changes driven by thermal energy to directed movement.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fischer, Niels -- Konevega, Andrey L -- Wintermeyer, Wolfgang -- Rodnina, Marina V -- Stark, Holger -- England -- Nature. 2010 Jul 15;466(7304):329-33. doi: 10.1038/nature09206.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉3D Electron Cryomicroscopy Group, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20631791" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; Escherichia coli ; Kinetics ; Models, Molecular ; Molecular Conformation ; *Movement ; *Protein Biosynthesis ; RNA, Transfer/genetics/*metabolism ; Ribosome Subunits, Large, Bacterial/chemistry/metabolism ; Ribosome Subunits, Small, Bacterial/chemistry/metabolism ; Ribosomes/chemistry/*metabolism ; Temperature ; Thermodynamics ; Time Factors
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    Structural mechanism of C-type inactivation in K(+) channels (2010)
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    Publication Date: 2010-07-09
    Description: Interconversion between conductive and non-conductive forms of the K(+) channel selectivity filter underlies a variety of gating events, from flicker transitions (at the microsecond timescale) to C-type inactivation (millisecond to second timescale). Here we report the crystal structure of the Streptomyces lividans K(+) channel KcsA in its open-inactivated conformation and investigate the mechanism of C-type inactivation gating at the selectivity filter from channels 'trapped' in a series of partially open conformations. Five conformer classes were identified with openings ranging from 12 A in closed KcsA (Calpha-Calpha distances at Thr 112) to 32 A when fully open. They revealed a remarkable correlation between the degree of gate opening and the conformation and ion occupancy of the selectivity filter. We show that a gradual filter backbone reorientation leads first to a loss of the S2 ion binding site and a subsequent loss of the S3 binding site, presumably abrogating ion conduction. These structures indicate a molecular basis for C-type inactivation in K(+) channels.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3033749/" 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/PMC3033749/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cuello, Luis G -- Jogini, Vishwanath -- Cortes, D Marien -- Perozo, Eduardo -- R01 GM057846/GM/NIGMS NIH HHS/ -- R01 GM057846-15/GM/NIGMS NIH HHS/ -- R01-GM57846/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jul 8;466(7303):203-8. doi: 10.1038/nature09153.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, University of Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20613835" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*antagonists & inhibitors/*chemistry/metabolism ; Binding Sites ; Crystallography, X-Ray ; Electrons ; *Ion Channel Gating ; Kinetics ; Models, Biological ; Models, Molecular ; Potassium/metabolism ; Potassium Channels/*chemistry/metabolism ; Protein Conformation ; Streptomyces lividans/*chemistry ; Structure-Activity Relationship
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    Chagas disease 101 (2010)
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    Publication Date: 2010-06-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clayton, Julie -- England -- Nature. 2010 Jun 24;465(7301):S4-5. doi: 10.1038/nature09220.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20571553" target="_blank"〉PubMed〈/a〉
    Keywords: Acute Disease ; Animals ; Carrier State/epidemiology/immunology/parasitology ; *Chagas Disease/drug therapy/epidemiology/parasitology/transmission ; Chronic Disease/drug therapy/epidemiology ; Clinical Trials as Topic ; History, 16th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; Humans ; Insect Vectors/parasitology ; Latin America/epidemiology/ethnology ; Neglected Diseases/economics ; Nitroimidazoles/pharmacology/therapeutic use ; Trypanocidal Agents/pharmacology/therapeutic use ; Trypanosoma cruzi/immunology/pathogenicity/physiology
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    Two enzymes bound to one transfer RNA assume alternative conformations for consecutive reactions (2010)
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    Publication Date: 2010-10-01
    Description: In most bacteria and all archaea, glutamyl-tRNA synthetase (GluRS) glutamylates both tRNA(Glu) and tRNA(Gln), and then Glu-tRNA(Gln) is selectively converted to Gln-tRNA(Gln) by a tRNA-dependent amidotransferase. The mechanisms by which the two enzymes recognize their substrate tRNA(s), and how they cooperate with each other in Gln-tRNA(Gln) synthesis, remain to be determined. Here we report the formation of the 'glutamine transamidosome' from the bacterium Thermotoga maritima, consisting of tRNA(Gln), GluRS and the heterotrimeric amidotransferase GatCAB, and its crystal structure at 3.35 A resolution. The anticodon-binding body of GluRS recognizes the common features of tRNA(Gln) and tRNA(Glu), whereas the tail body of GatCAB recognizes the outer corner of the L-shaped tRNA(Gln) in a tRNA(Gln)-specific manner. GluRS is in the productive form, as its catalytic body binds to the amino-acid-acceptor arm of tRNA(Gln). In contrast, GatCAB is in the non-productive form: the catalytic body of GatCAB contacts that of GluRS and is located near the acceptor stem of tRNA(Gln), in an appropriate site to wait for the completion of Glu-tRNA(Gln) formation by GluRS. We identified the hinges between the catalytic and anticodon-binding bodies of GluRS and between the catalytic and tail bodies of GatCAB, which allow both GluRS and GatCAB to adopt the productive and non-productive forms. The catalytic bodies of the two enzymes compete for the acceptor arm of tRNA(Gln) and therefore cannot assume their productive forms simultaneously. The transition from the present glutamylation state, with the productive GluRS and the non-productive GatCAB, to the putative amidation state, with the non-productive GluRS and the productive GatCAB, requires an intermediate state with the two enzymes in their non-productive forms, for steric reasons. The proposed mechanism explains how the transamidosome efficiently performs the two consecutive steps of Gln-tRNA(Gln) formation, with a low risk of releasing the unstable intermediate Glu-tRNA(Gln).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ito, Takuhiro -- Yokoyama, Shigeyuki -- England -- Nature. 2010 Sep 30;467(7315):612-6. doi: 10.1038/nature09411.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20882017" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon/genetics ; Biocatalysis ; Crystallography, X-Ray ; Electrophoretic Mobility Shift Assay ; Glutamate-tRNA Ligase/*chemistry/*metabolism ; Models, Molecular ; Molecular Conformation ; Nitrogenous Group Transferases/*chemistry/*metabolism ; Protein Binding ; RNA, Transfer, Gln/biosynthesis/*chemistry/*metabolism ; RNA, Transfer, Glu/chemistry/metabolism ; Staphylococcus aureus/enzymology ; Substrate Specificity ; Thermotoga maritima/*enzymology
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    Galileo's send-off (2010)
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    Publication Date: 2010-11-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Nov 4;468(7320):6. doi: 10.1038/468006a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21048719" target="_blank"〉PubMed〈/a〉
    Keywords: Astronomy/history ; Famous Persons ; History, 17th Century ; History, 18th Century ; History, 21st Century ; Italy ; *Jupiter ; *Space Flight ; United States ; United States National Aeronautics and Space Administration/trends
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    Multiple personal genomes await (2010)
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    Publication Date: 2010-04-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Venter, J Craig -- England -- Nature. 2010 Apr 1;464(7289):676-7. doi: 10.1038/464676a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉J. Craig Venter Institute, La Jolla, California 92121, USA. jcventer@jcvi.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360717" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Continental Population Groups/genetics ; Diploidy ; Female ; Genetic Predisposition to Disease/genetics ; Genetic Variation/genetics ; Genetics, Medical/*trends ; Genome, Human/*genetics ; Genomics/economics/history/*trends ; Haploidy ; Haplotypes/genetics ; History, 20th Century ; History, 21st Century ; Human Genome Project/economics/history ; Humans ; Male ; Phenotype ; Precision Medicine/*trends ; Sequence Analysis, DNA/economics/history/instrumentation/methods
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    Genomics: The tough new variants (2010)
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    Publication Date: 2010-10-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Oct 28;467(7319):1136. doi: 10.1038/4671136a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20981104" target="_blank"〉PubMed〈/a〉
    Keywords: DNA Copy Number Variations/*genetics ; Genome, Human/*genetics ; Genomics/*methods ; Humans ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide/genetics ; Reproducibility of Results
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    Structural basis of oligomerization in the stalk region of dynamin-like MxA (2010)
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    Publication Date: 2010-04-30
    Description: The interferon-inducible dynamin-like myxovirus resistance protein 1 (MxA; also called MX1) GTPase is a key mediator of cell-autonomous innate immunity against pathogens such as influenza viruses. MxA partially localizes to COPI-positive membranes of the smooth endoplasmic reticulum-Golgi intermediate compartment. At the point of infection, it redistributes to sites of viral replication and promotes missorting of essential viral constituents. It has been proposed that the middle domain and the GTPase effector domain of dynamin-like GTPases constitute a stalk that mediates oligomerization and transmits conformational changes from the G domain to the target structure; however, the molecular architecture of this stalk has remained elusive. Here we report the crystal structure of the stalk of human MxA, which folds into a four-helical bundle. This structure tightly oligomerizes in the crystal in a criss-cross pattern involving three distinct interfaces and one loop. Mutations in each of these interaction sites interfere with native assembly, oligomerization, membrane binding and antiviral activity of MxA. On the basis of these results, we propose a structural model for dynamin oligomerization and stimulated GTP hydrolysis that is consistent with previous structural predictions and has functional implications for all members of the dynamin family.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gao, Song -- von der Malsburg, Alexander -- Paeschke, Susann -- Behlke, Joachim -- Haller, Otto -- Kochs, Georg -- Daumke, Oliver -- England -- Nature. 2010 May 27;465(7297):502-6. doi: 10.1038/nature08972. Epub 2010 Apr 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Delbruck-Centrum for Molecular Medicine, Crystallography, Robert-Rossle-Strasse 10, 13125 Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20428112" target="_blank"〉PubMed〈/a〉
    Keywords: Antiviral Agents/chemistry/metabolism/pharmacology ; Binding Sites ; Cell Line ; Crystallography, X-Ray ; Dynamins/*chemistry/metabolism ; GTP Phosphohydrolases/metabolism ; GTP-Binding Proteins/*chemistry/genetics/*metabolism/pharmacology ; Guanosine Triphosphate/metabolism ; Humans ; Hydrolysis ; Hydrophobic and Hydrophilic Interactions ; Influenza A Virus, H5N1 Subtype/drug effects/physiology ; Models, Molecular ; Myxovirus Resistance Proteins ; Protein Conformation ; *Protein Multimerization ; Virus Replication/drug effects
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    NRMT is an alpha-N-methyltransferase that methylates RCC1 and retinoblastoma protein (2010)
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    Publication Date: 2010-07-30
    Description: The post-translational methylation of alpha-amino groups was first discovered over 30 years ago on the bacterial ribosomal proteins L16 and L33 (refs 1, 2), but almost nothing is known about the function or enzymology of this modification. Several other bacterial and eukaryotic proteins have since been shown to be alpha-N-methylated. However, the Ran guanine nucleotide-exchange factor, RCC1, is the only protein for which any biological function of alpha-N-methylation has been identified. Methylation-defective mutants of RCC1 have reduced affinity for DNA and cause mitotic defects, but further characterization of this modification has been hindered by ignorance of the responsible methyltransferase. All fungal and animal N-terminally methylated proteins contain a unique N-terminal motif, Met-(Ala/Pro/Ser)-Pro-Lys, indicating that they may be targets of the same, unknown enzyme. The initiating Met is cleaved, and the exposed alpha-amino group is mono-, di- or trimethylated. Here we report the discovery of the first alpha-N-methyltransferase, which we named N-terminal RCC1 methyltransferase (NRMT). Substrate docking and mutational analysis of RCC1 defined the NRMT recognition sequence and enabled the identification of numerous new methylation targets, including SET (also known as TAF-I or PHAPII) and the retinoblastoma protein, RB. Knockdown of NRMT recapitulates the multi-spindle phenotype seen with methylation-defective RCC1 mutants, demonstrating the importance of alpha-N-methylation for normal bipolar spindle formation and chromosome segregation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939154/" 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/PMC2939154/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tooley, Christine E Schaner -- Petkowski, Janusz J -- Muratore-Schroeder, Tara L -- Balsbaugh, Jeremy L -- Shabanowitz, Jeffrey -- Sabat, Michal -- Minor, Wladek -- Hunt, Donald F -- Macara, Ian G -- R01 GM050526/GM/NIGMS NIH HHS/ -- R01 GM050526-17/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Aug 26;466(7310):1125-8. doi: 10.1038/nature09343.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, Center for Cell Signaling, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA. ces5g@virginia.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20668449" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Cycle Proteins/*metabolism ; Cell Line ; Chromosome Segregation ; Gene Knockdown Techniques ; Guanine Nucleotide Exchange Factors/*metabolism ; HeLa Cells ; Histone Chaperones/metabolism ; Humans ; Methyltransferases/chemistry/genetics/*metabolism ; Models, Molecular ; Mutation/genetics ; Nuclear Proteins/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; Retinoblastoma Protein/*metabolism ; Spindle Apparatus/metabolism ; Transcription Factors/metabolism
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    Structural basis for the photoconversion of a phytochrome to the activated Pfr form (2010)
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    Publication Date: 2010-01-16
    Description: Phytochromes are a collection of bilin-containing photoreceptors that regulate numerous photoresponses in plants and microorganisms through their ability to photointerconvert between a red-light-absorbing, ground state (Pr) and a far-red-light-absorbing, photoactivated state (Pfr). Although the structures of several phytochromes as Pr have been determined, little is known about the structure of Pfr and how it initiates signalling. Here we describe the three-dimensional solution structure of the bilin-binding domain as Pfr, using the cyanobacterial phytochrome from Synechococcus OSB'. Contrary to predictions, light-induced rotation of the A pyrrole ring but not the D ring is the primary motion of the chromophore during photoconversion. Subsequent rearrangements within the protein then affect intradomain and interdomain contact sites within the phytochrome dimer. On the basis of our models, we propose that phytochromes act by propagating reversible light-driven conformational changes in the bilin to altered contacts between the adjacent output domains, which in most phytochromes direct differential phosphotransfer.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2807988/" 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/PMC2807988/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ulijasz, Andrew T -- Cornilescu, Gabriel -- Cornilescu, Claudia C -- Zhang, Junrui -- Rivera, Mario -- Markley, John L -- Vierstra, Richard D -- P41 RR002301/RR/NCRR NIH HHS/ -- P41 RR002301-237748/RR/NCRR NIH HHS/ -- U54 GM074901/GM/NIGMS NIH HHS/ -- U54 GM074901-05/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jan 14;463(7278):250-4. doi: 10.1038/nature08671.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Genetics and, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075921" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/chemistry/metabolism/radiation effects ; Bacterial Proteins/*chemistry/genetics/metabolism/*radiation effects ; Bile Pigments/chemistry/metabolism/radiation effects ; Binding Sites ; *Light ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Phytochrome/*chemistry/genetics/metabolism/*radiation effects ; Protein Kinases/*chemistry/genetics/metabolism/*radiation effects ; Protein Structure, Tertiary/radiation effects ; Rotation ; Synechococcus/*chemistry/genetics
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    Neurological disease mutations compromise a C-terminal ion pathway in the Na(+)/K(+)-ATPase (2010)
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    Publication Date: 2010-08-20
    Description: The Na(+)/K(+)-ATPase pumps three sodium ions out of and two potassium ions into the cell for each ATP molecule that is split, thereby generating the chemical and electrical gradients across the plasma membrane that are essential in, for example, signalling, secondary transport and volume regulation in animal cells. Crystal structures of the potassium-bound form of the pump revealed an intimate docking of the alpha-subunit carboxy terminus at the transmembrane domain. Here we show that this element is a key regulator of a previously unrecognized ion pathway. Current models of P-type ATPases operate with a single ion conduit through the pump, but our data suggest an additional pathway in the Na(+)/K(+)-ATPase between the ion-binding sites and the cytoplasm. The C-terminal pathway allows a cytoplasmic proton to enter and stabilize site III when empty in the potassium-bound state, and when potassium is released the proton will also return to the cytoplasm, thus allowing an overall asymmetric stoichiometry of the transported ions. The C terminus controls the gate to the pathway. Its structure is crucial for pump function, as demonstrated by at least eight mutations in the region that cause severe neurological diseases. This novel model for ion transport by the Na(+)/K(+)-ATPase is established by electrophysiological studies of C-terminal mutations in familial hemiplegic migraine 2 (FHM2) and is further substantiated by molecular dynamics simulations. A similar ion regulation is likely to apply to the H(+)/K(+)-ATPase and the Ca(2+)-ATPase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Poulsen, Hanne -- Khandelia, Himanshu -- Morth, J Preben -- Bublitz, Maike -- Mouritsen, Ole G -- Egebjerg, Jan -- Nissen, Poul -- England -- Nature. 2010 Sep 2;467(7311):99-102. doi: 10.1038/nature09309. Epub 2010 Aug 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉PUMPKIN - Centre for Membrane Pumps in Cells and Disease, Danish National Research Foundation, Department of Molecular Biology, Aarhus University, DK-8000 Aarhus C, Denmark. hp@mb.au.dk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20720542" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Crystallography, X-Ray ; Humans ; *Ion Transport ; Migraine with Aura/genetics/*metabolism ; Models, Molecular ; Molecular Dynamics Simulation ; Oocytes/metabolism ; Potassium/metabolism ; Protons ; Sodium-Potassium-Exchanging ATPase/*chemistry/*metabolism ; Squalus acanthias/metabolism ; Sus scrofa/metabolism ; Xenopus
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    Biologists tackle cells' identity crisis (2010)
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    Publication Date: 2010-06-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Katsnelson, Alla -- England -- Nature. 2010 Jun 3;465(7298):537. doi: 10.1038/465537a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20520682" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Culture Techniques/*methods/*standards ; Cell Line/*classification ; Cell Lineage ; *DNA Fingerprinting/methods/standards ; HeLa Cells ; Humans ; Organ Specificity ; Reproducibility of Results
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    Super-resolution biomolecular crystallography with low-resolution data (2010)
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    Publication Date: 2010-04-09
    Description: X-ray diffraction plays a pivotal role in the understanding of biological systems by revealing atomic structures of proteins, nucleic acids and their complexes, with much recent interest in very large assemblies like the ribosome. As crystals of such large assemblies often diffract weakly (resolution worse than 4 A), we need methods that work at such low resolution. In macromolecular assemblies, some of the components may be known at high resolution, whereas others are unknown: current refinement methods fail as they require a high-resolution starting structure for the entire complex. Determining the structure of such complexes, which are often of key biological importance, should be possible in principle as the number of independent diffraction intensities at a resolution better than 5 A generally exceeds the number of degrees of freedom. Here we introduce a method that adds specific information from known homologous structures but allows global and local deformations of these homology models. Our approach uses the observation that local protein structure tends to be conserved as sequence and function evolve. Cross-validation with R(free) (the free R-factor) determines the optimum deformation and influence of the homology model. For test cases at 3.5-5 A resolution with known structures at high resolution, our method gives significant improvements over conventional refinement in the model as monitored by coordinate accuracy, the definition of secondary structure and the quality of electron density maps. For re-refinements of a representative set of 19 low-resolution crystal structures from the Protein Data Bank, we find similar improvements. Thus, a structure derived from low-resolution diffraction data can have quality similar to a high-resolution structure. Our method is applicable to the study of weakly diffracting crystals using X-ray micro-diffraction as well as data from new X-ray light sources. Use of homology information is not restricted to X-ray crystallography and cryo-electron microscopy: as optical imaging advances to subnanometre resolution, it can use similar tools.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2859093/" 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/PMC2859093/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schroder, Gunnar F -- Levitt, Michael -- Brunger, Axel T -- EY016525/EY/NEI NIH HHS/ -- GM63718/GM/NIGMS NIH HHS/ -- R01 GM063817/GM/NIGMS NIH HHS/ -- U54 GM072970/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Apr 22;464(7292):1218-22. doi: 10.1038/nature08892. Epub 2010 Apr 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Strukturbiologie und Biophysik (ISB-3), Forschungszentrum Julich, 52425 Julich, Germany. gu.schroeder@fz-juelich.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20376006" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallization ; Crystallography, X-Ray/*methods ; Databases, Protein ; Electrons ; Likelihood Functions ; Models, Molecular ; Oligopeptides/chemistry ; Protein Conformation ; Software ; Static Electricity
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    Has the revolution arrived? (2010)
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    Publication Date: 2010-04-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Collins, Francis -- England -- Nature. 2010 Apr 1;464(7289):674-5. doi: 10.1038/464674a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Institutes of Health, Bethesda, Maryland 20892, USA. francis.collins@nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360716" target="_blank"〉PubMed〈/a〉
    Keywords: Access to Information ; Genetic Predisposition to Disease/genetics ; Genetics, Medical/*trends ; Genome, Human/*genetics ; Genome-Wide Association Study ; Genomics/economics/history/*trends ; Haplotypes/genetics ; History, 20th Century ; History, 21st Century ; Humans ; Precision Medicine/*trends ; Sequence Analysis, DNA/economics/history/trends
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    Upbeat oil report questioned (2010)
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    Publication Date: 2010-08-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schrope, Mark -- England -- Nature. 2010 Aug 12;466(7308):802. doi: 10.1038/466802a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20703275" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Disasters/*statistics & numerical data ; Ecology ; *Ecosystem ; Marine Biology ; Oceanography ; Oceans and Seas ; Petroleum/adverse effects/*analysis ; Reproducibility of Results ; Seawater/*chemistry ; *Uncertainty ; Volatilization
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    Deepwater Horizon: A scientist at the centre of the spill (2010)
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    Publication Date: 2010-08-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schrope, Mark -- England -- Nature. 2010 Aug 5;466(7307):680-4. doi: 10.1038/466680a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20686546" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Disasters/*statistics & numerical data ; *Expeditions/trends ; Food Chain ; Geologic Sediments/analysis/chemistry ; History, 21st Century ; Industry/legislation & jurisprudence ; Liability, Legal ; Methane/analysis/metabolism ; Oceans and Seas ; Oxygen/analysis/metabolism ; Petroleum/*adverse effects/*analysis/poisoning ; *Research ; *Research Personnel ; Seawater/analysis/*chemistry ; United States ; United States Government Agencies/legislation & jurisprudence ; Water Microbiology
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    The lost legacy of the last great oil spill (2010)
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    Publication Date: 2010-07-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Schrope, Mark -- England -- Nature. 2010 Jul 15;466(7304):304-5. doi: 10.1038/466304a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20631769" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Disasters/history ; *Ecosystem ; Fisheries/history/statistics & numerical data ; History, 20th Century ; History, 21st Century ; Marine Biology/history/trends ; Mexico ; Oceans and Seas ; Ostreidae ; Petroleum/*analysis/*toxicity ; Population Dynamics ; Research/history/*statistics & numerical data/trends ; Seawater/*chemistry
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    Standard issue (2010)
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    Publication Date: 2010-08-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Aug 12;466(7308):797. doi: 10.1038/466797a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20703263" target="_blank"〉PubMed〈/a〉
    Keywords: *Consumer Advocacy ; Genetic Testing/*legislation & jurisprudence/*standards ; Government Regulation ; Humans ; Marketing/standards ; Oligonucleotide Array Sequence Analysis ; Reproducibility of Results ; United States ; United States Food and Drug Administration/legislation & jurisprudence
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    Chemistry: Breaking the billion-hertz barrier (2010)
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    Publication Date: 2010-02-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhattacharya, Ananyo -- England -- Nature. 2010 Feb 4;463(7281):605-6. doi: 10.1038/463605a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20130626" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Child ; Crystallization ; Crystallography, X-Ray ; Diacylglycerol Kinase/chemistry ; Humans ; Magnetic Resonance Spectroscopy/*instrumentation/*methods ; Metabolomics/instrumentation/methods ; Models, Molecular ; Protein Conformation
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    How accurate are cancer cell lines? (2010)
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    Publication Date: 2010-02-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Borrell, Brendan -- England -- Nature. 2010 Feb 18;463(7283):858. doi: 10.1038/463858a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20164888" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line, Tumor/*metabolism ; Genetics, Medical/*methods/*trends ; Genomics/*methods/*trends ; Humans ; Neoplasms/*genetics/*pathology ; Reproducibility of Results ; Sequence Analysis, DNA/trends
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    The weight of evidence (2010)
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    Publication Date: 2010-04-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Apr 22;464(7292):1103-4. doi: 10.1038/4641103b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20414265" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Benzhydryl Compounds ; Chemical Industry/*legislation & jurisprudence/*standards ; *Evaluation Studies as Topic ; *Federal Government ; Guidelines as Topic ; Humans ; Phenols/adverse effects/toxicity ; Reproducibility of Results ; Safety/*legislation & jurisprudence/*standards ; *Toxicity Tests/methods/standards ; United States
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    Obituary: Harry Whittington (1916-2010) (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-08-06
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Briggs, Derek E G -- England -- Nature. 2010 Aug 5;466(7307):706. doi: 10.1038/466706a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geology and Geophysics, and the Peabody Museum of Natural History, Yale University, New Haven, Connecticut 06520, USA. derek.briggs@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20686564" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; British Columbia ; *Fossils ; Geologic Sediments/analysis/chemistry ; Great Britain ; History, 20th Century ; History, 21st Century ; Paleontology/*history ; United States
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    Floods linked to San Andreas quakes (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-01-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2010 Jan 7;463(7277):16. doi: 10.1038/463016a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20054370" target="_blank"〉PubMed〈/a〉
    Keywords: California ; Disasters/prevention & control/statistics & numerical data ; Earthquakes/history/*statistics & numerical data ; Floods/history/*statistics & numerical data ; Fresh Water ; History, 15th Century ; History, 18th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; *Risk Management ; Rivers ; Water Movements
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Climate e-mails: man's mark is clear in thermometer record (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-01-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉von Storch, Hans -- Allen, Myles -- England -- Nature. 2010 Jan 7;463(7277):25. doi: 10.1038/463025a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20054378" target="_blank"〉PubMed〈/a〉
    Keywords: *Electronic Mail ; *Global Warming/statistics & numerical data ; Great Britain ; *Human Activities/statistics & numerical data ; Reproducibility of Results ; Research Personnel/ethics ; *Temperature
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    Crystal structure of DNA-PKcs reveals a large open-ring cradle comprised of HEAT repeats (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-12-22
    Description: Broken chromosomes arising from DNA double-strand breaks result from endogenous events such as the production of reactive oxygen species during cellular metabolism, as well as from exogenous sources such as ionizing radiation. Left unrepaired or incorrectly repaired they can lead to genomic changes that may result in cell death or cancer. DNA-dependent protein kinase (DNA-PK), a holoenzyme that comprises the DNA-PK catalytic subunit (DNA-PKcs) and the heterodimer Ku70/Ku80, has a major role in non-homologous end joining-the main pathway in mammals used to repair double-strand breaks. DNA-PKcs is a serine/threonine protein kinase comprising a single polypeptide chain of 4,128 amino acids and belonging to the phosphatidylinositol-3-OH kinase (PI(3)K)-related protein family. DNA-PKcs is involved in the sensing and transmission of DNA damage signals to proteins such as p53, setting off events that lead to cell cycle arrest. It phosphorylates a wide range of substrates in vitro, including Ku70/Ku80, which is translocated along DNA. Here we present the crystal structure of human DNA-PKcs at 6.6 A resolution, in which the overall fold is clearly visible, to our knowledge, for the first time. The many alpha-helical HEAT repeats (helix-turn-helix motifs) facilitate bending and allow the polypeptide chain to fold into a hollow circular structure. The carboxy-terminal kinase domain is located on top of this structure, and a small HEAT repeat domain that probably binds DNA is inside. The structure provides a flexible cradle to promote DNA double-strand-break repair.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2811870/" 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/PMC2811870/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sibanda, Bancinyane L -- Chirgadze, Dimitri Y -- Blundell, Tom L -- 079281/Wellcome Trust/United Kingdom -- A3846/Cancer Research UK/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2010 Jan 7;463(7277):118-21. doi: 10.1038/nature08648. Epub 2009 Dec 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Cambridge, Old Addenbrooke's site, 80 Tennis Court Road, Cambridge CB2 1GA, UK. lynn@cryst.bioc.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20023628" target="_blank"〉PubMed〈/a〉
    Keywords: Antigens, Nuclear/chemistry ; Catalytic Domain ; Crystallography, X-Ray ; DNA/metabolism ; DNA Breaks, Double-Stranded ; DNA-Activated Protein Kinase/*chemistry/metabolism ; DNA-Binding Proteins/chemistry ; HeLa Cells ; *Helix-Turn-Helix Motifs ; Humans ; Models, Molecular ; Nuclear Proteins/*chemistry/metabolism ; Protein Folding ; Protein Structure, Secondary
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    A conserved spider silk domain acts as a molecular switch that controls fibre assembly (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-05-14
    Description: A huge variety of proteins are able to form fibrillar structures, especially at high protein concentrations. Hence, it is surprising that spider silk proteins can be stored in a soluble form at high concentrations and transformed into extremely stable fibres on demand. Silk proteins are reminiscent of amphiphilic block copolymers containing stretches of polyalanine and glycine-rich polar elements forming a repetitive core flanked by highly conserved non-repetitive amino-terminal and carboxy-terminal domains. The N-terminal domain comprises a secretion signal, but further functions remain unassigned. The C-terminal domain was implicated in the control of solubility and fibre formation initiated by changes in ionic composition and mechanical stimuli known to align the repetitive sequence elements and promote beta-sheet formation. However, despite recent structural data, little is known about this remarkable behaviour in molecular detail. Here we present the solution structure of the C-terminal domain of a spider dragline silk protein and provide evidence that the structural state of this domain is essential for controlled switching between the storage and assembly forms of silk proteins. In addition, the C-terminal domain also has a role in the alignment of secondary structural features formed by the repetitive elements in the backbone of spider silk proteins, which is known to be important for the mechanical properties of the fibre.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hagn, Franz -- Eisoldt, Lukas -- Hardy, John G -- Vendrely, Charlotte -- Coles, Murray -- Scheibel, Thomas -- Kessler, Horst -- England -- Nature. 2010 May 13;465(7295):239-42. doi: 10.1038/nature08936.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Integrated Protein Science (CIPSM), Technische Universitat Munchen, 85747 Garching, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20463741" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Calorimetry, Differential Scanning ; Circular Dichroism ; *Conserved Sequence ; Hydrophobic and Hydrophilic Interactions ; Magnetic Resonance Spectroscopy ; Models, Molecular ; Protein Structure, Tertiary ; Silk/*chemistry/*metabolism ; Spectrometry, Fluorescence ; Spectroscopy, Fourier Transform Infrared ; Spiders/*chemistry
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    Science in court: head case (2010)
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    Publication Date: 2010-03-20
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hughes, Virginia -- England -- Nature. 2010 Mar 18;464(7287):340-2. doi: 10.1038/464340a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20237536" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Antisocial Personality Disorder/physiopathology/psychology ; Child ; Female ; Forensic Sciences/ethics/*methods/trends ; Homicide/*legislation & jurisprudence/*psychology ; Humans ; Insanity Defense ; Magnetic Resonance Imaging/standards/*utilization ; Male ; *Neurosciences ; Positron-Emission Tomography/utilization ; Rape/legislation & jurisprudence/psychology ; Reproducibility of Results
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    Network organization of the human autophagy system (2010)
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    Publication Date: 2010-06-22
    Description: Autophagy, the process by which proteins and organelles are sequestered in autophagosomal vesicles and delivered to the lysosome/vacuole for degradation, provides a primary route for turnover of stable and defective cellular proteins. Defects in this system are linked with numerous human diseases. Although conserved protein kinase, lipid kinase and ubiquitin-like protein conjugation subnetworks controlling autophagosome formation and cargo recruitment have been defined, our understanding of the global organization of this system is limited. Here we report a proteomic analysis of the autophagy interaction network in human cells under conditions of ongoing (basal) autophagy, revealing a network of 751 interactions among 409 candidate interacting proteins with extensive connectivity among subnetworks. Many new autophagy interaction network components have roles in vesicle trafficking, protein or lipid phosphorylation and protein ubiquitination, and affect autophagosome number or flux when depleted by RNA interference. The six ATG8 orthologues in humans (MAP1LC3/GABARAP proteins) interact with a cohort of 67 proteins, with extensive binding partner overlap between family members, and frequent involvement of a conserved surface on ATG8 proteins known to interact with LC3-interacting regions in partner proteins. These studies provide a global view of the mammalian autophagy interaction landscape and a resource for mechanistic analysis of this critical protein homeostasis pathway.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2901998/" 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/PMC2901998/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Behrends, Christian -- Sowa, Mathew E -- Gygi, Steven P -- Harper, J Wade -- R01 AG011085/AG/NIA NIH HHS/ -- R01 AG011085-18/AG/NIA NIH HHS/ -- R01 GM054137/GM/NIGMS NIH HHS/ -- R01 GM054137-14/GM/NIGMS NIH HHS/ -- R01 GM054137-14S1/GM/NIGMS NIH HHS/ -- R01 GM054137-15/GM/NIGMS NIH HHS/ -- R01 GM070565/GM/NIGMS NIH HHS/ -- R01 GM070565-05S1/GM/NIGMS NIH HHS/ -- R01 GM095567/GM/NIGMS NIH HHS/ -- England -- Nature. 2010 Jul 1;466(7302):68-76. doi: 10.1038/nature09204. Epub 2010 Jun 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20562859" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/genetics/metabolism ; Autophagy/genetics/*physiology ; Homeostasis ; Humans ; Microfilament Proteins/genetics/metabolism ; Phagosomes ; Phosphorylation ; Protein Binding ; *Protein Interaction Mapping ; Proteomics ; RNA Interference ; Reproducibility of Results ; Ubiquitination
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    A painful remedy (2010)
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    Publication Date: 2010-11-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Nov 4;468(7320):6. doi: 10.1038/468006b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21048718" target="_blank"〉PubMed〈/a〉
    Keywords: Periodicals as Topic/*standards/statistics & numerical data ; Reproducibility of Results ; Research Personnel/ethics/statistics & numerical data ; *Retraction of Publication as Topic ; Scientific Misconduct/statistics & numerical data
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    Ligand-specific regulation of the extracellular surface of a G-protein-coupled receptor (2010)
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    Publication Date: 2010-01-08
    Description: G-protein-coupled receptors (GPCRs) are seven-transmembrane proteins that mediate most cellular responses to hormones and neurotransmitters. They are the largest group of therapeutic targets for a broad spectrum of diseases. Recent crystal structures of GPCRs have revealed structural conservation extending from the orthosteric ligand-binding site in the transmembrane core to the cytoplasmic G-protein-coupling domains. In contrast, the extracellular surface (ECS) of GPCRs is remarkably diverse and is therefore an ideal target for the discovery of subtype-selective drugs. However, little is known about the functional role of the ECS in receptor activation, or about conformational coupling of this surface to the native ligand-binding pocket. Here we use NMR spectroscopy to investigate ligand-specific conformational changes around a central structural feature in the ECS of the beta(2) adrenergic receptor: a salt bridge linking extracellular loops 2 and 3. Small-molecule drugs that bind within the transmembrane core and exhibit different efficacies towards G-protein activation (agonist, neutral antagonist and inverse agonist) also stabilize distinct conformations of the ECS. We thereby demonstrate conformational coupling between the ECS and the orthosteric binding site, showing that drugs targeting this diverse surface could function as allosteric modulators with high subtype selectivity. Moreover, these studies provide a new insight into the dynamic behaviour of GPCRs not addressable by static, inactive-state crystal structures.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805469/" 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/PMC2805469/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bokoch, Michael P -- Zou, Yaozhong -- Rasmussen, Soren G F -- Liu, Corey W -- Nygaard, Rie -- Rosenbaum, Daniel M -- Fung, Juan Jose -- Choi, Hee-Jung -- Thian, Foon Sun -- Kobilka, Tong Sun -- Puglisi, Joseph D -- Weis, William I -- Pardo, Leonardo -- Prosser, R Scott -- Mueller, Luciano -- Kobilka, Brian K -- GM56169/GM/NIGMS NIH HHS/ -- NS028471/NS/NINDS NIH HHS/ -- R01 GM056169/GM/NIGMS NIH HHS/ -- R01 GM056169-13/GM/NIGMS NIH HHS/ -- R21 MH082313/MH/NIMH NIH HHS/ -- R21 MH082313-01A1/MH/NIMH NIH HHS/ -- R37 NS028471/NS/NINDS NIH HHS/ -- R37 NS028471-19/NS/NINDS NIH HHS/ -- England -- Nature. 2010 Jan 7;463(7277):108-12. doi: 10.1038/nature08650.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20054398" target="_blank"〉PubMed〈/a〉
    Keywords: Adrenergic beta-2 Receptor Agonists ; Adrenergic beta-2 Receptor Antagonists ; Allosteric Regulation/drug effects ; Binding Sites ; Crystallography, X-Ray ; Drug Inverse Agonism ; Ethanolamines/pharmacology ; Formoterol Fumarate ; Humans ; Ligands ; Lysine/analogs & derivatives/metabolism ; Methylation ; Models, Molecular ; Mutant Proteins ; Nuclear Magnetic Resonance, Biomolecular ; Propanolamines/metabolism/pharmacology ; Protein Structure, Tertiary/drug effects ; Receptors, Adrenergic, beta-2/*chemistry/*metabolism ; Static Electricity ; Substrate Specificity
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    To make progress we must remember and learn from the past (2010)
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    Publication Date: 2010-02-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Penders, Bart -- Vermeulen, Niki -- Parker, John N -- England -- Nature. 2010 Jan 14;463(7278):157. doi: 10.1038/463157d.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20075896" target="_blank"〉PubMed〈/a〉
    Keywords: Government ; History, 20th Century ; History, 21st Century ; *Learning ; Private Sector ; Public Policy ; Science/*history/*methods/trends ; *Search Engine ; Universities
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    The prion protein as a receptor for amyloid-beta (2010)
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    Publication Date: 2010-08-13
    Description: Increased levels of brain amyloid-beta, a secreted peptide cleavage product of amyloid precursor protein (APP), is believed to be critical in the aetiology of Alzheimer's disease. Increased amyloid-beta can cause synaptic depression, reduce the number of spine protrusions (that is, sites of synaptic contacts) and block long-term synaptic potentiation (LTP), a form of synaptic plasticity; however, the receptor through which amyloid-beta produces these synaptic perturbations has remained elusive. Lauren et al. suggested that binding between oligomeric amyloid-beta (a form of amyloid-beta thought to be most active) and the cellular prion protein (PrP(C)) is necessary for synaptic perturbations. Here we show that PrP(C) is not required for amyloid-beta-induced synaptic depression, reduction in spine density, or blockade of LTP; our results indicate that amyloid-beta-mediated synaptic defects do not require PrP(c).〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057871/" 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/PMC3057871/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kessels, Helmut W -- Nguyen, Louis N -- Nabavi, Sadegh -- Malinow, Roberto -- R01 AG032132/AG/NIA NIH HHS/ -- R01 AG032132-14/AG/NIA NIH HHS/ -- R01 AG032132-15/AG/NIA NIH HHS/ -- R01 AG032132-17/AG/NIA NIH HHS/ -- R01 AG032132-18/AG/NIA NIH HHS/ -- R01 MH049159/MH/NIMH NIH HHS/ -- R01 MH049159-09/MH/NIMH NIH HHS/ -- R01 MH049159-21/MH/NIMH NIH HHS/ -- R01 MH049159-22/MH/NIMH NIH HHS/ -- England -- Nature. 2010 Aug 12;466(7308):E3-4; discussion E4-5. doi: 10.1038/nature09217.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Neural Circuits and Behavior, 9500 Gilman Drive 0634, University of California at San Diego, La Jolla, California 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20703260" target="_blank"〉PubMed〈/a〉
    Keywords: Alzheimer Disease/metabolism/pathology ; Amyloid beta-Peptides/chemistry/genetics/*metabolism ; Animals ; Learning/physiology ; Mice ; Mice, Inbred C57BL ; Mice, Transgenic ; PrPC Proteins/deficiency/genetics/*metabolism ; Reproducibility of Results ; Serotonin/metabolism ; Synapses/*metabolism/*pathology ; Synaptic Transmission
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    The human genome at ten (2010)
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    Publication Date: 2010-04-03
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2010 Apr 1;464(7289):649-50. doi: 10.1038/464649a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20360688" target="_blank"〉PubMed〈/a〉
    Keywords: Data Collection ; Genetic Testing/trends ; Genetics, Medical/*trends ; Genome, Human/*genetics ; Genomics/economics/*history/trends ; Haplotypes/genetics ; History, 20th Century ; History, 21st Century ; Human Genome Project/*history ; Humans ; Time Factors
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    Inferring echolocation in ancient bats (2010)
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    Publication Date: 2010-08-21
    Description: Laryngeal echolocation, used by most living bats to form images of their surroundings and to detect and capture flying prey, is considered to be a key innovation for the evolutionary success of bats, and palaeontologists have long sought osteological correlates of echolocation that can be used to infer the behaviour of fossil bats. Veselka et al. argued that the most reliable trait indicating echolocation capabilities in bats is an articulation between the stylohyal bone (part of the hyoid apparatus that supports the throat and larynx) and the tympanic bone, which forms the floor of the middle ear. They examined the oldest and most primitive known bat, Onychonycteris finneyi (early Eocene, USA), and argued that it showed evidence of this stylohyal-tympanic articulation, from which they concluded that O. finneyi may have been capable of echolocation. We disagree with their interpretation of key fossil data and instead argue that O. finneyi was probably not an echolocating bat.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simmons, Nancy B -- Seymour, Kevin L -- Habersetzer, Jorg -- Gunnell, Gregg F -- England -- Nature. 2010 Aug 19;466(7309):E8; discussion E9. doi: 10.1038/nature09219.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉American Museum of Natural History, Central Park West at 79th Street, New York, New York 10024, USA. simmons@amnh.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20724993" target="_blank"〉PubMed〈/a〉
    Keywords: Animal Structures/physiology ; Animals ; Bone and Bones/physiology ; Chiroptera/anatomy & histology/*physiology ; Echolocation/*physiology ; *Fossils ; Models, Biological ; Reproducibility of Results
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    Genomics goes beyond DNA sequence (2010)
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    Publication Date: 2010-05-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Katsnelson, Alla -- England -- Nature. 2010 May 13;465(7295):145. doi: 10.1038/465145a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20463710" target="_blank"〉PubMed〈/a〉
    Keywords: *DNA Methylation ; Epigenesis, Genetic/*genetics ; Genome, Human/genetics ; Genomics/*methods ; Humans ; Models, Molecular ; Neoplasms/genetics ; Sequence Analysis, DNA/*methods
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    Benoit Mandelbrot (1924-2010) (2010)
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    Publication Date: 2010-11-19
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gomory, Ralph -- England -- Nature. 2010 Nov 18;468(7322):378. doi: 10.1038/468378a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21085164" target="_blank"〉PubMed〈/a〉
    Keywords: Fractals/*history ; France ; History, 20th Century ; History, 21st Century ; Mathematics/history ; Nature ; Poland ; United States
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    Palaeogenetics: Icy resolve (2010)
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    Publication Date: 2010-02-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2010 Feb 11;463(7282):724-5. doi: 10.1038/463724a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20148008" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arctic Regions ; Cryopreservation ; DNA/genetics/isolation & purification ; DNA, Mitochondrial/analysis/genetics ; Denmark ; Emigration and Immigration/*history ; Feces ; Fossils ; Genetics, Medical/history ; Genome, Human/*genetics ; Greenland/ethnology ; History, 20th Century ; History, 21st Century ; History, Ancient ; Humans ; Inuits/*ethnology/*history ; Male ; Paleontology/*history ; Phylogeny ; Reproducibility of Results ; Sequence Analysis, DNA ; Siberia/ethnology
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    Still looking for that woodpecker (2010)
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    Publication Date: 2010-02-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dalton, Rex -- England -- Nature. 2010 Feb 11;463(7282):718-9. doi: 10.1038/463718a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20148004" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Birds ; Conservation of Natural Resources/economics/*trends ; *Extinction, Biological ; Reproducibility of Results
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    Predicting protein structures with a multiplayer online game (2010)
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    Publication Date: 2010-08-06
    Description: People exert large amounts of problem-solving effort playing computer games. Simple image- and text-recognition tasks have been successfully 'crowd-sourced' through games, but it is not clear if more complex scientific problems can be solved with human-directed computing. Protein structure prediction is one such problem: locating the biologically relevant native conformation of a protein is a formidable computational challenge given the very large size of the search space. Here we describe Foldit, a multiplayer online game that engages non-scientists in solving hard prediction problems. Foldit players interact with protein structures using direct manipulation tools and user-friendly versions of algorithms from the Rosetta structure prediction methodology, while they compete and collaborate to optimize the computed energy. We show that top-ranked Foldit players excel at solving challenging structure refinement problems in which substantial backbone rearrangements are necessary to achieve the burial of hydrophobic residues. Players working collaboratively develop a rich assortment of new strategies and algorithms; unlike computational approaches, they explore not only the conformational space but also the space of possible search strategies. The integration of human visual problem-solving and strategy development capabilities with traditional computational algorithms through interactive multiplayer games is a powerful new approach to solving computationally-limited scientific problems.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956414/" 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/PMC2956414/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cooper, Seth -- Khatib, Firas -- Treuille, Adrien -- Barbero, Janos -- Lee, Jeehyung -- Beenen, Michael -- Leaver-Fay, Andrew -- Baker, David -- Popovic, Zoran -- Players, Foldit -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Aug 5;466(7307):756-60. doi: 10.1038/nature09304.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Computer Science and Engineering, University of Washington, Box 352350, Seattle, Washington 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20686574" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Computational Biology/*methods ; Computer Graphics ; Computer Simulation ; Cooperative Behavior ; Cues ; *Games, Experimental ; *Group Processes ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Imaging, Three-Dimensional ; *Internet ; Leisure Activities ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Photic Stimulation ; *Problem Solving ; Protein Conformation ; *Protein Folding ; Proteins/*chemistry/metabolism ; Stochastic Processes ; Thermodynamics
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    James Watson's genome sequenced at high speed (2008)
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    Publication Date: 2008-04-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wadman, Meredith -- England -- Nature. 2008 Apr 17;452(7189):788. doi: 10.1038/452788b.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18431822" target="_blank"〉PubMed〈/a〉
    Keywords: Genetic Counseling/trends ; *Genome, Human ; Genomics/economics/*trends ; History, 21st Century ; Humans ; Individuality ; Male ; Reference Standards ; Sequence Analysis, DNA/economics/*trends ; Time Factors
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    Pyruvate kinase M2 is a phosphotyrosine-binding protein (2008)
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    Publication Date: 2008-03-14
    Description: Growth factors stimulate cells to take up excess nutrients and to use them for anabolic processes. The biochemical mechanism by which this is accomplished is not fully understood but it is initiated by phosphorylation of signalling proteins on tyrosine residues. Using a novel proteomic screen for phosphotyrosine-binding proteins, we have made the observation that an enzyme involved in glycolysis, the human M2 (fetal) isoform of pyruvate kinase (PKM2), binds directly and selectively to tyrosine-phosphorylated peptides. We show that binding of phosphotyrosine peptides to PKM2 results in release of the allosteric activator fructose-1,6-bisphosphate, leading to inhibition of PKM2 enzymatic activity. We also provide evidence that this regulation of PKM2 by phosphotyrosine signalling diverts glucose metabolites from energy production to anabolic processes when cells are stimulated by certain growth factors. Collectively, our results indicate that expression of this phosphotyrosine-binding form of pyruvate kinase is critical for rapid growth in cancer cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Christofk, Heather R -- Vander Heiden, Matthew G -- Wu, Ning -- Asara, John M -- Cantley, Lewis C -- R01 GM056203/GM/NIGMS NIH HHS/ -- T32 CA009172/CA/NCI NIH HHS/ -- England -- Nature. 2008 Mar 13;452(7184):181-6. doi: 10.1038/nature06667.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Systems Biology.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18337815" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Site ; Animals ; Catalysis ; Cell Line ; Cell Proliferation/drug effects ; Cells/drug effects/metabolism ; HeLa Cells ; Humans ; Lysine/metabolism ; Models, Molecular ; Peptide Library ; Phosphotyrosine/*metabolism ; Protein Binding ; Proteomics ; Pyruvate Kinase/antagonists & inhibitors/*metabolism ; Substrate Specificity
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    History of science: quinine steps back in time (2008)
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    Publication Date: 2008-02-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ball, Philip -- England -- Nature. 2008 Feb 28;451(7182):1065-6. doi: 10.1038/4511065a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18305535" target="_blank"〉PubMed〈/a〉
    Keywords: History, 20th Century ; Quinine/*chemical synthesis/chemistry/*history ; Reproducibility of Results
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    Structural recognition and functional activation of FcgammaR by innate pentraxins (2008)
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    Publication Date: 2008-11-18
    Description: Pentraxins are a family of ancient innate immune mediators conserved throughout evolution. The classical pentraxins include serum amyloid P component (SAP) and C-reactive protein, which are two of the acute-phase proteins synthesized in response to infection. Both recognize microbial pathogens and activate the classical complement pathway through C1q (refs 3 and 4). More recently, members of the pentraxin family were found to interact with cell-surface Fcgamma receptors (FcgammaR) and activate leukocyte-mediated phagocytosis. Here we describe the structural mechanism for pentraxin's binding to FcgammaR and its functional activation of FcgammaR-mediated phagocytosis and cytokine secretion. The complex structure between human SAP and FcgammaRIIa reveals a diagonally bound receptor on each SAP pentamer with both D1 and D2 domains of the receptor contacting the ridge helices from two SAP subunits. The 1:1 stoichiometry between SAP and FcgammaRIIa infers the requirement for multivalent pathogen binding for receptor aggregation. Mutational and binding studies show that pentraxins are diverse in their binding specificity for FcgammaR isoforms but conserved in their recognition structure. The shared binding site for SAP and IgG results in competition for FcgammaR binding and the inhibition of immune-complex-mediated phagocytosis by soluble pentraxins. These results establish antibody-like functions for pentraxins in the FcgammaR pathway, suggest an evolutionary overlap between the innate and adaptive immune systems, and have new therapeutic implications for autoimmune diseases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688732/" 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/PMC2688732/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Jinghua -- Marnell, Lorraine L -- Marjon, Kristopher D -- Mold, Carolyn -- Du Clos, Terry W -- Sun, Peter D -- R01 AI28358/AI/NIAID NIH HHS/ -- T32 AI007538/AI/NIAID NIH HHS/ -- Z01 AI000853-09/Intramural NIH HHS/ -- England -- Nature. 2008 Dec 18;456(7224):989-92. doi: 10.1038/nature07468. Epub 2008 Nov 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Immunology Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19011614" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Binding, Competitive ; C-Reactive Protein/chemistry/*immunology/*metabolism ; Crystallography, X-Ray ; Cytokines/immunology/secretion ; Humans ; Immunity, Innate/*immunology ; Immunoglobulin G/immunology/metabolism ; Macrophages/cytology/immunology ; Models, Molecular ; Phagocytosis ; Protein Conformation ; Receptors, IgG/chemistry/*immunology/*metabolism ; Serum Amyloid P-Component/chemistry/*immunology/*metabolism
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    Structural basis for gibberellin recognition by its receptor GID1 (2008)
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    Publication Date: 2008-11-28
    Description: Gibberellins (GAs) are phytohormones essential for many developmental processes in plants. A nuclear GA receptor, GIBBERELLIN INSENSITIVE DWARF1 (GID1), has a primary structure similar to that of the hormone-sensitive lipases (HSLs). Here we analyse the crystal structure of Oryza sativa GID1 (OsGID1) bound with GA(4) and GA(3) at 1.9 A resolution. The overall structure of both complexes shows an alpha/beta-hydrolase fold similar to that of HSLs except for an amino-terminal lid. The GA-binding pocket corresponds to the substrate-binding site of HSLs. On the basis of the OsGID1 structure, we mutagenized important residues for GA binding and examined their binding activities. Almost all of them showed very little or no activity, confirming that the residues revealed by structural analysis are important for GA binding. The replacement of Ile 133 with Leu or Val-residues corresponding to those of the lycophyte Selaginella moellendorffii GID1s-caused an increase in the binding affinity for GA(34), a 2beta-hydroxylated GA(4). These observations indicate that GID1 originated from HSL and was further modified to have higher affinity and more strict selectivity for bioactive GAs by adapting the amino acids involved in GA binding in the course of plant evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shimada, Asako -- Ueguchi-Tanaka, Miyako -- Nakatsu, Toru -- Nakajima, Masatoshi -- Naoe, Youichi -- Ohmiya, Hiroko -- Kato, Hiroaki -- Matsuoka, Makoto -- England -- Nature. 2008 Nov 27;456(7221):520-3. doi: 10.1038/nature07546.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19037316" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Gibberellins/*chemistry/*metabolism ; Hydrolases/chemistry/metabolism ; Hydroxylation ; Models, Molecular ; Oryza/*chemistry/genetics/metabolism ; Plant Growth Regulators/*chemistry/*metabolism ; Plant Proteins/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Conformation ; Substrate Specificity ; Two-Hybrid System Techniques
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    Complex speciation of humans and chimpanzees (2008)
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    Publication Date: 2008-03-14
    Description: Genetic data from two or more species provide information about the process of speciation. In their analysis of DNA from humans, chimpanzees, gorillas, orangutans and macaques (HCGOM), Patterson et al. suggest that the apparently short divergence time between humans and chimpanzees on the X chromosome is explained by a massive interspecific hybridization event in the ancestry of these two species. However, Patterson et al. do not statistically test their own null model of simple speciation before concluding that speciation was complex, and--even if the null model could be rejected--they do not consider other explanations of a short divergence time on the X chromosome. These include natural selection on the X chromosome in the common ancestor of humans and chimpanzees, changes in the ratio of male-to-female mutation rates over time, and less extreme versions of divergence with gene flow (see ref. 2, for example). I therefore believe that their claim of hybridization is unwarranted.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wakeley, John -- England -- Nature. 2008 Mar 13;452(7184):E3-4; discussion E4. doi: 10.1038/nature06805.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Avenue, Cambridge, Massachusetts 02138, USA. wakeley@fas.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18337768" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Chromosomes, Mammalian/genetics ; Female ; *Genetic Speciation ; Humans ; Male ; *Models, Genetic ; Mutagenesis/genetics ; Pan troglodytes/*genetics ; Phylogeny ; Reproducibility of Results ; Selection, Genetic ; Sex Characteristics ; Time Factors ; X Chromosome/genetics
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    Science & music: lost in music (2008)
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    Publication Date: 2008-05-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huron, David -- England -- Nature. 2008 May 22;453(7194):456-7. doi: 10.1038/453456a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Music & Center for Cognitive Science, Ohio State University, Columbus, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497806" target="_blank"〉PubMed〈/a〉
    Keywords: *Cultural Diversity ; *Cultural Evolution ; History, 17th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; Humans ; *Music/history ; *Neurosciences
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    Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning (2008)
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    Publication Date: 2008-02-19
    Description: Cytosine DNA methylation is important in regulating gene expression and in silencing transposons and other repetitive sequences. Recent genomic studies in Arabidopsis thaliana have revealed that many endogenous genes are methylated either within their promoters or within their transcribed regions, and that gene methylation is highly correlated with transcription levels. However, plants have different types of methylation controlled by different genetic pathways, and detailed information on the methylation status of each cytosine in any given genome is lacking. To this end, we generated a map at single-base-pair resolution of methylated cytosines for Arabidopsis, by combining bisulphite treatment of genomic DNA with ultra-high-throughput sequencing using the Illumina 1G Genome Analyser and Solexa sequencing technology. This approach, termed BS-Seq, unlike previous microarray-based methods, allows one to sensitively measure cytosine methylation on a genome-wide scale within specific sequence contexts. Here we describe methylation on previously inaccessible components of the genome and analyse the DNA methylation sequence composition and distribution. We also describe the effect of various DNA methylation mutants on genome-wide methylation patterns, and demonstrate that our newly developed library construction and computational methods can be applied to large genomes such as that of mouse.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2377394/" 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/PMC2377394/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cokus, Shawn J -- Feng, Suhua -- Zhang, Xiaoyu -- Chen, Zugen -- Merriman, Barry -- Haudenschild, Christian D -- Pradhan, Sriharsa -- Nelson, Stanley F -- Pellegrini, Matteo -- Jacobsen, Steven E -- Howard Hughes Medical Institute/ -- England -- Nature. 2008 Mar 13;452(7184):215-9. doi: 10.1038/nature06745. Epub 2008 Feb 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18278030" target="_blank"〉PubMed〈/a〉
    Keywords: 5-Methylcytosine/metabolism ; Animals ; Arabidopsis/*genetics ; Base Sequence ; Computational Biology ; Cytosine/metabolism ; *DNA Methylation ; Gene Expression Regulation, Plant/genetics ; Gene Library ; Genome, Plant/*genetics ; Mice ; Mutation/genetics ; Promoter Regions, Genetic/genetics ; Reproducibility of Results ; Sequence Analysis, DNA/*methods ; Sulfites/*metabolism ; Uracil/metabolism
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    Beyond the origin (2008)
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    Publication Date: 2008-11-21
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉England -- Nature. 2008 Nov 20;456(7220):281. doi: 10.1038/456281a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19020564" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anniversaries and Special Events ; *Biological Evolution ; Biological Science Disciplines/history ; Genetic Speciation ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; Selection, Genetic
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    Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants (2008)
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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
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    Net carbon dioxide losses of northern ecosystems in response to autumn warming (2008)
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    Publication Date: 2008-01-04
    Description: The carbon balance of terrestrial ecosystems is particularly sensitive to climatic changes in autumn and spring, with spring and autumn temperatures over northern latitudes having risen by about 1.1 degrees C and 0.8 degrees C, respectively, over the past two decades. A simultaneous greening trend has also been observed, characterized by a longer growing season and greater photosynthetic activity. These observations have led to speculation that spring and autumn warming could enhance carbon sequestration and extend the period of net carbon uptake in the future. Here we analyse interannual variations in atmospheric carbon dioxide concentration data and ecosystem carbon dioxide fluxes. We find that atmospheric records from the past 20 years show a trend towards an earlier autumn-to-winter carbon dioxide build-up, suggesting a shorter net carbon uptake period. This trend cannot be explained by changes in atmospheric transport alone and, together with the ecosystem flux data, suggest increasing carbon losses in autumn. We use a process-based terrestrial biosphere model and satellite vegetation greenness index observations to investigate further the observed seasonal response of northern ecosystems to autumnal warming. We find that both photosynthesis and respiration increase during autumn warming, but the increase in respiration is greater. In contrast, warming increases photosynthesis more than respiration in spring. Our simulations and observations indicate that northern terrestrial ecosystems may currently lose carbon dioxide in response to autumn warming, with a sensitivity of about 0.2 PgC degrees C(-1), offsetting 90% of the increased carbon dioxide uptake during spring. If future autumn warming occurs at a faster rate than in spring, the ability of northern ecosystems to sequester carbon may be diminished earlier than previously suggested.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Piao, Shilong -- Ciais, Philippe -- Friedlingstein, Pierre -- Peylin, Philippe -- Reichstein, Markus -- Luyssaert, Sebastiaan -- Margolis, Hank -- Fang, Jingyun -- Barr, Alan -- Chen, Anping -- Grelle, Achim -- Hollinger, David Y -- Laurila, Tuomas -- Lindroth, Anders -- Richardson, Andrew D -- Vesala, Timo -- England -- Nature. 2008 Jan 3;451(7174):49-52. doi: 10.1038/nature06444.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉LSCE, UMR CEA-CNRS, Batiment 709, CE, L'Orme des Merisiers, F-91191 Gif-sur-Yvette, France. slpiao@lsce.ipsl.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18172494" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Biomass ; Carbon Dioxide/analysis/*metabolism ; Cell Respiration ; *Ecosystem ; Fossil Fuels ; Geography ; Greenhouse Effect ; History, 20th Century ; History, 21st Century ; Oceans and Seas ; Photosynthesis ; Plant Transpiration ; Plants/metabolism ; Rain ; *Seasons ; Soil/analysis ; *Temperature ; Water/metabolism
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    Structure of the 30S translation initiation complex (2008)
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    Publication Date: 2008-09-02
    Description: Translation initiation, the rate-limiting step of the universal process of protein synthesis, proceeds through sequential, tightly regulated steps. In bacteria, the correct messenger RNA start site and the reading frame are selected when, with the help of initiation factors IF1, IF2 and IF3, the initiation codon is decoded in the peptidyl site of the 30S ribosomal subunit by the fMet-tRNA(fMet) anticodon. This yields a 30S initiation complex (30SIC) that is an intermediate in the formation of the 70S initiation complex (70SIC) that occurs on joining of the 50S ribosomal subunit to the 30SIC and release of the initiation factors. The localization of IF2 in the 30SIC has proved to be difficult so far using biochemical approaches, but could now be addressed using cryo-electron microscopy and advanced particle separation techniques on the basis of three-dimensional statistical analysis. Here we report the direct visualization of a 30SIC containing mRNA, fMet-tRNA(fMet) and initiation factors IF1 and GTP-bound IF2. We demonstrate that the fMet-tRNA(fMet) is held in a characteristic and precise position and conformation by two interactions that contribute to the formation of a stable complex: one involves the transfer RNA decoding stem which is buried in the 30S peptidyl site, and the other occurs between the carboxy-terminal domain of IF2 and the tRNA acceptor end. The structure provides insights into the mechanism of 70SIC assembly and rationalizes the rapid activation of GTP hydrolysis triggered on 30SIC-50S joining by showing that the GTP-binding domain of IF2 would directly face the GTPase-activated centre of the 50S subunit.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Simonetti, Angelita -- Marzi, Stefano -- Myasnikov, Alexander G -- Fabbretti, Attilio -- Yusupov, Marat -- Gualerzi, Claudio O -- Klaholz, Bruno P -- England -- Nature. 2008 Sep 18;455(7211):416-20. doi: 10.1038/nature07192. Epub 2008 Aug 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Genetics and of Molecular and Cellular Biology, Department of Structural Biology and Genomics, Illkirch F-67404, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18758445" target="_blank"〉PubMed〈/a〉
    Keywords: Cryoelectron Microscopy ; Crystallography, X-Ray ; Guanosine Triphosphate/chemistry/metabolism ; Models, Molecular ; Multiprotein Complexes/*chemistry/genetics/metabolism/*ultrastructure ; *Peptide Chain Initiation, Translational ; Prokaryotic Initiation Factor-1/chemistry/genetics/metabolism/ultrastructure ; Prokaryotic Initiation Factor-2/chemistry/genetics/metabolism/ultrastructure ; Protein Conformation ; RNA, Messenger/chemistry/genetics/metabolism ; RNA, Transfer, Met/chemistry/genetics/metabolism/ultrastructure ; Ribosome Subunits/chemistry/metabolism/ultrastructure ; Ribosomes/chemistry/*metabolism/*ultrastructure ; Thermus thermophilus/*enzymology/genetics/*ultrastructure
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    Old-growth forests as global carbon sinks (2008)
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    Publication Date: 2008-09-12
    Description: Old-growth forests remove carbon dioxide from the atmosphere at rates that vary with climate and nitrogen deposition. The sequestered carbon dioxide is stored in live woody tissues and slowly decomposing organic matter in litter and soil. Old-growth forests therefore serve as a global carbon dioxide sink, but they are not protected by international treaties, because it is generally thought that ageing forests cease to accumulate carbon. Here we report a search of literature and databases for forest carbon-flux estimates. We find that in forests between 15 and 800 years of age, net ecosystem productivity (the net carbon balance of the forest including soils) is usually positive. Our results demonstrate that old-growth forests can continue to accumulate carbon, contrary to the long-standing view that they are carbon neutral. Over 30 per cent of the global forest area is unmanaged primary forest, and this area contains the remaining old-growth forests. Half of the primary forests (6 x 10(8) hectares) are located in the boreal and temperate regions of the Northern Hemisphere. On the basis of our analysis, these forests alone sequester about 1.3 +/- 0.5 gigatonnes of carbon per year. Thus, our findings suggest that 15 per cent of the global forest area, which is currently not considered when offsetting increasing atmospheric carbon dioxide concentrations, provides at least 10 per cent of the global net ecosystem productivity. Old-growth forests accumulate carbon for centuries and contain large quantities of it. We expect, however, that much of this carbon, even soil carbon, will move back to the atmosphere if these forests are disturbed.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Luyssaert, Sebastiaan -- Schulze, E-Detlef -- Borner, Annett -- Knohl, Alexander -- Hessenmoller, Dominik -- Law, Beverly E -- Ciais, Philippe -- Grace, John -- England -- Nature. 2008 Sep 11;455(7210):213-5. doi: 10.1038/nature07276.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, University of Antwerp, 2610 Wilrijk, Belgium. sebastiaan.luyssaert@ua.ac.be〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18784722" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Atmosphere/chemistry ; Biomass ; Carbon/*metabolism ; Carbon Dioxide/metabolism ; Databases, Factual ; Disasters ; *Ecosystem ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Ancient ; History, Medieval ; Human Activities ; Time Factors ; Trees/*metabolism
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    Science & music: raising the roof (2008)
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    Publication Date: 2008-06-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Barron, Michael -- England -- Nature. 2008 Jun 12;453(7197):859-60. doi: 10.1038/453859a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Architecture and Civil Engineering, University of Bath, BA2 7AY, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18548056" target="_blank"〉PubMed〈/a〉
    Keywords: Absorption ; *Acoustics ; Auditory Perception ; *Facility Design and Construction/history ; Hearing/physiology ; History, 19th Century ; History, 20th Century ; History, 21st Century ; Humans ; *Music/history
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    The advent and development of organocatalysis (2008)
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    Publication Date: 2008-09-19
    Description: The use of small organic molecules as catalysts has been known for more than a century. But only in the past decade has organocatalysis become a thriving area of general concepts and widely applicable asymmetric reactions. Here I present my opinion on why the field of organocatalysis has blossomed so dramatically over the past decade.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉MacMillan, David W C -- R01 GM078201-01-01/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Sep 18;455(7211):304-8. doi: 10.1038/nature07367.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Merck Center for Catalysis at Princeton University, 116 Frick Laboratory, Princeton University, Princeton, New Jersey 08540, USA. dmacmill@princeton.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18800128" target="_blank"〉PubMed〈/a〉
    Keywords: Catalysis ; Chemistry, Organic/*history/*methods ; History, 20th Century ; History, 21st Century ; Hydrogen Bonding ; Ions/chemistry
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    Celebrations for Darwin downplay Wallace's role (2008)
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    Publication Date: 2008-02-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Beccaloni, George W -- Smith, Vincent S -- England -- Nature. 2008 Feb 28;451(7182):1050. doi: 10.1038/4511050d.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18305520" target="_blank"〉PubMed〈/a〉
    Keywords: Biology/*history ; History, 19th Century ; History, 20th Century ; History, 21st Century ; *Selection, Genetic
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    Computational biochemistry: old enzymes, new tricks (2008)
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    Publication Date: 2008-05-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ghirlanda, Giovanna -- England -- Nature. 2008 May 8;453(7192):164-6. doi: 10.1038/453164a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18464727" target="_blank"〉PubMed〈/a〉
    Keywords: Biochemistry/*methods ; Catalysis ; Computational Biology/*methods ; Directed Molecular Evolution/*methods ; Drug Design ; Drug Evaluation, Preclinical ; Enzymes/*chemistry/*metabolism ; Models, Molecular ; Protein Engineering/*methods
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    Argentina's pivotal moment (2008)
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    Publication Date: 2008-02-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smaglik, Paul -- England -- Nature. 2008 Jan 24;451(7177):494-6. doi: 10.1038/nj7177-494a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18290265" target="_blank"〉PubMed〈/a〉
    Keywords: Argentina ; Emigration and Immigration/history/trends ; *Federal Government ; History, 20th Century ; History, 21st Century ; Politics ; Research Personnel/economics/history/*trends ; Research Support as Topic/economics/history ; Salaries and Fringe Benefits ; Science/*economics/history/manpower/*organization & administration
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    Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex (2008)
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    Publication Date: 2008-12-19
    Description: Here we report on a 3.0 A crystal structure of a ternary complex of wild-type Thermus thermophilus argonaute bound to a 5'-phosphorylated 21-nucleotide guide DNA and a 20-nucleotide target RNA containing cleavage-preventing mismatches at the 10-11 step. The seed segment (positions 2 to 8) adopts an A-helical-like Watson-Crick paired duplex, with both ends of the guide strand anchored in the complex. An arginine, inserted between guide-strand bases 10 and 11 in the binary complex, locking it in an inactive conformation, is released on ternary complex formation. The nucleic-acid-binding channel between the PAZ- and PIWI-containing lobes of argonaute widens on formation of a more open ternary complex. The relationship of structure to function was established by determining cleavage activity of ternary complexes containing position-dependent base mismatch, bulge and 2'-O-methyl modifications. Consistent with the geometry of the ternary complex, bulges residing in the seed segments of the target, but not the guide strand, were better accommodated and their complexes were catalytically active.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2765400/" 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/PMC2765400/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Yanli -- Juranek, Stefan -- Li, Haitao -- Sheng, Gang -- Tuschl, Thomas -- Patel, Dinshaw J -- R01 AI068776/AI/NIAID NIH HHS/ -- R01 AI068776-02/AI/NIAID NIH HHS/ -- England -- Nature. 2008 Dec 18;456(7224):921-6. doi: 10.1038/nature07666.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program, Memorial-Sloan Kettering Cancer Center, New York, New York 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19092929" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/*chemistry/genetics/*metabolism ; Base Pair Mismatch ; Base Pairing ; Base Sequence ; Crystallography, X-Ray ; DNA/chemistry/genetics/*metabolism ; Methylation ; Models, Molecular ; Phosphorylation ; Protein Conformation ; RNA/chemistry/genetics/*metabolism ; RNA Interference ; RNA-Induced Silencing Complex/*chemistry/genetics/*metabolism ; Substrate Specificity ; Thermus thermophilus/*chemistry
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    The replisome uses mRNA as a primer after colliding with RNA polymerase (2008)
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    Publication Date: 2008-11-21
    Description: Replication forks are impeded by DNA damage and protein-nucleic acid complexes such as transcribing RNA polymerase. For example, head-on collision of the replisome with RNA polymerase results in replication fork arrest. However, co-directional collision of the replisome with RNA polymerase has little or no effect on fork progression. Here we examine co-directional collisions between a replisome and RNA polymerase in vitro. We show that the Escherichia coli replisome uses the RNA transcript as a primer to continue leading-strand synthesis after the collision with RNA polymerase that is displaced from the DNA. This action results in a discontinuity in the leading strand, yet the replisome remains intact and bound to DNA during the entire process. These findings underscore the notable plasticity by which the replisome operates to circumvent obstacles in its path and may explain why the leading strand is synthesized discontinuously in vivo.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2605185/" 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/PMC2605185/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pomerantz, Richard T -- O'Donnell, Mike -- R01 GM038839/GM/NIGMS NIH HHS/ -- R01 GM038839-21/GM/NIGMS NIH HHS/ -- R37 GM038839/GM/NIGMS NIH HHS/ -- R37 GM038839-20/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Dec 11;456(7223):762-6. doi: 10.1038/nature07527. Epub 2008 Nov 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, New York 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19020502" target="_blank"〉PubMed〈/a〉
    Keywords: DNA Polymerase III/*metabolism ; DNA Replication ; DNA, Bacterial/metabolism ; DNA-Directed RNA Polymerases/*metabolism ; Escherichia coli/genetics/*metabolism ; Models, Molecular ; *Rna ; RNA, Bacterial/*metabolism ; RNA, Messenger/*metabolism
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    Population biology: Case of the absent lemmings (2008)
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    Publication Date: 2008-11-07
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Coulson, Tim -- Malo, Aurelio -- England -- Nature. 2008 Nov 6;456(7218):43-4. doi: 10.1038/456043a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18987726" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arvicolinae/*physiology ; *Ecosystem ; Female ; *Greenhouse Effect ; History, 20th Century ; History, 21st Century ; Norway ; Population Dynamics ; Seasons ; Snow ; Temperature
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    Structure of the Tribolium castaneum telomerase catalytic subunit TERT (2008)
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    Publication Date: 2008-09-02
    Description: A common hallmark of human cancers is the overexpression of telomerase, a ribonucleoprotein complex that is responsible for maintaining the length and integrity of chromosome ends. Telomere length deregulation and telomerase activation is an early, and perhaps necessary, step in cancer cell evolution. Here we present the high-resolution structure of the Tribolium castaneum catalytic subunit of telomerase, TERT. The protein consists of three highly conserved domains, organized into a ring-like structure that shares common features with retroviral reverse transcriptases, viral RNA polymerases and B-family DNA polymerases. Domain organization places motifs implicated in substrate binding and catalysis in the interior of the ring, which can accommodate seven to eight bases of double-stranded nucleic acid. Modelling of an RNA-DNA heteroduplex in the interior of this ring demonstrates a perfect fit between the protein and the nucleic acid substrate, and positions the 3'-end of the DNA primer at the active site of the enzyme, providing evidence for the formation of an active telomerase elongation complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gillis, Andrew J -- Schuller, Anthony P -- Skordalakes, Emmanuel -- England -- Nature. 2008 Oct 2;455(7213):633-7. doi: 10.1038/nature07283. Epub 2008 Aug 31.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gene Expression and Regulation Program, The Wistar Institute, 3601 Spruce Street, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18758444" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Animals ; Binding Sites ; Catalysis ; Catalytic Domain ; Conserved Sequence ; Crystallization ; Crystallography, X-Ray ; Humans ; Models, Molecular ; Nucleotides/metabolism ; Protein Structure, Tertiary ; Telomerase/*chemistry/metabolism ; Tribolium/*enzymology
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    Science prizes: Best in class (2008)
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    Publication Date: 2008-09-27
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Powell, Kendall -- England -- Nature. 2008 Sep 25;455(7212):455-8. doi: 10.1038/455455a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18818627" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Awards and Prizes ; Creativity ; Elephants/physiology ; *Foundations/economics ; Greenhouse Effect ; Hand/physiology ; History, 20th Century ; History, 21st Century ; Humans ; Hybridization, Genetic ; Illinois ; Neurosciences ; *Research Personnel/economics/psychology ; Robotics ; *Science/economics ; Selection, Genetic
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Structure of a beta1-adrenergic G-protein-coupled receptor (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-07-03
    Description: G-protein-coupled receptors have a major role in transmembrane signalling in most eukaryotes and many are important drug targets. Here we report the 2.7 A resolution crystal structure of a beta(1)-adrenergic receptor in complex with the high-affinity antagonist cyanopindolol. The modified turkey (Meleagris gallopavo) receptor was selected to be in its antagonist conformation and its thermostability improved by earlier limited mutagenesis. The ligand-binding pocket comprises 15 side chains from amino acid residues in 4 transmembrane alpha-helices and extracellular loop 2. This loop defines the entrance of the ligand-binding pocket and is stabilized by two disulphide bonds and a sodium ion. Binding of cyanopindolol to the beta(1)-adrenergic receptor and binding of carazolol to the beta(2)-adrenergic receptor involve similar interactions. A short well-defined helix in cytoplasmic loop 2, not observed in either rhodopsin or the beta(2)-adrenergic receptor, directly interacts by means of a tyrosine with the highly conserved DRY motif at the end of helix 3 that is essential for receptor activation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923055/" 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/PMC2923055/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Warne, Tony -- Serrano-Vega, Maria J -- Baker, Jillian G -- Moukhametzianov, Rouslan -- Edwards, Patricia C -- Henderson, Richard -- Leslie, Andrew G W -- Tate, Christopher G -- Schertler, Gebhard F X -- MC_U105178937/Medical Research Council/United Kingdom -- MC_U105184322/Medical Research Council/United Kingdom -- MC_U105184325/Medical Research Council/United Kingdom -- MC_U105197215/Medical Research Council/United Kingdom -- U.1051.04.020(78937)/Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2008 Jul 24;454(7203):486-91. doi: 10.1038/nature07101. Epub 2008 Jun 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18594507" target="_blank"〉PubMed〈/a〉
    Keywords: Adrenergic beta-1 Receptor Agonists ; Adrenergic beta-1 Receptor Antagonists ; Adrenergic beta-Antagonists/chemistry/metabolism ; Amino Acid Motifs ; Animals ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Ligands ; Models, Molecular ; Mutant Proteins/chemistry/genetics/metabolism ; Mutation ; Pindolol/analogs & derivatives/chemistry/metabolism ; Propanolamines/chemistry/metabolism ; Protein Conformation ; Receptors, Adrenergic, beta-1/*chemistry/metabolism ; Thermodynamics ; Turkeys
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Obituary: Bert Bolin (1925-2008) (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-02-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Watson, Bob -- England -- Nature. 2008 Feb 7;451(7179):642. doi: 10.1038/451642a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Watson@defra.gsi.gov.uk.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18256656" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere/chemistry ; Carbon Dioxide/metabolism ; Ecosystem ; *Greenhouse Effect ; History, 20th Century ; History, 21st Century ; Sweden
    Print ISSN: 0028-0836
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    Increasing risk of Amazonian drought due to decreasing aerosol pollution (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-05-10
    Description: The Amazon rainforest plays a crucial role in the climate system, helping to drive atmospheric circulations in the tropics by absorbing energy and recycling about half of the rainfall that falls on it. This region (Amazonia) is also estimated to contain about one-tenth of the total carbon stored in land ecosystems, and to account for one-tenth of global, net primary productivity. The resilience of the forest to the combined pressures of deforestation and global warming is therefore of great concern, especially as some general circulation models (GCMs) predict a severe drying of Amazonia in the twenty-first century. Here we analyse these climate projections with reference to the 2005 drought in western Amazonia, which was associated with unusually warm North Atlantic sea surface temperatures (SSTs). We show that reduction of dry-season (July-October) rainfall in western Amazonia correlates well with an index of the north-south SST gradient across the equatorial Atlantic (the 'Atlantic N-S gradient'). Our climate model is unusual among current GCMs in that it is able to reproduce this relationship and also the observed twentieth-century multidecadal variability in the Atlantic N-S gradient, provided that the effects of aerosols are included in the model. Simulations for the twenty-first century using the same model show a strong tendency for the SST conditions associated with the 2005 drought to become much more common, owing to continuing reductions in reflective aerosol pollution in the Northern Hemisphere.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cox, Peter M -- Harris, Phil P -- Huntingford, Chris -- Betts, Richard A -- Collins, Matthew -- Jones, Chris D -- Jupp, Tim E -- Marengo, Jose A -- Nobre, Carlos A -- England -- Nature. 2008 May 8;453(7192):212-5. doi: 10.1038/nature06960.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Engineering, Computing and Mathematics, University of Exeter, Exeter EX4 4QF, UK. p.m.cox@exeter.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18464740" target="_blank"〉PubMed〈/a〉
    Keywords: Aerosols/*analysis ; Atlantic Ocean ; Carbon Dioxide/analysis ; Disasters/history/*statistics & numerical data ; *Ecosystem ; Environmental Pollution/*statistics & numerical data ; *Greenhouse Effect ; History, 20th Century ; History, 21st Century ; *Models, Theoretical ; Pacific Ocean ; Probability ; Rain ; Seasons ; South America ; Temperature ; Trees/*physiology
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    Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy (2008)
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    Publication Date: 2008-02-29
    Description: A half-century after the determination of the first three-dimensional crystal structure of a protein, more than 40,000 structures ranging from single polypeptides to large assemblies have been reported. The challenge for crystallographers, however, remains the growing of a diffracting crystal. Here we report the 4.5-A resolution structure of a 22-MDa macromolecular assembly, the capsid of the infectious epsilon15 (epsilon15) particle, by single-particle electron cryomicroscopy. From this density map we constructed a complete backbone trace of its major capsid protein, gene product 7 (gp7). The structure reveals a similar protein architecture to that of other tailed double-stranded DNA viruses, even in the absence of detectable sequence similarity. However, the connectivity of the secondary structure elements (topology) in gp7 is unique. Protruding densities are observed around the two-fold axes that cannot be accounted for by gp7. A subsequent proteomic analysis of the whole virus identifies these densities as gp10, a 12-kDa protein. Its structure, location and high binding affinity to the capsid indicate that the gp10 dimer functions as a molecular staple between neighbouring capsomeres to ensure the particle's stability. Beyond epsilon15, this method potentially offers a new approach for modelling the backbone conformations of the protein subunits in other macromolecular assemblies at near-native solution states.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jiang, Wen -- Baker, Matthew L -- Jakana, Joanita -- Weigele, Peter R -- King, Jonathan -- Chiu, Wah -- England -- Nature. 2008 Feb 28;451(7182):1130-4. doi: 10.1038/nature06665.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA. jiang12@purdue.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18305544" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophages/*chemistry/genetics/*ultrastructure ; Capsid/*chemistry/*ultrastructure ; Capsid Proteins/chemistry/ultrastructure ; Cryoelectron Microscopy ; DNA Viruses/chemistry/genetics/ultrastructure ; Models, Molecular ; Molecular Conformation ; Salmonella/*virology
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    Defence research: still in the lead? (2008)
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    Publication Date: 2008-01-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weinberger, Sharon -- England -- Nature. 2008 Jan 24;451(7177):390-3. doi: 10.1038/451390a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18216826" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bionics/trends ; History, 20th Century ; History, 21st Century ; Humans ; Internet ; Research/history/*trends ; Robotics/trends ; Security Measures/history/organization & administration/*trends ; Technology/history/*trends ; Terrorism/prevention & control ; United States ; United States Government Agencies/economics/history/organization & ; administration/*trends
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins (2008)
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    Publication Date: 2008-05-27
    Description: Understanding the energetics of molecular interactions is fundamental to all of the central quests of structural biology including structure prediction and design, mapping evolutionary pathways, learning how mutations cause disease, drug design, and relating structure to function. Hydrogen-bonding is widely regarded as an important force in a membrane environment because of the low dielectric constant of membranes and a lack of competition from water. Indeed, polar residue substitutions are the most common disease-causing mutations in membrane proteins. Because of limited structural information and technical challenges, however, there have been few quantitative tests of hydrogen-bond strength in the context of large membrane proteins. Here we show, by using a double-mutant cycle analysis, that the average contribution of eight interhelical side-chain hydrogen-bonding interactions throughout bacteriorhodopsin is only 0.6 kcal mol(-1). In agreement with these experiments, we find that 4% of polar atoms in the non-polar core regions of membrane proteins have no hydrogen-bond partner and the lengths of buried hydrogen bonds in soluble proteins and membrane protein transmembrane regions are statistically identical. Our results indicate that most hydrogen-bond interactions in membrane proteins are only modestly stabilizing. Weak hydrogen-bonding should be reflected in considerations of membrane protein folding, dynamics, design, evolution and function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734483/" 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/PMC2734483/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Joh, Nathan Hyunjoong -- Min, Andrew -- Faham, Salem -- Whitelegge, Julian P -- Yang, Duan -- Woods, Virgil L -- Bowie, James U -- R01 CA081000/CA/NCI NIH HHS/ -- R01 CA081000-07/CA/NCI NIH HHS/ -- R01 CA081000-08/CA/NCI NIH HHS/ -- R01 CA081000-09/CA/NCI NIH HHS/ -- R01 GM063919/GM/NIGMS NIH HHS/ -- R01 GM063919-06/GM/NIGMS NIH HHS/ -- R01 GM063919-07/GM/NIGMS NIH HHS/ -- R01 GM063919-08/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Jun 26;453(7199):1266-70. doi: 10.1038/nature06977. Epub 2008 May 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, UCLA-DOE Center for Genomics and Proteomics, Molecular Biology Institute, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18500332" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriorhodopsins/chemistry/genetics/metabolism ; Crystallography, X-Ray ; Deuterium Exchange Measurement ; Hydrogen Bonding ; Membrane Proteins/*chemistry/genetics/*metabolism ; Models, Molecular ; Mutation/genetics ; Protein Folding ; Solubility ; Thermodynamics
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    When authorship met authenticity (2008)
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    Publication Date: 2008-02-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Johns, Adrian -- England -- Nature. 2008 Feb 28;451(7182):1058-9. doi: 10.1038/4511058a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Chicago, 1126 East 59th Street Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18305531" target="_blank"〉PubMed〈/a〉
    Keywords: Authorship ; Drug-Related Side Effects and Adverse Reactions ; Fraud/*history ; History, 17th Century ; History, 18th Century ; History, 21st Century ; Internationality ; Patents as Topic/*history ; Pharmaceutical Preparations/economics/*history/*standards
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    The science of doping (2008)
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    Publication Date: 2008-08-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berry, Donald A -- England -- Nature. 2008 Aug 7;454(7205):692-3. doi: 10.1038/454692a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Quantitative Sciences, Department of Biostatistics, MD Anderson Cancer Center, University of Texas, 1400 Pressler Street, Houston, Texas 77030-1402, USA. dberry@mdanderson.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18685682" target="_blank"〉PubMed〈/a〉
    Keywords: Doping in Sports/*prevention & control ; False Positive Reactions ; Female ; Humans ; Male ; Probability ; Reproducibility of Results ; Sample Size ; Sensitivity and Specificity ; *Sports/ethics/standards ; Substance Abuse Detection/methods/*standards
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    Eyewitness identification: line-ups on trial (2008)
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    Publication Date: 2008-05-24
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spinney, Laura -- England -- Nature. 2008 May 22;453(7194):442-4. doi: 10.1038/453442a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497791" target="_blank"〉PubMed〈/a〉
    Keywords: Crime/*legislation & jurisprudence ; Criminal Law/*methods/standards ; DNA Fingerprinting ; Evaluation Studies as Topic ; Great Britain ; Humans ; Police ; Reproducibility of Results ; *Research ; United States
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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    Human behaviour: killer instincts (2008)
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    Publication Date: 2008-02-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jones, Dan -- England -- Nature. 2008 Jan 31;451(7178):512-5. doi: 10.1038/451512a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18235473" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Aggression/*physiology/psychology ; Altruism ; Anger/physiology ; Animals ; Antisocial Personality Disorder/physiopathology ; *Biological Evolution ; Conflict (Psychology) ; Female ; History, 15th Century ; History, 16th Century ; History, 17th Century ; History, 18th Century ; History, 19th Century ; History, 20th Century ; History, 21st Century ; History, Medieval ; *Homicide/history/psychology ; Humans ; Male ; Models, Biological ; Morals ; Pan troglodytes/physiology ; Prefrontal Cortex/anatomy & histology/physiology ; Sex Characteristics ; United Nations ; Violence/psychology ; Warfare
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