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  • Binding Sites  (51)
  • Fisheries
  • Inorganic Chemistry
  • Seismology
  • American Association for the Advancement of Science (AAAS)  (57)
  • Victoria: Seychelles Fishing Authority  (2)
  • WIOMSA  (1)
  • Am. Meteor. Soc.
  • WWF Programa Marino para Latinoamérica y el Caribe
  • 2005-2009  (60)
  • 1950-1954
  • 2006  (60)
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Keywords
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  • 2005-2009  (60)
  • 1950-1954
Year
  • 1
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    Seychelles fisheries country profile : 1990-1994. (2006)
    Victoria: Seychelles Fishing Authority
    Details
    Publication Date: 2021-05-19
    Description: Seychelles is composed of over 100 islands with a land area of approximately 455 km², centred close to 4°30'S and 55°30'E. The combined coastline is approximately 600 km long, the oceanic shelf totals about 50 000 km² and the Exclusive Economic Zone (EEZ) is over 1 370 000 km². The total population (1994 census) stands at just under 74 000. in 1994, the population registered a growth rate of 2.2%. The GDP (1994) was SR 2373.8 million, fisheries representing 4.8% of this sum. Licensing agreements for foreign fishing activities provided a yearly revenue of SR8 million. Port Victoria is seen as a prime centre for tuna fishing operations in the Indian Ocean. In the artisanal fishery just under 900 persons are working. The largest contributor to catch by vessel type are the traditional whaler vessels representing 47.8% of the total catch. Over 66.3% of the catch is by the handline method. Carangidae representing 24% and Lutjanidae 19% of total landings. There are six specific objectives to the fisheries sector policy, which aims as resource development and maximisation of potential benefits. Nearshore fishery resources are considered to be heavily exploited, however opportunities exist around the distant islands and in deeper waters off the Mahe plateau shelf. Aquaculture of molluscs and prawns is being developed and carried out. The main constraints to development are seen as the lack of skilled manpower and foreign exchange.
    Description: Published
    Keywords: Country profile ; Fisheries ; Seychelles ; Statistics ; Fisheries ; Fishery statistics
    Repository Name: AquaDocs
    Type: Report , Non-Refereed
    Format: 186058 bytes
    Format: 520444 bytes
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  • 2
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    Feeding partitioning among tuna taken in surface and mid-water layers: the case of yellowfin (Thunnus albacares) and bigeye (T. obesus) in the Western Tropical Indian Ocean (2006)
    WIOMSA
    Details
    Publication Date: 2021-05-19
    Description: The trophic relations of two apex predators, yellowfin and bigeye tuna (Thunnus albacares and T. obesus), and their prey were investigated in the western tropical Indian Ocean. The contents of 173 non-empty stomachs were analysed from specimens caught with longlines and purse seine during scientific and fishing cruises. Diet data were processed by occurrence, by number, and by wet weight and a comparison of diets between surface and deep swimmers made. Crustaceans were the almost exclusive food source of surface-swimming bigeye tuna, with the stomatopod (Natosquilla investigatoris) being the sole prey item recorded in this category. The diet of deep-swimming yellowfin tuna was balanced between epipelagic fish, crustaceans and cephalopods. Bigeye tuna fed predominantly on cephalopods and mesopelagic fish (Scopelarchidae and Paralepididae), for which this predator appeared to be the most active chaser. The diet of the two predators reflects their ability to catch the prey, and their vertical distribution.
    Description: Published
    Description: Natosquilla investigatoris; Thunnus albacares; T. obesus; Feeding ecology; Vertical habitat
    Keywords: Tuna ; Fisheries ; Diets ; Tuna fisheries ; Analysis
    Repository Name: AquaDocs
    Type: Journal Contribution , Non-Refereed , Article
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  • 3
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    The industrial tuna fishing activity in the Western Indian Ocean: report for the year 2001 (2006)
    Victoria: Seychelles Fishing Authority | Victoria
    Details
    Publication Date: 2021-08-09
    Description: Published
    Description: Industrial tuna fishing
    Keywords: Tuna ; Fisheries ; Fishery economics ; Fishery industry ; Fishery statistics ; Tuna fisheries
    Repository Name: AquaDocs
    Type: Report , Non-Refereed
    Format: 1589602 bytes
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  • 4
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    Sustainability. Resolving mismatches in U.S. ocean governance (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-08-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Crowder, L B -- Osherenko, G -- Young, O R -- Airame, S -- Norse, E A -- Baron, N -- Day, J C -- Douvere, F -- Ehler, C N -- Halpern, B S -- Langdon, S J -- McLeod, K L -- Ogden, J C -- Peach, R E -- Rosenberg, A A -- Wilson, J A -- New York, N.Y. -- Science. 2006 Aug 4;313(5787):617-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Marine Conservation, Nicholas School of the Environment and Earth Sciences, Duke University Marine Laboratory, Beaufort, NC 28516, USA. lcrowder@duke.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16888124" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Conservation of Natural Resources ; *Ecosystem ; Environment ; Fisheries ; Fishes ; *Government Regulation ; *Marine Biology ; Oceans and Seas ; Population Dynamics ; Seawater ; United States
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Molecular recognition in the selective oxygenation of saturated C-H bonds by a dimanganese catalyst (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-01
    Description: Although enzymes often incorporate molecular recognition elements to orient substrates selectively, such strategies are rarely achieved by synthetic catalysts. We combined molecular recognition through hydrogen bonding with C-H activation to obtain high-turnover catalytic regioselective functionalization of sp3 C-H bonds remote from the -COOH recognition group. The catalyst contains a Mn(mu-O)2Mn reactive center and a ligand based on Kemp's triacid that directs a -COOH group to anchor the carboxylic acid group of the substrate and thus modify the usual selectivity for oxidation. Control experiments supported the role of hydrogen bonding in orienting the substrate to achieve high selectivity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Das, Siddhartha -- Incarvito, Christopher D -- Crabtree, Robert H -- Brudvig, Gary W -- GM32715/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Jun 30;312(5782):1941-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Yale University, 225 Prospect Street, Post Office Box 208107, New Haven, CT 06520-8107, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16809537" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Carbon/*chemistry ; Carboxylic Acids/*chemistry ; *Catalysis ; Chemistry, Physical ; Hydrogen/*chemistry ; Hydrogen Bonding ; Ibuprofen/*chemistry ; Ligands ; Magnetic Resonance Spectroscopy ; Manganese/*chemistry ; Models, Chemical ; Models, Molecular ; Molecular Structure ; Organometallic Compounds/*chemistry ; Oxidation-Reduction ; Physicochemical Phenomena
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    Evolution of hormone-receptor complexity by molecular exploitation (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-04-08
    Description: According to Darwinian theory, complexity evolves by a stepwise process of elaboration and optimization under natural selection. Biological systems composed of tightly integrated parts seem to challenge this view, because it is not obvious how any element's function can be selected for unless the partners with which it interacts are already present. Here we demonstrate how an integrated molecular system-the specific functional interaction between the steroid hormone aldosterone and its partner the mineralocorticoid receptor-evolved by a stepwise Darwinian process. Using ancestral gene resurrection, we show that, long before the hormone evolved, the receptor's affinity for aldosterone was present as a structural by-product of its partnership with chemically similar, more ancient ligands. Introducing two amino acid changes into the ancestral sequence recapitulates the evolution of present-day receptor specificity. Our results indicate that tight interactions can evolve by molecular exploitation-recruitment of an older molecule, previously constrained for a different role, into a new functional complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bridgham, Jamie T -- Carroll, Sean M -- Thornton, Joseph W -- F32-GM074398/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Apr 7;312(5770):97-101.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Ecology and Evolutionary Biology, University of Oregon, Eugene, OR 97403, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16601189" target="_blank"〉PubMed〈/a〉
    Keywords: Aldosterone/chemistry/*metabolism ; Amino Acid Substitution ; Animals ; Bayes Theorem ; Binding Sites ; Desoxycorticosterone/metabolism ; *Evolution, Molecular ; Gene Duplication ; Hagfishes ; Hydrocortisone/metabolism ; Lampreys ; Ligands ; Mutation ; Perciformes ; Phylogeny ; Rats ; Receptors, Glucocorticoid/chemistry/genetics/metabolism ; Receptors, Mineralocorticoid/chemistry/*genetics/*metabolism ; Receptors, Steroid/chemistry/*genetics/*metabolism ; Skates (Fish)
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
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    A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-05-27
    Description: We describe a pathogenetic mechanism underlying a variant form of the inherited blood disorder alpha thalassemia. Association studies of affected individuals from Melanesia localized the disease trait to the telomeric region of human chromosome 16, which includes the alpha-globin gene cluster, but no molecular defects were detected by conventional approaches. After resequencing and using a combination of chromatin immunoprecipitation and expression analysis on a tiled oligonucleotide array, we identified a gain-of-function regulatory single-nucleotide polymorphism (rSNP) in a nongenic region between the alpha-globin genes and their upstream regulatory elements. The rSNP creates a new promoterlike element that interferes with normal activation of all downstream alpha-like globin genes. Thus, our work illustrates a strategy for distinguishing between neutral and functionally important rSNPs, and it also identifies a pathogenetic mechanism that could potentially underlie other genetic diseases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉De Gobbi, Marco -- Viprakasit, Vip -- Hughes, Jim R -- Fisher, Chris -- Buckle, Veronica J -- Ayyub, Helena -- Gibbons, Richard J -- Vernimmen, Douglas -- Yoshinaga, Yuko -- de Jong, Pieter -- Cheng, Jan-Fang -- Rubin, Edward M -- Wood, William G -- Bowden, Don -- Higgs, Douglas R -- MC_U137961143/Medical Research Council/United Kingdom -- MC_U137961145/Medical Research Council/United Kingdom -- MC_U137961147/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2006 May 26;312(5777):1215-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, OX3 9DS, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16728641" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cells, Cultured ; Chromatin Immunoprecipitation ; Chromosomes, Human, Pair 16/*genetics ; Erythroblasts ; GATA1 Transcription Factor/metabolism ; Gene Expression ; Gene Expression Profiling ; Globins/*genetics ; Haplotypes ; Humans ; Melanesia ; Minisatellite Repeats ; Multigene Family ; Oligonucleotide Array Sequence Analysis ; *Polymorphism, Single Nucleotide ; *Promoter Regions, Genetic ; Regulatory Elements, Transcriptional ; Transcription, Genetic ; alpha-Thalassemia/*genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    Selective silencing of foreign DNA with low GC content by the H-NS protein in Salmonella (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-06-10
    Description: Horizontal gene transfer plays a major role in microbial evolution. However, newly acquired sequences can decrease fitness unless integrated into preexisting regulatory networks. We found that the histone-like nucleoid structuring protein (H-NS) selectively silences horizontally acquired genes by targeting sequences with GC content lower than the resident genome. Mutations in hns are lethal in Salmonella unless accompanied by compensatory mutations in other regulatory loci. Thus, H-NS provides a previously unrecognized mechanism of bacterial defense against foreign DNA, enabling the acquisition of DNA from exogenous sources while avoiding detrimental consequences from unregulated expression of newly acquired genes. Characteristic GC/AT ratios of bacterial genomes may facilitate discrimination between a cell's own DNA and foreign DNA.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Navarre, William Wiley -- Porwollik, Steffen -- Wang, Yipeng -- McClelland, Michael -- Rosen, Henry -- Libby, Stephen J -- Fang, Ferric C -- AI034829/AI/NIAID NIH HHS/ -- AI049417/AI/NIAID NIH HHS/ -- AI052237/AI/NIAID NIH HHS/ -- AI057733/AI/NIAID NIH HHS/ -- AI39557/AI/NIAID NIH HHS/ -- AI48622/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2006 Jul 14;313(5784):236-8. Epub 2006 Jun 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16763111" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/genetics/*metabolism ; Base Composition ; Binding Sites ; Chromatin Immunoprecipitation ; DNA, Bacterial/*chemistry/*genetics ; DNA-Binding Proteins/genetics/*metabolism ; Gene Expression Regulation, Bacterial ; *Gene Silencing ; *Gene Transfer, Horizontal ; Genome, Bacterial ; Helicobacter pylori/genetics ; Models, Genetic ; Mutation ; Oligonucleotide Array Sequence Analysis ; Repressor Proteins/genetics/*metabolism ; Salmonella typhimurium/*genetics/physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    Transcriptional repression distinguishes somatic from germ cell lineages in a plant (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-29
    Description: In flowering plants, the male germline begins with an asymmetric division, after which one of the resulting cells, the generative cell, divides symmetrically to produce two sperm cells. We show here that the male germline is initiated by transcriptional control. We identify GRSF, germline-restrictive silencing factor, from the lily. GRSF is ubiquitous in nongerm cells and is absent from male germ cells. GRSF recognizes silencer sequences in promoters of genes specific to the germline, stably repressing these genes in cells that are not destined to become germ cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haerizadeh, Farzad -- Singh, Mohan B -- Bhalla, Prem L -- New York, N.Y. -- Science. 2006 Jul 28;313(5786):496-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Molecular Biology and Biotechnology Laboratory, Australian Research Council Centre of Excellence for Integrative Legume Research, Faculty of Land and Food Resources, University of Melbourne, Parkville, Victoria 3010, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16873660" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Arabidopsis/cytology/genetics/metabolism ; Binding Sites ; Cell Lineage ; Cell Nucleus/metabolism ; Chromatin Immunoprecipitation ; Conserved Sequence ; *Gene Expression Regulation, Plant ; Gene Silencing ; Genes, Plant ; Germ Cells/*cytology/metabolism ; Lilium/cytology/*genetics/metabolism ; Plant Proteins/chemistry/*genetics/metabolism ; Promoter Regions, Genetic ; Recombinant Fusion Proteins ; Repressor Proteins/chemistry/genetics/*metabolism ; *Silencer Elements, Transcriptional ; *Transcription, Genetic ; Transformation, Genetic
    Print ISSN: 0036-8075
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  • 10
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    Biochemistry. Proteins in a small world (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yeates, Todd O -- Beeby, Morgan -- New York, N.Y. -- Science. 2006 Dec 22;314(5807):1882-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA90024-1569, USA. yeates@mbi.ucla.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17185587" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Evolution, Molecular ; Gene Duplication ; Gene Transfer, Horizontal ; *Metabolic Networks and Pathways ; Mutation ; Protein Binding ; *Protein Interaction Mapping ; Proteins/*chemistry/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 11
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    Transcript-assisted transcriptional proofreading (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-29
    Description: Fidelity of template-dependent nucleic acid synthesis is the main determinant of stable heredity and error-free gene expression. The mechanism (or mechanisms) ensuring fidelity of transcription by DNA-dependent RNA polymerases (RNAPs) is not fully understood. Here, we show that the 3' end-proximal nucleotide of the nascent transcript stimulates hydrolysis of the penultimate phosphodiester bond by providing active groups and coordination bonds to the RNAP active center. This stimulation is much higher in the case of misincorporated nucleotide. We show that during transcription elongation, the hydrolytic reaction stimulated by misincorporated nucleotides proofreads most of the misincorporation events and thus serves as an intrinsic mechanism of transcription fidelity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zenkin, Nikolay -- Yuzenkova, Yulia -- Severinov, Konstantin -- New York, N.Y. -- Science. 2006 Jul 28;313(5786):518-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA. nicserzen@mail.ru〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16873663" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/metabolism ; Base Pairing ; Binding Sites ; Catalysis ; Cytidine Monophosphate/metabolism ; DNA/metabolism ; DNA-Directed RNA Polymerases/*metabolism ; Hydrogen Bonding ; Hydrolysis ; Kinetics ; Magnesium/metabolism ; Models, Genetic ; Nucleotides/metabolism ; RNA, Messenger/*metabolism ; Templates, Genetic ; Thermus/enzymology ; *Transcription, Genetic
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 12
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    S6K1- and betaTRCP-mediated degradation of PDCD4 promotes protein translation and cell growth (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-10-21
    Description: The tumor suppressor programmed cell death protein 4 (PDCD4) inhibits the translation initiation factor eIF4A, an RNA helicase that catalyzes the unwinding of secondary structure at the 5' untranslated region (5'UTR) of messenger RNAs (mRNAs). In response to mitogens, PDCD4 was rapidly phosphorylated on Ser67 by the protein kinase S6K1 and subsequently degraded via the ubiquitin ligase SCF(betaTRCP). Expression in cultured cells of a stable PDCD4 mutant that is unable to bind betaTRCP inhibited translation of an mRNA with a structured 5'UTR, resulted in smaller cell size, and slowed down cell cycle progression. We propose that regulated degradation of PDCD4 in response to mitogens allows efficient protein synthesis and consequently cell growth.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dorrello, N Valerio -- Peschiaroli, Angelo -- Guardavaccaro, Daniele -- Colburn, Nancy H -- Sherman, Nicholas E -- Pagano, Michele -- R01-CA76584/CA/NCI NIH HHS/ -- R01-GM57587/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Oct 20;314(5798):467-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pathology, NYU Cancer Institute, New York University School of Medicine, 550 First Avenue, MSB 599, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17053147" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions ; Amino Acid Motifs ; Apoptosis Regulatory Proteins/chemistry/genetics/*metabolism ; Binding Sites ; Cell Line ; Cell Line, Tumor ; *Cell Proliferation ; Cell Size ; Eukaryotic Initiation Factor-4A/antagonists & inhibitors/metabolism ; Eukaryotic Initiation Factor-4F/metabolism ; Eukaryotic Initiation Factor-4G/metabolism ; Eukaryotic Initiation Factors/metabolism ; Humans ; Mitogens/pharmacology ; Phosphorylation ; *Protein Biosynthesis ; RNA, Small Interfering ; RNA-Binding Proteins/chemistry/genetics/*metabolism ; Ribosomal Protein S6 Kinases/metabolism ; SKP Cullin F-Box Protein Ligases/*metabolism ; Serine/metabolism ; Serum ; Signal Transduction ; beta-Transducin Repeat-Containing Proteins/genetics/*metabolism
    Print ISSN: 0036-8075
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  • 13
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    Electric fields at the active site of an enzyme: direct comparison of experiment with theory (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-15
    Description: The electric fields produced in folded proteins influence nearly every aspect of protein function. We present a vibrational spectroscopy technique that measures changes in electric field at a specific site of a protein as shifts in frequency (Stark shifts) of a calibrated nitrile vibration. A nitrile-containing inhibitor is used to deliver a unique probe vibration to the active site of human aldose reductase, and the response of the nitrile stretch frequency is measured for a series of mutations in the enzyme active site. These shifts yield quantitative information on electric fields that can be directly compared with electrostatics calculations. We show that extensive molecular dynamics simulations and ensemble averaging are required to reproduce the observed changes in field.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Suydam, Ian T -- Snow, Christopher D -- Pande, Vijay S -- Boxer, Steven G -- New York, N.Y. -- Science. 2006 Jul 14;313(5784):200-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16840693" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Reductase/antagonists & inhibitors/*chemistry/genetics/metabolism ; Binding Sites ; Circular Dichroism ; Computer Simulation ; *Electricity ; Enzyme Inhibitors/metabolism/pharmacology ; Humans ; Models, Molecular ; Mutation ; Nitriles/metabolism/pharmacology ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Spectrophotometry, Infrared ; Spectrum Analysis ; Static Electricity
    Print ISSN: 0036-8075
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  • 14
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    Viruses: making friends with old foes (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-05-13
    Description: The study of viruses has traditionally focused on their roles as infectious agents and as tools for understanding cell biology. Viruses are now finding a new expanded role as nanoplatforms with applications in materials science and medicine. Viruses form highly symmetrical monodisperse architectures and are ideal templates for engineering multifunctionality, including multivalent display of surface ligands and encapsulation of inorganic and organic materials. These developments assure that viruses will find applications as versatile nanoscale materials.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Douglas, Trevor -- Young, Mark -- R01EB000432/EB/NIBIB NIH HHS/ -- R01GM61340/GM/NIGMS NIH HHS/ -- R21EB005364/EB/NIBIB NIH HHS/ -- New York, N.Y. -- Science. 2006 May 12;312(5775):873-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Bio-Inspired Nanomaterials, Montana State University, Bozeman, MT 59717, USA. tdouglas@chemistry.montana.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16690856" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Biomimetics ; *Biotechnology ; *Capsid/chemistry/ultrastructure ; Genetic Vectors ; Inorganic Chemicals ; Ligands ; Metals/chemistry/metabolism ; *Nanostructures ; *Nanotechnology ; Organic Chemicals ; Peptide Library ; Surface Properties ; Virus Assembly ; *Viruses/chemistry/genetics/ultrastructure
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Marine parks need sharks? (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-04-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chapman, Demian D F -- Pikitch, Ellen K -- Babcock, Elizabeth A -- New York, N.Y. -- Science. 2006 Apr 28;312(5773):526-8; author reply 526-8.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16645076" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Anthozoa ; Biomass ; Caribbean Region ; *Conservation of Natural Resources ; *Ecosystem ; Fisheries ; *Fishes ; Predatory Behavior ; *Sharks
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  • 16
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    Architecture of mammalian fatty acid synthase at 4.5 A resolution (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-03-04
    Description: The homodimeric mammalian fatty acid synthase is one of the most complex cellular multienzymes, in that each 270-kilodalton polypeptide chain carries all seven functional domains required for fatty acid synthesis. We have calculated a 4.5 angstrom-resolution x-ray crystallographic map of porcine fatty acid synthase, highly homologous to the human multienzyme, and placed homologous template structures of all individual catalytic domains responsible for the cyclic elongation of fatty acid chains into the electron density. The positioning of domains reveals the complex architecture of the multienzyme forming an intertwined dimer with two lateral semicircular reaction chambers, each containing a full set of catalytic domains required for fatty acid elongation. Large distances between active sites and conformational differences between the reaction chambers demonstrate that mobility of the acyl carrier protein and general flexibility of the multienzyme must accompany handover of the reaction intermediates during the reaction cycle.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maier, Timm -- Jenni, Simon -- Ban, Nenad -- New York, N.Y. -- Science. 2006 Mar 3;311(5765):1258-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology (ETH Zurich), 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16513975" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Carrier Protein/chemistry/metabolism ; Animals ; Binding Sites ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Fatty Acid Synthases/*chemistry/isolation & purification/metabolism ; Fatty Acids/biosynthesis ; Mammary Glands, Animal/enzymology ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Swine
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    Immunology. When F-actin becomes too much of a good thing (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-08-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dustin, Michael L -- New York, N.Y. -- Science. 2006 Aug 11;313(5788):767-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Progam in Molecular Pathogenesis, Skirball Institute, New York University Medical Center, 540 First Avenue, New York, NY 10016, USA. dustin@saturn.med.nyu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16902113" target="_blank"〉PubMed〈/a〉
    Keywords: Actin-Related Protein 2-3 Complex/antagonists & inhibitors/metabolism ; Actins/*metabolism ; Animals ; Apoptosis ; Binding Sites ; Cell Death ; Cell Movement ; *Chemotaxis, Leukocyte ; Homeostasis ; Intracellular Membranes/physiology ; Membrane Potentials ; Mice ; Microfilament Proteins/chemistry/*physiology ; Mitochondria/*physiology ; Protein Structure, Tertiary ; Receptors, Antigen, T-Cell/immunology ; T-Lymphocytes/immunology/*physiology ; Voltage-Dependent Anion Channels/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Biochemistry. Loop grafting and the origins of enzyme species (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-01-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tawfik, Dan S -- New York, N.Y. -- Science. 2006 Jan 27;311(5760):475-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel. tawfik@weizmann.ac.il〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16439649" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; *Directed Molecular Evolution ; Evolution, Molecular ; *Protein Engineering ; Substrate Specificity ; Thiolester Hydrolases/*chemistry/*metabolism ; beta-Lactamases/chemistry/*metabolism ; beta-Lactams/metabolism
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  • 19
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    Structure of the hydrophilic domain of respiratory complex I from Thermus thermophilus (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-02-14
    Description: Respiratory complex I plays a central role in cellular energy production in bacteria and mitochondria. Its dysfunction is implicated in many human neurodegenerative diseases, as well as in aging. The crystal structure of the hydrophilic domain (peripheral arm) of complex I from Thermus thermophilus has been solved at 3.3 angstrom resolution. This subcomplex consists of eight subunits and contains all the redox centers of the enzyme, including nine iron-sulfur clusters. The primary electron acceptor, flavin-mononucleotide, is within electron transfer distance of cluster N3, leading to the main redox pathway, and of the distal cluster N1a, a possible antioxidant. The structure reveals new aspects of the mechanism and evolution of the enzyme. The terminal cluster N2 is coordinated, uniquely, by two consecutive cysteines. The novel subunit Nqo15 has a similar fold to the mitochondrial iron chaperone frataxin, and it may be involved in iron-sulfur cluster regeneration in the complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sazanov, Leonid A -- Hinchliffe, Philip -- MC_U105674180/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2006 Mar 10;311(5766):1430-6. Epub 2006 Feb 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Dunn Human Nutrition Unit, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 2XY, U.K. sazanov@mrc-dunn.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16469879" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bacterial Proteins/*chemistry ; Binding Sites ; Crystallography, X-Ray ; Electron Transport Complex I/*chemistry ; Iron-Binding Proteins/chemistry ; Oxidation-Reduction ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Protein Subunits ; Thermus thermophilus/*chemistry
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    Atomic description of an enzyme reaction dominated by proton tunneling (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-04-15
    Description: We present an atomic-level description of the reaction chemistry of an enzyme-catalyzed reaction dominated by proton tunneling. By solving structures of reaction intermediates at near-atomic resolution, we have identified the reaction pathway for tryptamine oxidation by aromatic amine dehydrogenase. Combining experiment and computer simulation, we show proton transfer occurs predominantly to oxygen O2 of Asp(128)beta in a reaction dominated by tunneling over approximately 0.6 angstroms. The role of long-range coupled motions in promoting tunneling is controversial. We show that, in this enzyme system, tunneling is promoted by a short-range motion modulating proton-acceptor distance and no long-range coupled motion is required.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Masgrau, Laura -- Roujeinikova, Anna -- Johannissen, Linus O -- Hothi, Parvinder -- Basran, Jaswir -- Ranaghan, Kara E -- Mulholland, Adrian J -- Sutcliffe, Michael J -- Scrutton, Nigel S -- Leys, David -- New York, N.Y. -- Science. 2006 Apr 14;312(5771):237-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Manchester Interdisciplinary Biocentre, University of Manchester, Jackson's Mill, Post Office Box 88, Manchester M60 1QD, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16614214" target="_blank"〉PubMed〈/a〉
    Keywords: Alcaligenes faecalis/*enzymology ; Aspartic Acid/chemistry ; Binding Sites ; Catalysis ; Chemistry, Physical ; Computer Simulation ; Crystallography, X-Ray ; Kinetics ; Models, Chemical ; Motion ; Oxidation-Reduction ; Oxidoreductases Acting on CH-NH Group Donors/*chemistry/*metabolism ; Oxygen/chemistry ; Physicochemical Phenomena ; *Protons ; Temperature ; Thermodynamics ; Tryptamines/*metabolism ; Water/chemistry
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 21
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    Structure of a DNA glycosylase searching for lesions (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-02-25
    Description: DNA glycosylases must interrogate millions of base pairs of undamaged DNA in order to locate and then excise one damaged nucleobase. The nature of this search process remains poorly understood. Here we report the use of disulfide cross-linking (DXL) technology to obtain structures of a bacterial DNA glycosylase, MutM, interrogating undamaged DNA. These structures, solved to 2.0 angstrom resolution, reveal the nature of the search process: The protein inserts a probe residue into the helical stack and severely buckles the target base pair, which remains intrahelical. MutM therefore actively interrogates the intact DNA helix while searching for damage.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Banerjee, Anirban -- Santos, Webster L -- Verdine, Gregory L -- F32 GM067380/GM/NIGMS NIH HHS/ -- GM044853/GM/NIGMS NIH HHS/ -- R01 CA100742/CA/NCI NIH HHS/ -- R01 GM044853/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Feb 24;311(5764):1153-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16497933" target="_blank"〉PubMed〈/a〉
    Keywords: *Base Pairing ; Binding Sites ; Cross-Linking Reagents ; Crystallography, X-Ray ; DNA/*chemistry/metabolism ; *DNA Damage ; DNA Glycosylases/*chemistry/*metabolism ; Geobacillus stearothermophilus/*enzymology ; Guanine/*analogs & derivatives/analysis/metabolism ; Hydrogen Bonding ; Models, Molecular ; Nucleic Acid Conformation ; Oligodeoxyribonucleotides/chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary
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  • 22
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    Crystal structure of a divalent metal ion transporter CorA at 2.9 angstrom resolution (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-07-22
    Description: CorA family members are ubiquitously distributed transporters of divalent metal cations and are considered to be the primary Mg2+ transporter of Bacteria and Archaea. We have determined a 2.9 angstrom resolution structure of CorA from Thermotoga maritima that reveals a pentameric cone-shaped protein. Two potential regulatory metal binding sites are found in the N-terminal domain that bind both Mg2+ and Co2+. The structure of CorA supports an efflux system involving dehydration and rehydration of divalent metal ions potentially mediated by a ring of conserved aspartate residues at the cytoplasmic entrance and a carbonyl funnel at the periplasmic side of the pore.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eshaghi, Said -- Niegowski, Damian -- Kohl, Andreas -- Martinez Molina, Daniel -- Lesley, Scott A -- Nordlund, Par -- New York, N.Y. -- Science. 2006 Jul 21;313(5785):354-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77 Stockholm, Sweden. Said.Eshaghi@ki.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16857941" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Cation Transport Proteins/*chemistry/metabolism ; Chlorides/analysis/metabolism ; Cobalt/chemistry/*metabolism ; Crystallography, X-Ray ; Hydrophobic and Hydrophilic Interactions ; Magnesium/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; Thermotoga maritima/*chemistry ; Water/chemistry
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  • 23
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    An architectural framework that may lie at the core of the postsynaptic density (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-01-28
    Description: The postsynaptic density (PSD) is a complex assembly of proteins associated with the postsynaptic membrane that organizes neurotransmitter receptors, signaling pathways, and regulatory elements within a cytoskeletal matrix. Here we show that the sterile alpha motif domain of rat Shank3/ProSAP2, a master scaffolding protein located deep within the PSD, can form large sheets composed of helical fibers stacked side by side. Zn2+, which is found in high concentrations in the PSD, binds tightly to Shank3 and may regulate assembly. Sheets of the Shank protein could form a platform for the construction of the PSD complex.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baron, Marisa K -- Boeckers, Tobias M -- Vaida, Bianca -- Faham, Salem -- Gingery, Mari -- Sawaya, Michael R -- Salyer, Danielle -- Gundelfinger, Eckart D -- Bowie, James U -- R01 CA081000/CA/NCI NIH HHS/ -- R01 GM063919/GM/NIGMS NIH HHS/ -- R01 GM063919-07/GM/NIGMS NIH HHS/ -- R01 GM063919-08/GM/NIGMS NIH HHS/ -- R01 GM075922/GM/NIGMS NIH HHS/ -- R01 GM075922-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Jan 27;311(5760):531-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095-1570, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16439662" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/analysis/*chemistry/genetics/metabolism ; Animals ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Hippocampus/chemistry ; Microscopy, Electron ; Models, Molecular ; Mutation ; Nerve Tissue Proteins ; Neurons/chemistry ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Rats ; Recombinant Fusion Proteins/analysis ; Solubility ; Synapses/*chemistry ; Zinc/metabolism
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    Migration and Dispersal. Sound sightings (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-08-12
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Holden, Constance -- New York, N.Y. -- Science. 2006 Aug 11;313(5788):777.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16902121" target="_blank"〉PubMed〈/a〉
    Keywords: *Acoustics ; *Animal Identification Systems ; Animals ; *Ecosystem ; Environment ; Fisheries ; *Fishes ; International Cooperation ; Movement ; Oceans and Seas ; Seawater ; Telemetry
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  • 25
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    Biochemistry. Enzyme motions inside and out (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-04-15
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Benkovic, Stephen J -- Hammes-Schiffer, Sharon -- GM24129/GM/NIGMS NIH HHS/ -- GM56207/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Apr 14;312(5771):208-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA. sjb1@psu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16614206" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Chemistry, Physical ; Computer Simulation ; Hydrogen/chemistry ; Kinetics ; Models, Chemical ; Motion ; Oxidation-Reduction ; Oxidoreductases Acting on CH-NH Group Donors/*chemistry/*metabolism ; Physicochemical Phenomena ; Protein Conformation ; *Protons ; Thermodynamics ; Tryptamines/*metabolism
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  • 26
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    Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-04-08
    Description: Biological responses to histone methylation critically depend on the faithful readout and transduction of the methyl-lysine signal by "effector" proteins, yet our understanding of methyl-lysine recognition has so far been limited to the study of histone binding by chromodomain and WD40-repeat proteins. The double tudor domain of JMJD2A, a Jmjc domain-containing histone demethylase, binds methylated histone H3-K4 and H4-K20. We found that the double tudor domain has an interdigitated structure, and the unusual fold is required for its ability to bind methylated histone tails. The cocrystal structure of the JMJD2A double tudor domain with a trimethylated H3-K4 peptide reveals that the trimethyl-K4 is bound in a cage of three aromatic residues, two of which are from the tudor-2 motif, whereas the binding specificity is determined by side-chain interactions involving amino acids from the tudor-1 motif. Our study provides mechanistic insights into recognition of methylated histone tails by tudor domains and reveals the structural intricacy of methyl-lysine recognition by two closely spaced effector domains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Ying -- Fang, Jia -- Bedford, Mark T -- Zhang, Yi -- Xu, Rui-Ming -- DK62248/DK/NIDDK NIH HHS/ -- GM 63718/GM/NIGMS NIH HHS/ -- GM68804/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 May 5;312(5774):748-51. Epub 2006 Apr 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16601153" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Histones/*chemistry/*metabolism ; Humans ; Hydrogen Bonding ; Jumonji Domain-Containing Histone Demethylases ; Lysine/metabolism ; Methylation ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Oxidoreductases, N-Demethylating ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Static Electricity ; Transcription Factors/*chemistry/genetics/*metabolism
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  • 27
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    Conformational switches modulate protein interactions in peptide antibiotic synthetases (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-04-15
    Description: Protein dynamics plays an important role in protein function. Many functionally important motions occur on the microsecond and low millisecond time scale and can be characterized by nuclear magnetic resonance relaxation experiments. We describe the different states of a peptidyl carrier protein (PCP) that play a crucial role in its function as a peptide shuttle in the nonribosomal peptide synthetases of the tyrocidine A system. Both apo-PCP (without the bound 4'-phosphopantetheine cofactor) and holo-PCP exist in two different stable conformations. We show that one of the apo conformations and one of the holo conformations are identical, whereas the two remaining conformations are only detectable by nuclear magnetic resonance spectroscopy in either the apo or holo form. We further demonstrate that this conformational diversity is an essential prerequisite for the directed movement of the 4'-PP cofactor and its interaction with externally acting proteins such as thioesterases and 4'-PP transferase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koglin, Alexander -- Mofid, Mohammad R -- Lohr, Frank -- Schafer, Birgit -- Rogov, Vladimir V -- Blum, Marc-Michael -- Mittag, Tanja -- Marahiel, Mohamed A -- Bernhard, Frank -- Dotsch, Volker -- New York, N.Y. -- Science. 2006 Apr 14;312(5771):273-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance (BMRZ), J.W. Goethe University of Frankfurt, Marie-Curie-Strasse, D-60439 Frankfurt/Main, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16614225" target="_blank"〉PubMed〈/a〉
    Keywords: Apoproteins/chemistry/metabolism ; Bacterial Proteins/chemistry/metabolism ; Binding Sites ; Carrier Proteins/*chemistry/*metabolism ; Crystallography, X-Ray ; Fatty Acid Synthases/metabolism ; Holoenzymes/chemistry/metabolism ; Models, Molecular ; Nuclear Magnetic Resonance, Biomolecular ; Pantetheine/analogs & derivatives/metabolism ; Peptide Synthases/*chemistry/*metabolism ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Thiolester Hydrolases/metabolism ; Transferases/metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Direct demonstration of an adaptive constraint (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-10-21
    Description: The role of constraint in adaptive evolution is an open question. Directed evolution of an engineered beta-isopropylmalate dehydrogenase (IMDH), with coenzyme specificity switched from nicotinamide adenine dinucleotide (NAD) to nicotinamide adenine dinucleotide phosphate (NADP), always produces mutants with lower affinities for NADP. This result is the correlated response to selection for relief from inhibition by NADPH (the reduced form of NADP) expected of an adaptive landscape subject to three enzymatic constraints: an upper limit to the rate of maximum turnover (kcat), a correlation in NADP and NADPH affinities, and a trade-off between NAD and NADP usage. Two additional constraints, high intracellular NADPH abundance and the cost of compensatory protein synthesis, have ensured the conserved use of NAD by IMDH throughout evolution. Our results show that selective mechanisms and evolutionary constraints are to be understood in terms of underlying adaptive landscapes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, Stephen P -- Lunzer, Mark -- Dean, Antony M -- GM060611/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Oct 20;314(5798):458-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17053145" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Isopropylmalate Dehydrogenase/antagonists & ; inhibitors/chemistry/genetics/*metabolism ; *Adaptation, Physiological ; Amino Acid Substitution ; Binding Sites ; Codon ; *Directed Molecular Evolution ; Escherichia coli/*enzymology/growth & development/physiology ; *Evolution, Molecular ; Kinetics ; Mutation ; NAD/metabolism ; NADP/metabolism ; Phenotype ; Selection, Genetic
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    Molecular biology. Self-correcting messages (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cramer, Patrick -- New York, N.Y. -- Science. 2006 Jul 28;313(5786):447-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Gene Center Munich, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universitat Munchen, Feodor-Lynen-Strasse 25, 81377 Munich, Germany. cramer@lmb.uni-muenchen.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16873631" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; DNA-Directed DNA Polymerase/metabolism ; DNA-Directed RNA Polymerases/*metabolism ; Evolution, Molecular ; Magnesium/metabolism ; RNA, Messenger/*metabolism ; *Transcription, Genetic
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    Differential targeting of Gbetagamma-subunit signaling with small molecules (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-04-22
    Description: G protein betagamma subunits have potential as a target for therapeutic treatment of a number of diseases. We performed virtual docking of a small-molecule library to a site on Gbetagamma subunits that mediates protein interactions. We hypothesized that differential targeting of this surface could allow for selective modulation of Gbetagamma subunit functions. Several compounds bound to Gbetagamma subunits with affinities from 0.1 to 60 muM and selectively modulated functional Gbetagamma-protein-protein interactions in vitro, chemotactic peptide signaling pathways in HL-60 leukocytes, and opioid receptor-dependent analgesia in vivo. These data demonstrate an approach for modulation of G protein-coupled receptor signaling that may represent an important therapeutic strategy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bonacci, Tabetha M -- Mathews, Jennifer L -- Yuan, Chujun -- Lehmann, David M -- Malik, Sundeep -- Wu, Dianqing -- Font, Jose L -- Bidlack, Jean M -- Smrcka, Alan V -- GM60286/GM/NIGMS NIH HHS/ -- HL-T3207949/HL/NHLBI NIH HHS/ -- HL080706/HL/NHLBI NIH HHS/ -- K05-DA00360/DA/NIDA NIH HHS/ -- R01 CA132317/CA/NCI NIH HHS/ -- R01 GM054597/GM/NIGMS NIH HHS/ -- R01 GM054597-09/GM/NIGMS NIH HHS/ -- R01 HL080706/HL/NHLBI NIH HHS/ -- R01 HL080706-10/HL/NHLBI NIH HHS/ -- R01 HL080706-11/HL/NHLBI NIH HHS/ -- T32DA07232/DA/NIDA NIH HHS/ -- New York, N.Y. -- Science. 2006 Apr 21;312(5772):443-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology and Physiology, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16627746" target="_blank"〉PubMed〈/a〉
    Keywords: Analgesics/pharmacology ; Animals ; Binding Sites ; Binding, Competitive ; Cell Line ; Computer Simulation ; Cyclohexanes/chemistry/*metabolism/*pharmacology ; Drug Evaluation, Preclinical/*methods ; Enzyme-Linked Immunosorbent Assay ; G-Protein-Coupled Receptor Kinase 2 ; GTP-Binding Protein alpha Subunits/metabolism ; GTP-Binding Protein beta Subunits/chemistry/*metabolism ; GTP-Binding Protein gamma Subunits/chemistry/*metabolism ; HL-60 Cells ; Humans ; Isoenzymes/metabolism ; Mice ; Mice, Inbred ICR ; Mitogen-Activated Protein Kinases/metabolism ; Molecular Structure ; Morphine/pharmacology ; N-Formylmethionine Leucyl-Phenylalanine/metabolism ; Peptide Library ; Peptides/*metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Phospholipase C beta ; Protein Binding ; Protein Interaction Mapping ; *Signal Transduction ; Software ; Structure-Activity Relationship ; Type C Phospholipases/metabolism ; Xanthenes/chemistry/*metabolism/*pharmacology ; beta-Adrenergic Receptor Kinases/metabolism
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    N- to C-terminal SNARE complex assembly promotes rapid membrane fusion (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-08-05
    Description: Assembly of the soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) syntaxin 1, SNAP-25, and synaptobrevin 2 is thought to be the driving force for the exocytosis of synaptic vesicles. However, whereas exocytosis is triggered at a millisecond time scale, the SNARE-mediated fusion of liposomes requires hours for completion, which challenges the idea of a key role for SNAREs in the final steps of exocytosis. We found that liposome fusion was dramatically accelerated when a stabilized syntaxin/SNAP-25 acceptor complex was used. Thus, SNAREs do have the capacity to execute fusion at a speed required for neuronal secretion, demonstrating that the maintenance of acceptor complexes is a critical step in biological fusion reactions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pobbati, Ajaybabu V -- Stein, Alexander -- Fasshauer, Dirk -- P01 GM072694/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Aug 4;313(5787):673-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, 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/16888141" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Circular Dichroism ; Dimerization ; Exocytosis ; Liposomes/*chemistry ; *Membrane Fusion ; Molecular Sequence Data ; Peptide Fragments/chemistry/metabolism ; Protein Binding ; Protein Folding ; Protein Structure, Secondary ; Qa-SNARE Proteins/chemistry/*metabolism ; R-SNARE Proteins/chemistry/metabolism ; Rats ; Synaptosomal-Associated Protein 25/chemistry/*metabolism
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    Structural basis for ribosome recruitment and manipulation by a viral IRES RNA (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-11-25
    Description: Canonical cap-dependent translation initiation requires a large number of protein factors that act in a stepwise assembly process. In contrast, internal ribosomal entry sites (IRESs) are cis-acting RNAs that in some cases completely supplant these factors by recruiting and activating the ribosome using a single structured RNA. Here we present the crystal structures of the ribosome-binding domain from a Dicistroviridae intergenic region IRES at 3.1 angstrom resolution, providing a view of the prefolded architecture of an all-RNA translation initiation apparatus. Docking of the structure into cryo-electron microscopy reconstructions of an IRES-ribosome complex suggests a model for ribosome manipulation by a dynamic IRES RNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2669756/" 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/PMC2669756/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pfingsten, Jennifer S -- Costantino, David A -- Kieft, Jeffrey S -- R01 GM072560/GM/NIGMS NIH HHS/ -- R01 GM072560-01/GM/NIGMS NIH HHS/ -- R01 GM072560-02/GM/NIGMS NIH HHS/ -- R01 GM072560-03/GM/NIGMS NIH HHS/ -- R01 GM072560-04/GM/NIGMS NIH HHS/ -- R01 GM072560-05/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Dec 1;314(5804):1450-4. Epub 2006 Nov 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Mail Stop 8101, Post Office Box 6511, Aurora, CO 80045, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17124290" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cryoelectron Microscopy ; Crystallization ; Crystallography, X-Ray ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; *Protein Biosynthesis ; RNA Viruses/*genetics ; RNA, Viral/*chemistry/genetics/metabolism ; *Regulatory Sequences, Ribonucleic Acid/genetics ; Ribosomes/*metabolism
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    Architecture of a fungal fatty acid synthase at 5 A resolution (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-04
    Description: All steps of fatty acid synthesis in fungi are catalyzed by the fatty acid synthase, which forms a 2.6-megadalton alpha6beta6 complex. We have determined the molecular architecture of this multienzyme by fitting the structures of homologous enzymes that catalyze the individual steps of the reaction pathway into a 5 angstrom x-ray crystallographic electron density map. The huge assembly contains two separated reaction chambers, each equipped with three sets of active sites separated by distances up to approximately 130 angstroms, across which acyl carrier protein shuttles substrates during the reaction cycle. Regions of the electron density arising from well-defined structural features outside the catalytic domains separate the two reaction chambers and serve as a matrix in which domains carrying the various active sites are embedded. The structure rationalizes the compartmentalization of fatty acid synthesis, and the spatial arrangement of the active sites has specific implications for our understanding of the reaction cycle mechanism and of the architecture of multienzymes in general.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jenni, Simon -- Leibundgut, Marc -- Maier, Timm -- Ban, Nenad -- New York, N.Y. -- Science. 2006 Mar 3;311(5765):1263-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, Department of Biology, Swiss Federal Institute of Technology (ETH Zurich), 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16513976" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Carrier Protein/chemistry/metabolism ; Ascomycota/*enzymology ; Binding Sites ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Fatty Acid Synthases/*chemistry/isolation & purification/metabolism ; Fatty Acids/biosynthesis ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Homology, Amino Acid
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    Structure of dual function iron regulatory protein 1 complexed with ferritin IRE-RNA (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-12-23
    Description: Iron regulatory protein 1 (IRP1) binds iron-responsive elements (IREs) in messenger RNAs (mRNAs), to repress translation or degradation, or binds an iron-sulfur cluster, to become a cytosolic aconitase enzyme. The 2.8 angstrom resolution crystal structure of the IRP1:ferritin H IRE complex shows an open protein conformation compared with that of cytosolic aconitase. The extended, L-shaped IRP1 molecule embraces the IRE stem-loop through interactions at two sites separated by approximately 30 angstroms, each involving about a dozen protein:RNA bonds. Extensive conformational changes related to binding the IRE or an iron-sulfur cluster explain the alternate functions of IRP1 as an mRNA regulator or enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Walden, William E -- Selezneva, Anna I -- Dupuy, Jerome -- Volbeda, Anne -- Fontecilla-Camps, Juan C -- Theil, Elizabeth C -- Volz, Karl -- DK20251/DK/NIDDK NIH HHS/ -- DK47281/DK/NIDDK NIH HHS/ -- GM47522/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Dec 22;314(5807):1903-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612-7344, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17185597" target="_blank"〉PubMed〈/a〉
    Keywords: Apoferritins/*genetics ; Binding Sites ; Crystallography, X-Ray ; Hydrogen Bonding ; Iron/metabolism ; Iron Regulatory Protein 1/*chemistry/*metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Messenger/chemistry/genetics/metabolism ; *Regulatory Sequences, Ribonucleic Acid ; *Response Elements ; Sulfur/metabolism ; Untranslated Regions/*chemistry/*metabolism
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    Regulation of adult bone mass by the zinc finger adapter protein Schnurri-3 (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-05-27
    Description: Genetic mutations that disrupt osteoblast function can result in skeletal dysmorphogenesis or, more rarely, in increased postnatal bone formation. Here we show that Schnurri-3 (Shn3), a mammalian homolog of the Drosophila zinc finger adapter protein Shn, is an essential regulator of adult bone formation. Mice lacking Shn3 display adult-onset osteosclerosis with increased bone mass due to augmented osteoblast activity. Shn3 was found to control protein levels of Runx2, the principal transcriptional regulator of osteoblast differentiation, by promoting its degradation through recruitment of the E3 ubiquitin ligase WWP1 to Runx2. By this means, Runx2-mediated extracellular matrix mineralization was antagonized, revealing an essential role for Shn3 as a central regulator of postnatal bone mass.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jones, Dallas C -- Wein, Marc N -- Oukka, Mohamed -- Hofstaetter, Jochen G -- Glimcher, Melvin J -- Glimcher, Laurie H -- AI29673/AI/NIAID NIH HHS/ -- AR46983/AR/NIAMS NIH HHS/ -- New York, N.Y. -- Science. 2006 May 26;312(5777):1223-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16728642" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; *Bone Density ; Bone and Bones/*anatomy & histology/chemistry/physiology ; Cell Line ; Cells, Cultured ; Core Binding Factor Alpha 1 Subunit/genetics/metabolism ; DNA-Binding Proteins/analysis/genetics/*metabolism ; Gene Expression Regulation ; Immunoprecipitation ; Mice ; Osteoblasts/chemistry/physiology ; Osteoclasts/physiology ; Osteogenesis ; Protein Binding ; Protein Structure, Tertiary ; RNA Interference ; RNA, Messenger/genetics/metabolism ; Transcriptional Activation ; Transfection ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/chemistry/metabolism ; Zinc Fingers
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    The dynamic energy landscape of dihydrofolate reductase catalysis (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-09-16
    Description: We used nuclear magnetic resonance relaxation dispersion to characterize higher energy conformational substates of Escherichia coli dihydrofolate reductase. Each intermediate in the catalytic cycle samples low-lying excited states whose conformations resemble the ground-state structures of preceding and following intermediates. Substrate and cofactor exchange occurs through these excited substates. The maximum hydride transfer and steady-state turnover rates are governed by the dynamics of transitions between ground and excited states of the intermediates. Thus, the modulation of the energy landscape by the bound ligands funnels the enzyme through its reaction cycle along a preferred kinetic path.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boehr, David D -- McElheny, Dan -- Dyson, H Jane -- Wright, Peter E -- GM56879/GM/NIGMS NIH HHS/ -- GM75995/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Sep 15;313(5793):1638-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Skaggs Institute for Chemical Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16973882" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Catalysis ; Escherichia coli/*enzymology ; Kinetics ; Ligands ; Models, Molecular ; NADP/metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Protein Binding ; *Protein Conformation ; Tetrahydrofolate Dehydrogenase/*chemistry/*metabolism ; Tetrahydrofolates/metabolism ; Thermodynamics
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    The Ste5 scaffold allosterically modulates signaling output of the yeast mating pathway (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-01-21
    Description: Scaffold proteins organize signaling proteins into pathways and are often viewed as passive assembly platforms. We found that the Ste5 scaffold has a more active role in the yeast mating pathway: A fragment of Ste5 allosterically activated autophosphorylation of the mitogen-activated protein kinase Fus3. The resulting form of Fus3 is partially active-it is phosphorylated on only one of two key residues in the activation loop. Unexpectedly, at a systems level, autoactivated Fus3 appears to have a negative regulatory role, promoting Ste5 phosphorylation and a decrease in pathway transcriptional output. Thus, scaffolds not only direct basic pathway connectivity but can precisely tune quantitative pathway input-output properties.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bhattacharyya, Roby P -- Remenyi, Attila -- Good, Matthew C -- Bashor, Caleb J -- Falick, Arnold M -- Lim, Wendell A -- New York, N.Y. -- Science. 2006 Feb 10;311(5762):822-6. Epub 2006 Jan 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California-San Francisco, 600 16th Street, San Francisco, CA 94143-2240, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16424299" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/*chemistry/genetics/*metabolism ; Allosteric Regulation ; Amino Acid Motifs ; Binding Sites ; Crystallography, X-Ray ; Down-Regulation ; Enzyme Activation ; *MAP Kinase Signaling System ; Mitogen-Activated Protein Kinases/*chemistry/*metabolism ; Models, Biological ; Models, Molecular ; Mutation ; Pheromones/*physiology ; Phosphorylation ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism ; Transcription, Genetic
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    Structural biology. Architectural options for a fatty acid synthase (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Smith, Stuart -- New York, N.Y. -- Science. 2006 Mar 3;311(5765):1251-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA. ssmith@chori.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16513973" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Dimerization ; Evolution, Molecular ; Fatty Acid Synthases/*chemistry/metabolism ; Fatty Acids/biosynthesis ; Fungi/enzymology ; Models, Molecular ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry
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    Synthesis-mediated release of a small RNA inhibitor of RNA polymerase (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-12-13
    Description: Noncoding small RNAs regulate gene expression in all organisms, in some cases through direct association with RNA polymerase (RNAP). Here we report that the mechanism of 6S RNA inhibition of transcription is through specific, stable interactions with the active site of Escherichia coli RNAP that exclude promoter DNA binding. In fact, the DNA-dependent RNAP uses bound 6S RNA as a template for RNA synthesis, producing 14-to 20-nucleotide RNA products (pRNA). These results demonstrate that 6S RNA is functionally engaged in the active site of RNAP. Synthesis of pRNA destabilizes 6S RNA-RNAP complexes leading to release of the pRNA-6S RNA hybrid. In vivo, 6S RNA-directed RNA synthesis occurs during outgrowth from the stationary phase and likely is responsible for liberating RNAP from 6S RNA in response to nutrient availability.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wassarman, Karen M -- Saecker, Ruth M -- GM23467/GM/NIGMS NIH HHS/ -- GM67955/GM/NIGMS NIH HHS/ -- R01 GM067955/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Dec 8;314(5805):1601-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA. wassarman@bact.wisc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17158328" target="_blank"〉PubMed〈/a〉
    Keywords: Base Sequence ; Binding Sites ; DNA, Bacterial/chemistry/metabolism ; DNA-Directed RNA Polymerases/antagonists & inhibitors/chemistry/*metabolism ; Escherichia coli/genetics/growth & development/*metabolism ; Molecular Sequence Data ; Nucleic Acid Conformation ; Promoter Regions, Genetic ; RNA Stability ; RNA, Bacterial/biosynthesis/chemistry/genetics/*metabolism ; RNA, Double-Stranded/chemistry/metabolism ; RNA, Untranslated/chemistry/genetics/*metabolism ; Sigma Factor/*metabolism ; Templates, Genetic ; Transcription, Genetic
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    Structure and receptor specificity of the hemagglutinin from an H5N1 influenza virus (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-18
    Description: The hemagglutinin (HA) structure at 2.9 angstrom resolution, from a highly pathogenic Vietnamese H5N1 influenza virus, is more related to the 1918 and other human H1 HAs than to a 1997 duck H5 HA. Glycan microarray analysis of this Viet04 HA reveals an avian alpha2-3 sialic acid receptor binding preference. Introduction of mutations that can convert H1 serotype HAs to human alpha2-6 receptor specificity only enhanced or reduced affinity for avian-type receptors. However, mutations that can convert avian H2 and H3 HAs to human receptor specificity, when inserted onto the Viet04 H5 HA framework, permitted binding to a natural human alpha2-6 glycan, which suggests a path for this H5N1 virus to gain a foothold in the human population.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stevens, James -- Blixt, Ola -- Tumpey, Terrence M -- Taubenberger, Jeffery K -- Paulson, James C -- Wilson, Ian A -- AI058113/AI/NIAID NIH HHS/ -- AI42266/AI/NIAID NIH HHS/ -- CA55896/CA/NCI NIH HHS/ -- GM060938/GM/NIGMS NIH HHS/ -- GM062116/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Apr 21;312(5772):404-10. Epub 2006 Mar 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. jstevens@scripps.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16543414" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Antigenic Variation ; Binding Sites ; Birds ; Carbohydrate Conformation ; Cloning, Molecular ; Crystallography, X-Ray ; Glycosylation ; Hemagglutinin Glycoproteins, Influenza ; Virus/*chemistry/genetics/immunology/*metabolism ; Humans ; Influenza A Virus, H5N1 Subtype/*chemistry/genetics/metabolism/*pathogenicity ; Lung/virology ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Polysaccharides/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Receptors, Virus/chemistry/*metabolism ; Respiratory Mucosa/virology ; Sialic Acids/chemistry/metabolism ; Species Specificity ; Virulence
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Cell signaling. A sophisticated scaffold wields a new trick (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-02-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Breitkreutz, Ashton -- Tyers, Mike -- New York, N.Y. -- Science. 2006 Feb 10;311(5762):789-90.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Campbell Family Institute for Breast Cancer Research, Toronto Medical Discovery Tower, Toronto, Canada M5G 1L7. abreitkr@uhnres.utoronto.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16469909" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/chemistry/genetics/*metabolism ; Binding Sites ; *MAP Kinase Signaling System ; Mitogen-Activated Protein Kinase Kinases ; Mitogen-Activated Protein Kinases/chemistry/*metabolism ; Models, Biological ; Mutation ; Pheromones/physiology ; Phosphorylation ; Protein Binding ; Protein Conformation ; Protein Kinases/metabolism ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Tyrosine/metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Fishing, trophic cascades, and the process of grazing on coral reefs (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-01-10
    Description: Since the mass mortality of the urchin Diadema antillarum in 1983, parrotfishes have become the dominant grazer on Caribbean reefs. The grazing capacity of these fishes could be impaired if marine reserves achieve their long-term goal of restoring large consumers, several of which prey on parrotfishes. Here we compare the negative impacts of enhanced predation with the positive impacts of reduced fishing mortality on parrotfishes inside reserves. Because large-bodied parrotfishes escape the risk of predation from a large piscivore (the Nassau grouper), the predation effect reduced grazing by only 4 to 8%. This impact was overwhelmed by the increase in density of large parrotfishes, resulting in a net doubling of grazing. Increased grazing caused a fourfold reduction in the cover of macroalgae, which, because they are the principal competitors of corals, highlights the potential importance of reserves for coral reef resilience.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mumby, Peter J -- Dahlgren, Craig P -- Harborne, Alastair R -- Kappel, Carrie V -- Micheli, Fiorenza -- Brumbaugh, Daniel R -- Holmes, Katherine E -- Mendes, Judith M -- Broad, Kenneth -- Sanchirico, James N -- Buch, Kevin -- Box, Steve -- Stoffle, Richard W -- Gill, Andrew B -- New York, N.Y. -- Science. 2006 Jan 6;311(5757):98-101.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Marine Spatial Ecology Lab, School of BioSciences, University of Exeter, Prince of Wales Road, Exeter EX4 4PS, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16400152" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Anthozoa/growth & development ; Bahamas ; Biomass ; Body Size ; *Conservation of Natural Resources ; *Ecosystem ; Fisheries ; *Fishes ; *Perciformes/anatomy & histology ; Population Density ; Population Dynamics ; Predatory Behavior
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    CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1 (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-04-15
    Description: Gene transcription may be regulated by remote enhancer or insulator regions through chromosome looping. Using a modification of chromosome conformation capture (3C) and fluorescence in situ hybridization, we found that one allele of the insulin-like growth factor 2 (Igf2)/H19 imprinting control region (ICR) on chromosome 7 colocalized with one allele of Wsb1/Nf1 on chromosome 11. Omission of CCCTC-binding factor (CTCF) or deletion of the maternal ICR abrogated this association and altered Wsb1/Nf1 gene expression. These findings demonstrate that CTCF mediates an interchromosomal association, perhaps by directing distant DNA segments to a common transcription factory, and the data provide a model for long-range allele-specific associations between gene regions on different chromosomes that suggest a framework for DNA recombination and RNA trans-splicing.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ling, Jian Qun -- Li, Tao -- Hu, Ji Fan -- Vu, Thanh H -- Chen, Hui Ling -- Qiu, Xin Wen -- Cherry, Athena M -- Hoffman, Andrew R -- DK036054/DK/NIDDK NIH HHS/ -- DK065283/DK/NIDDK NIH HHS/ -- HD047013/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2006 Apr 14;312(5771):269-72.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Service, Department of Veterans Affairs, Palo Alto Health Care System, and Department of Medicine, Stanford University, Palo Alto, CA 94304, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16614224" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Binding Sites ; Chromatin Immunoprecipitation ; Chromosomes, Mammalian/*genetics/metabolism ; DNA-Binding Proteins/*metabolism ; Epistasis, Genetic ; Female ; *Gene Expression Regulation ; Genomic Imprinting ; In Situ Hybridization, Fluorescence ; Insulin-Like Growth Factor II/genetics ; Male ; Mice ; Neurofibromin 1/genetics ; RNA, Long Noncoding ; RNA, Untranslated/genetics ; Regulatory Elements, Transcriptional ; Repressor Proteins/*metabolism ; Transcription, Genetic ; Ubiquitin-Protein Ligases/genetics
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    RNA recognition and cleavage by a splicing endonuclease (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-05-13
    Description: The RNA splicing endonuclease cleaves two phosphodiester bonds within folded precursor RNAs during intron removal, producing the functional RNAs required for protein synthesis. Here we describe at a resolution of 2.85 angstroms the structure of a splicing endonuclease from Archaeglobus fulgidus bound with a bulge-helix-bulge RNA containing a noncleaved and a cleaved splice site. The endonuclease dimer cooperatively recognized a flipped-out bulge base and stabilizes sharply bent bulge backbones that are poised for an in-line RNA cleavage reaction. Cooperativity arises because an arginine pair from one catalytic domain sandwiches a nucleobase within the bulge cleaved by the other catalytic domain.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xue, Song -- Calvin, Kate -- Li, Hong -- New York, N.Y. -- Science. 2006 May 12;312(5775):906-10.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16690865" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Archaeal Proteins/chemistry/metabolism ; Archaeoglobus fulgidus/*enzymology ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Dimerization ; Endoribonucleases/*chemistry/*metabolism ; Hydrogen Bonding ; Introns ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Protein Conformation ; Protein Subunits/chemistry/metabolism ; RNA Precursors/*chemistry/*metabolism ; *RNA Splicing ; RNA, Archaeal/chemistry/metabolism ; RNA, Transfer/chemistry/metabolism
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    Wildlife conservation. River dolphins down for the count, and perhaps out (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Guo, Jerry -- New York, N.Y. -- Science. 2006 Dec 22;314(5807):1860.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17185573" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; China ; *Conservation of Natural Resources ; *Dolphins ; Environment ; Extinction, Biological ; Fisheries ; *Fresh Water ; Population Density ; *Porpoises ; *Rivers ; Water Pollution
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    Where water is oxidized to dioxygen: structure of the photosynthetic Mn4Ca cluster (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-04
    Description: The oxidation of water to dioxygen is catalyzed within photosystem II (PSII) by a Mn(4)Ca cluster, the structure of which remains elusive. Polarized extended x-ray absorption fine structure (EXAFS) measurements on PSII single crystals constrain the Mn(4)Ca cluster geometry to a set of three similar high-resolution structures. Combining polarized EXAFS and x-ray diffraction data, the cluster was placed within PSII, taking into account the overall trend of the electron density of the metal site and the putative ligands. The structure of the cluster from the present study is unlike either the 3.0 or 3.5 angstrom-resolution x-ray structures or other previously proposed models.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3963817/" 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/PMC3963817/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yano, Junko -- Kern, Jan -- Sauer, Kenneth -- Latimer, Matthew J -- Pushkar, Yulia -- Biesiadka, Jacek -- Loll, Bernhard -- Saenger, Wolfram -- Messinger, Johannes -- Zouni, Athina -- Yachandra, Vittal K -- GM 55302/GM/NIGMS NIH HHS/ -- R01 GM055302/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 3;314(5800):821-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Melvin Calvin Laboratory, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17082458" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Calcium/*chemistry ; Crystallization ; Crystallography, X-Ray ; Cyanobacteria/*chemistry/metabolism ; Fourier Analysis ; Ligands ; Manganese/*chemistry ; Models, Molecular ; Oxidation-Reduction ; Oxygen/*chemistry/metabolism ; Photosystem II Protein Complex/*chemistry/metabolism ; Spectrum Analysis ; Water/*chemistry/metabolism ; X-Ray Diffraction ; X-Rays
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    GE Prize winner. How molecular motors move (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-02-14
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yildiz, Ahmet -- New York, N.Y. -- Science. 2006 Feb 10;311(5762):792-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, CA 94107, USA. yildiz@cmp.ucsf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16469911" target="_blank"〉PubMed〈/a〉
    Keywords: Awards and Prizes ; Binding Sites ; Calmodulin/metabolism ; Carbocyanines ; *Fluorescent Dyes ; Humans ; Kinesin/*physiology ; Models, Biological ; Molecular Motor Proteins/*physiology ; Movement ; Myosin Heavy Chains/*physiology ; Myosin Type V/*physiology ; Nanotechnology ; Rhodamines
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    Signal recognition particle receptor exposes the ribosomal translocon binding site (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-05-06
    Description: Signal sequences of secretory and membrane proteins are recognized by the signal recognition particle (SRP) as they emerge from the ribosome. This results in their targeting to the membrane by docking with the SRP receptor, which facilitates transfer of the ribosome to the translocon. Here, we present the 8 angstrom cryo-electron microscopy structure of a "docking complex" consisting of a SRP-bound 80S ribosome and the SRP receptor. Interaction of the SRP receptor with both SRP and the ribosome rearranged the S domain of SRP such that a ribosomal binding site for the translocon, the L23e/L35 site, became exposed, whereas Alu domain-mediated elongation arrest persisted.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Halic, Mario -- Gartmann, Marco -- Schlenker, Oliver -- Mielke, Thorsten -- Pool, Martin R -- Sinning, Irmgard -- Beckmann, Roland -- New York, N.Y. -- Science. 2006 May 5;312(5774):745-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biochemistry, Charite, University Medical School Berlin, Monbijoustrasse 2, 10117 Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16675701" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cryoelectron Microscopy ; Dogs ; Guanosine Triphosphate/metabolism ; Models, Biological ; Models, Molecular ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport ; Receptors, Cytoplasmic and Nuclear/*chemistry/*metabolism ; Receptors, Peptide/*chemistry/*metabolism ; Ribosomes/*chemistry/*metabolism ; Signal Recognition Particle/*chemistry/*metabolism
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    Molecular biology. "X"-rated chromosomal rendezvous (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-02-25
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carrel, Laura -- New York, N.Y. -- Science. 2006 Feb 24;311(5764):1107-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA. lcarrel@psu.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16497921" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Cell Differentiation ; Chromosome Pairing ; Female ; In Situ Hybridization, Fluorescence ; Mice ; Mutation ; RNA, Long Noncoding ; RNA, Untranslated/genetics/metabolism ; Regulatory Elements, Transcriptional ; Stem Cells/cytology/physiology ; Transgenes ; X Chromosome/genetics/*physiology ; *X Chromosome Inactivation
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    Pharmacology. Hitting the hot spots of cell signaling cascades (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-04-22
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tesmer, John Joseph Grubb -- New York, N.Y. -- Science. 2006 Apr 21;312(5772):377-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, MI 48109, USA. tesmerjj@umich.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16627730" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Site ; Animals ; Binding Sites ; Computer Simulation ; Drug Design ; Drug Evaluation, Preclinical/*methods ; GTP-Binding Protein alpha Subunits/metabolism ; GTP-Binding Protein beta Subunits/chemistry/*metabolism ; GTP-Binding Protein gamma Subunits/chemistry/*metabolism ; Models, Molecular ; Peptide Library ; Peptides/*metabolism ; Protein Binding ; *Signal Transduction ; Software ; Structure-Activity Relationship
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    Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-05-06
    Description: Riboswitches are untranslated regions of messenger RNA, which adopt alternate structures depending on the binding of specific metabolites. Such conformational switching regulates the expression of proteins involved in the biosynthesis of riboswitch substrates. Here, we present the 2.9 angstrom-resolution crystal structure of the eukaryotic Arabidopsis thaliana thiamine pyrophosphate (TPP)-specific riboswitch in complex with its natural ligand. The riboswitch specifically recognizes the TPP via conserved residues located within two highly distorted parallel "sensor" helices. The structure provides the basis for understanding the reorganization of the riboswitch fold upon TPP binding and explains the mechanism of resistance to the antibiotic pyrithiamine.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thore, Stephane -- Leibundgut, Marc -- Ban, Nenad -- New York, N.Y. -- Science. 2006 May 26;312(5777):1208-11. Epub 2006 May 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉ETH Zurich, Institute of Molecular Biology and Biophysics, 8092 Zurich, Switzerland. ban@mol.biol.ethz.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16675665" target="_blank"〉PubMed〈/a〉
    Keywords: 3' Untranslated Regions/*chemistry/*metabolism ; Arabidopsis/*chemistry/genetics ; Base Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Drug Resistance ; Genes, Plant ; Hydrogen Bonding ; Ligands ; Magnesium/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Pyrithiamine/pharmacology ; Thiamine Pyrophosphate/chemistry/*metabolism
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    Structural basis of RNA-dependent recruitment of glutamine to the genetic code (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-07-01
    Description: Glutaminyl-transfer RNA (Gln-tRNA(Gln)) in archaea is synthesized in a pretranslational amidation of misacylated Glu-tRNA(Gln) by the heterodimeric Glu-tRNA(Gln) amidotransferase GatDE. Here we report the crystal structure of the Methanothermobacter thermautotrophicus GatDE complexed to tRNA(Gln) at 3.15 angstroms resolution. Biochemical analysis of GatDE and of tRNA(Gln) mutants characterized the catalytic centers for the enzyme's three reactions (glutaminase, kinase, and amidotransferase activity). A 40 angstrom-long channel for ammonia transport connects the active sites in GatD and GatE. tRNA(Gln) recognition by indirect readout based on shape complementarity of the D loop suggests an early anticodon-independent RNA-based mechanism for adding glutamine to the genetic code.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oshikane, Hiroyuki -- Sheppard, Kelly -- Fukai, Shuya -- Nakamura, Yuko -- Ishitani, Ryuichiro -- Numata, Tomoyuki -- Sherrer, R Lynn -- Feng, Liang -- Schmitt, Emmanuelle -- Panvert, Michel -- Blanquet, Sylvain -- Mechulam, Yves -- Soll, Dieter -- Nureki, Osamu -- New York, N.Y. -- Science. 2006 Jun 30;312(5782):1950-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama-shi, Kanagawa 226-8501, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16809540" target="_blank"〉PubMed〈/a〉
    Keywords: Acylation ; Adenosine Triphosphate/metabolism ; Ammonia/metabolism ; Anticodon ; Binding Sites ; Catalytic Domain ; Computer Simulation ; Crystallography, X-Ray ; Dimerization ; *Genetic Code ; Glutamine/*metabolism ; Hydrogen Bonding ; Magnesium/metabolism ; Methanobacteriaceae/*enzymology/genetics ; Models, Molecular ; Mutation ; Nitrogenous Group Transferases/*chemistry/*metabolism ; Nucleic Acid Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Archaeal/*chemistry/metabolism ; RNA, Transfer, Gln/*chemistry/metabolism
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    Relating three-dimensional structures to protein networks provides evolutionary insights (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-23
    Description: Most studies of protein networks operate on a high level of abstraction, neglecting structural and chemical aspects of each interaction. Here, we characterize interactions by using atomic-resolution information from three-dimensional protein structures. We find that some previously recognized relationships between network topology and genomic features (e.g., hubs tending to be essential proteins) are actually more reflective of a structural quantity, the number of distinct binding interfaces. Subdividing hubs with respect to this quantity provides insight into their evolutionary rate and indicates that additional mechanisms of network growth are active in evolution (beyond effective preferential attachment through gene duplication).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Philip M -- Lu, Long J -- Xia, Yu -- Gerstein, Mark B -- N01-HV-28186/HV/NHLBI NIH HHS/ -- RR19895/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2006 Dec 22;314(5807):1938-41.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17185604" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Substitution ; Binding Sites ; Computational Biology ; *Evolution, Molecular ; Gene Duplication ; *Metabolic Networks and Pathways ; Mutation ; Protein Binding ; Protein Conformation ; *Protein Interaction Mapping ; Proteome ; Saccharomyces cerevisiae Proteins/*chemistry/*metabolism
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Design and evolution of new catalytic activity with an existing protein scaffold (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-01-28
    Description: The design of enzymes with new functions and properties has long been a goal in protein engineering. Here, we report a strategy to change the catalytic activity of an existing protein scaffold. This was achieved by simultaneous incorporation and adjustment of functional elements through insertion, deletion, and substitution of several active site loops, followed by point mutations to fine-tune the activity. Using this approach, we were able to introduce beta-lactamase activity into the alphabeta/betaalpha metallohydrolase scaffold of glyoxalase II. The resulting enzyme, evMBL8 (evolved metallo beta-lactamase 8), completely lost its original activity and, instead, catalyzed the hydrolysis of cefotaxime with a (kcat/Km)app of 1.8 x 10(2) (mole/liter)(-1) second(-1), thus increasing resistance to Escherichia coli growth on cefotaxime by a factor of about 100.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Park, Hee-Sung -- Nam, Sung-Hun -- Lee, Jin Kak -- Yoon, Chang No -- Mannervik, Bengt -- Benkovic, Stephen J -- Kim, Hak-Sung -- New York, N.Y. -- Science. 2006 Jan 27;311(5760):535-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 373-1, Kusung-Dong, Yusung-Gu, Daejon 305-701, Korea.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16439663" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Catalysis ; Catalytic Domain ; Cefotaxime/metabolism/pharmacology ; *Directed Molecular Evolution ; Drug Resistance, Bacterial ; Escherichia coli/drug effects ; Evolution, Molecular ; Humans ; Hydrophobic and Hydrophilic Interactions ; Iron/metabolism ; Kinetics ; Metals/metabolism ; Models, Molecular ; Molecular Sequence Data ; Point Mutation ; Protein Conformation ; *Protein Engineering ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Substrate Specificity ; Thiolester Hydrolases/*chemistry/genetics/*metabolism ; Zinc/metabolism ; beta-Lactamases/chemistry/*metabolism
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    X-ray Structure of a self-compartmentalizing sulfur cycle metalloenzyme (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-02-18
    Description: Numerous microorganisms oxidize sulfur for energy conservation and contribute to the global biogeochemical sulfur cycle. We have determined the 1.7 angstrom-resolution structure of the sulfur oxygenase reductase from the thermoacidophilic archaeon Acidianus ambivalens, which catalyzes an oxygen-dependent disproportionation of elemental sulfur. Twenty-four monomers form a large hollow sphere enclosing a positively charged nanocompartment. Apolar channels provide access for linear sulfur species. A cysteine persulfide and a low-potential mononuclear non-heme iron site ligated by a 2-His-1-carboxylate facial triad in a pocket of each subunit constitute the active sites, accessible from the inside of the sphere. The iron is likely the site of both sulfur oxidation and sulfur reduction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Urich, Tim -- Gomes, Claudio M -- Kletzin, Arnulf -- Frazao, Carlos -- New York, N.Y. -- Science. 2006 Feb 17;311(5763):996-1000.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Darmstadt University of Technology, Institute of Microbiology and Genetics, Schnittspahnstrasse 10, 64287 Darmstadt, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16484493" target="_blank"〉PubMed〈/a〉
    Keywords: Acidianus/*enzymology/physiology ; Amino Acid Sequence ; Archaeal Proteins/*chemistry/metabolism ; Binding Sites ; Catalysis ; Catalytic Domain ; Crystallization ; Crystallography, X-Ray ; Hot Temperature ; Hydrophobic and Hydrophilic Interactions ; Iron/chemistry/metabolism ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Oxidation-Reduction ; Oxidoreductases Acting on Sulfur Group Donors/*chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Recombinant Proteins/chemistry ; Static Electricity ; Sulfur/*metabolism
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 56
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    Ion selectivity in a semisynthetic K+ channel locked in the conductive conformation (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-11
    Description: Potassium channels are K+-selective protein pores in cell membrane. The selectivity filter is the functional unit that allows K+ channels to distinguish potassium (K+) and sodium (Na+) ions. The filter's structure depends on whether K+ or Na+ ions are bound inside it. We synthesized a K+ channel containing the d-enantiomer of alanine in place of a conserved glycine and found by x-ray crystallography that its filter maintains the K+ (conductive) structure in the presence of Na+ and very low concentrations of K+. This channel conducts Na+ in the absence of K+ but not in the presence of K+. These findings demonstrate that the ability of the channel to adapt its structure differently to K+ and Na+ is a fundamental aspect of ion selectivity, as is the ability of multiple K+ ions to compete effectively with Na+ for the conductive filter.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Valiyaveetil, Francis I -- Leonetti, Manuel -- Muir, Tom W -- Mackinnon, Roderick -- EB001991/EB/NIBIB NIH HHS/ -- GM43949/GM/NIGMS NIH HHS/ -- GM55843/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 10;314(5801):1004-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratories of Molecular Neurobiology and Biophysics and Synthetic Protein Chemistry, Rockefeller University and Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095703" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Crystallography, X-Ray ; Electrophysiology ; Lipid Bilayers ; Liposomes ; Models, Molecular ; Potassium/*metabolism ; Potassium Channels/*chemistry/*metabolism ; Protein Conformation
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Ecological role of purple sea urchins (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-11-11
    Description: Sea urchins are major components of marine communities. Their grazing limits algal biomass, and they are preyed upon by many predators. Purple sea urchins (Strongylocentrotus purpuratus) are among the best studied species. They live in environments that alternate between two stable states: luxuriant, species-rich kelp forests and sea urchin-dominated "barrens." The transition from one state to the other can be initiated by several factors, including the abundance of algal food, predators, storm intensities, and incidence of disease. Purple sea urchins compete with other grazers, some of which are important fishery resources (such as abalones and red sea urchins), and they are harvested for scientific research. Revelations from their genome will lead to a better understanding of how they maintain their ecological importance, and may in turn enhance their economic potential.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pearse, John S -- New York, N.Y. -- Science. 2006 Nov 10;314(5801):940-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Long Marine Laboratory, University of California, Santa Cruz, 100 Shaffer Road, Santa Cruz, CA 95060, USA. pearse@biology.ucsc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095690" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Biodiversity ; *Ecosystem ; Feeding Behavior ; Fisheries ; Fishes ; Gastropoda ; Genome ; Kelp ; Population Dynamics ; Strongylocentrotus ; Strongylocentrotus purpuratus/genetics/*physiology
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    Molecular biology. Versatility of self-cleaving ribozymes (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-09-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Been, Michael D -- New York, N.Y. -- Science. 2006 Sep 22;313(5794):1745-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Duke University Medical School, Durham, NC 27710, USA. mdbeen@duke.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16990539" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; *Evolution, Molecular ; Gene Expression Regulation ; Glucosamine/analogs & derivatives/metabolism ; Glucose-6-Phosphate/analogs & derivatives/metabolism ; Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing)/*genetics/metabolism ; Hepatitis Delta Virus/enzymology ; Humans ; Introns ; Ligands ; Nucleic Acid Conformation ; RNA, Catalytic/*chemistry/isolation & purification/*metabolism ; RNA, Messenger/genetics/metabolism ; Replicon ; Thermoanaerobacter/enzymology/*genetics ; mRNA Cleavage and Polyadenylation Factors/genetics
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Structural basis of glmS ribozyme activation by glucosamine-6-phosphate (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-23
    Description: The glmS ribozyme is the only natural catalytic RNA known to require a small-molecule activator for catalysis. This catalytic RNA functions as a riboswitch, with activator-dependent RNA cleavage regulating glmS messenger RNA expression. We report crystal structures of the glmS ribozyme in precleavage states that are unliganded or bound to the competitive inhibitor glucose-6-phosphate and in the postcleavage state. All structures superimpose closely, revealing a remarkably rigid RNA that contains a preformed active and coenzyme-binding site. Unlike other riboswitches, the glmS ribozyme binds its activator in an open, solvent-accessible pocket. Our structures suggest that the amine group of the glmS ribozyme-bound coenzyme performs general acid-base and electrostatic catalysis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Klein, Daniel J -- Ferre-D'Amare, Adrian R -- GM63576/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Sep 22;313(5794):1752-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16990543" target="_blank"〉PubMed〈/a〉
    Keywords: 5' Untranslated Regions ; Base Pairing ; Base Sequence ; Binding Sites ; Catalysis ; Crystallization ; Crystallography, X-Ray ; Enzyme Activation ; Enzyme Inhibitors/metabolism/pharmacology ; Glucosamine/*analogs & derivatives/metabolism ; Glucose-6-Phosphate/*analogs & derivatives/metabolism/pharmacology ; Glutamine-Fructose-6-Phosphate Transaminase (Isomerizing)/*genetics/metabolism ; Hydrogen Bonding ; Ligands ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA, Catalytic/*chemistry/*metabolism ; Thermoanaerobacter/enzymology/*genetics
    Print ISSN: 0036-8075
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    MOSFET-Embedded microcantilevers for measuring deflection in biomolecular sensors (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-02-04
    Description: A promising approach for detecting biomolecules follows their binding to immobilized probe molecules on microfabricated cantilevers; binding causes surface stresses that bend the cantilever. We measured this deflection, which is on the order of tens of nanometers, by embedding a metal-oxide semiconductor field-effect transistor (MOSFET) into the base of the cantilever and recording decreases in drain current with deflections as small as 5 nanometers. The gate region of the MOSFET responds to surface stresses and thus is embedded in silicon nitride so as to avoid direct contact with the sample solution. This approach, which offers low noise, high sensitivity, and direct readout, was used to detect specific binding events with biotin and antibodies.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shekhawat, Gajendra -- Tark, Soo-Hyun -- Dravid, Vinayak P -- New York, N.Y. -- Science. 2006 Mar 17;311(5767):1592-5. Epub 2006 Feb 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉International Institute for Nanotechnology, Northwestern University, Evanston, IL 60208, USA. g-shekhawat@northwestern.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16456038" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; *Biosensing Techniques ; Biotin/*analysis/metabolism ; Finite Element Analysis ; Immunoglobulin G/*analysis/metabolism ; Nanotechnology ; Protein Binding ; Sensitivity and Specificity ; Streptavidin/metabolism ; *Transistors, Electronic
    Print ISSN: 0036-8075
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