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  • Articles  (173)
  • *Ecosystem  (107)
  • Protein Conformation  (52)
  • Models, Molecular
  • 2005-2009  (173)
  • 2006  (173)
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  • Articles  (173)
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  • 2005-2009  (173)
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  • 1
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    A "silent" polymorphism in the MDR1 gene changes substrate specificity (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-23
    Description: Synonymous single-nucleotide polymorphisms (SNPs) do not produce altered coding sequences, and therefore they are not expected to change the function of the protein in which they occur. We report that a synonymous SNP in the Multidrug Resistance 1 (MDR1) gene, part of a haplotype previously linked to altered function of the MDR1 gene product P-glycoprotein (P-gp), nonetheless results in P-gp with altered drug and inhibitor interactions. Similar mRNA and protein levels, but altered conformations, were found for wild-type and polymorphic P-gp. We hypothesize that the presence of a rare codon, marked by the synonymous polymorphism, affects the timing of cotranslational folding and insertion of P-gp into the membrane, thereby altering the structure of substrate and inhibitor interaction sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kimchi-Sarfaty, Chava -- Oh, Jung Mi -- Kim, In-Wha -- Sauna, Zuben E -- Calcagno, Anna Maria -- Ambudkar, Suresh V -- Gottesman, Michael M -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2007 Jan 26;315(5811):525-8. Epub 2006 Dec 21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA. kimchi@cber.fda.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17185560" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Cell Line ; Cell Membrane/metabolism ; Cercopithecus aethiops ; Codon ; Cyclosporine/pharmacology ; *Genes, MDR ; Haplotypes ; HeLa Cells ; Humans ; Mutagenesis, Site-Directed ; P-Glycoprotein/antagonists & inhibitors/*chemistry/genetics/*metabolism ; *Polymorphism, Single Nucleotide ; Protein Biosynthesis ; Protein Conformation ; *Protein Folding ; Protein Structure, Tertiary ; RNA, Messenger/genetics/metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Rhodamine 123/metabolism/pharmacology ; Sirolimus/pharmacology ; Substrate Specificity ; Transfection ; Verapamil/metabolism/pharmacology
    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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  • 2
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    Scientific publishing. A scientist's nightmare: software problem leads to five retractions (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miller, Greg -- New York, N.Y. -- Science. 2006 Dec 22;314(5807):1856-7.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17185570" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry ; Antiporters/*chemistry ; Bacterial Proteins/*chemistry ; Crystallography, X-Ray ; Escherichia coli Proteins/*chemistry ; Protein Conformation ; *Retraction of Publication as Topic ; *Software
    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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  • 3
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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)
    Details
    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
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Biochemistry. If the RNA fits, use it (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-23
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rouault, Tracey A -- New York, N.Y. -- Science. 2006 Dec 22;314(5807):1886-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, Bethesda, MD 20892, USA. trou@helix.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17185590" target="_blank"〉PubMed〈/a〉
    Keywords: Apoferritins/*genetics ; Apoproteins/chemistry/metabolism ; Crystallography, X-Ray ; Evolution, Molecular ; Iron/metabolism ; Iron Regulatory Protein 1/*chemistry/*metabolism ; Ligands ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Messenger/chemistry/genetics/metabolism ; *Regulatory Sequences, Ribonucleic Acid ; *Response Elements ; Sulfur/metabolism ; Untranslated Regions/*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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  • 5
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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
    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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    Lineages of acidophilic archaea revealed by community genomic analysis (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-23
    Description: Novel, low-abundance microbial species can be easily overlooked in standard polymerase chain reaction (PCR)-based surveys. We used community genomic data obtained without PCR or cultivation to reconstruct DNA fragments bearing unusual 16S ribosomal RNA (rRNA) and protein-coding genes from organisms belonging to novel archaeal lineages. The organisms are minor components of all biofilms growing in pH 0.5 to 1.5 solutions within the Richmond Mine, California. Probes specific for 16S rRNA showed that the fraction less than 0.45 micrometers in diameter is dominated by these organisms. Transmission electron microscope images revealed that the cells are pleomorphic with unusual folded membrane protrusions and have apparent volumes of 〈0.006 cubic micrometer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baker, Brett J -- Tyson, Gene W -- Webb, Richard I -- Flanagan, Judith -- Hugenholtz, Philip -- Allen, Eric E -- Banfield, Jillian F -- New York, N.Y. -- Science. 2006 Dec 22;314(5807):1933-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth and Planetary Sciences, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17185602" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; *Biofilms ; California ; Cell Membrane/ultrastructure ; DNA Transposable Elements ; DNA, Archaeal ; Databases, Genetic ; *Ecosystem ; *Euryarchaeota/genetics/physiology/ultrastructure ; Genes, Archaeal ; Genes, rRNA ; *Genome, Archaeal ; Hydrogen-Ion Concentration ; Microscopy, Electron, Transmission ; Mining ; Molecular Sequence Data ; Oligonucleotide Probes ; Phylogeny ; Pyrophosphatases/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; Temperature
    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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    Microbiology. Ramping up the heat on nitrogenase (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-16
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Capone, Douglas G -- New York, N.Y. -- Science. 2006 Dec 15;314(5806):1691-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA. capone@usc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17170282" target="_blank"〉PubMed〈/a〉
    Keywords: Archaea/*enzymology/growth & development/*isolation & purification/metabolism ; *Ecosystem ; *Hot Temperature ; Nitrogen/metabolism ; *Nitrogen Fixation/genetics ; Nitrogenase/*metabolism ; Oceans and Seas ; Operon ; Seawater/*microbiology
    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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    Nitrogen fixation at 92 degrees C by a hydrothermal vent archaeon (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-16
    Description: A methanogenic archaeon isolated from deep-sea hydrothermal vent fluid was found to reduce N(2) to NH(3) at up to 92 degrees C, which is 28 degrees C higher than the current upper temperature limit of biological nitrogen fixation. The 16S ribosomal RNA gene of the hyperthermophilic nitrogen fixer, designated FS406-22, was 99% similar to that of non-nitrogen fixing Methanocaldococcus jannaschii DSM 2661. At its optimal growth temperature of 90 degrees C, FS406-22 incorporated (15)N(2) and expressed nifH messenger RNA. This increase in the temperature limit of nitrogen fixation could reveal a broader range of conditions for life in the subseafloor biosphere and other nitrogen-limited ecosystems than previously estimated.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mehta, Mausmi P -- Baross, John A -- New York, N.Y. -- Science. 2006 Dec 15;314(5806):1783-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Oceanography, University of Washington, Seattle, WA 98195, USA. mausmi@alum.mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17170307" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Archaea/classification/genetics/*isolation & purification/*metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Base Sequence ; *Ecosystem ; Genes, Archaeal ; Genes, rRNA ; Geologic Sediments/microbiology ; *Hot Temperature ; Molecular Sequence Data ; Nitrogen/metabolism ; *Nitrogen Fixation/genetics ; Nitrogenase/chemistry/*genetics/metabolism ; Operon ; Oxidation-Reduction ; Oxidoreductases/chemistry/genetics/metabolism ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Volcanic Eruptions
    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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    Biomass, size, and trophic status of top predators in the Pacific Ocean (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-16
    Description: Fisheries have removed at least 50 million tons of tuna and other top-level predators from the Pacific Ocean pelagic ecosystem since 1950, leading to concerns about a catastrophic reduction in population biomass and the collapse of oceanic food chains. We analyzed all available data from Pacific tuna fisheries for 1950-2004 to provide comprehensive estimates of fishery impacts on population biomass and size structure. Current biomass ranges among species from 36 to 91% of the biomass predicted in the absence of fishing, a level consistent with or higher than standard fisheries management targets. Fish larger than 175 centimeters fork length have decreased from 5% to approximately 1% of the total population. The trophic level of the catch has decreased slightly, but there is no detectable decrease in the trophic level of the population. These results indicate substantial, though not catastrophic, impacts of fisheries on these top-level predators and minor impacts on the ecosystem in the Pacific Ocean.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sibert, John -- Hampton, John -- Kleiber, Pierre -- Maunder, Mark -- New York, N.Y. -- Science. 2006 Dec 15;314(5806):1773-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Joint Institute for Marine and Atmospheric Research, University of Hawaii, Honolulu, HI 96822, USA. sibert@hawaii.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17170304" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biomass ; Body Size ; Conservation of Natural Resources ; *Ecosystem ; *Fisheries ; *Food Chain ; Pacific Ocean ; Perciformes/anatomy & histology/physiology ; Population Density ; Population Dynamics ; Predatory Behavior ; *Sharks/anatomy & histology/physiology ; *Tuna/anatomy & histology/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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  • 10
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    Nannoplankton extinction and origination across the Paleocene-Eocene Thermal Maximum (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-16
    Description: The Paleocene-Eocene Thermal Maximum (PETM, approximately 55 million years ago) was an interval of global warming and ocean acidification attributed to rapid release and oxidation of buried carbon. We show that the onset of the PETM coincided with a prominent increase in the origination and extinction of calcareous phytoplankton. Yet major perturbation of the surface-water saturation state across the PETM was not detrimental to the survival of most calcareous nannoplankton taxa and did not impart a calcification or ecological bias to the pattern of evolutionary turnover. Instead, the rate of environmental change appears to have driven turnover, preferentially affecting rare taxa living close to their viable limits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gibbs, Samantha J -- Bown, Paul R -- Sessa, Jocelyn A -- Bralower, Timothy J -- Wilson, Paul A -- New York, N.Y. -- Science. 2006 Dec 15;314(5806):1770-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Ocean and Earth Sciences, National Oceanography Centre, Southampton, European Way, Southampton, SO14 3ZH, UK. sxg@noc.soton.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17170303" target="_blank"〉PubMed〈/a〉
    Keywords: Atmosphere ; Biodiversity ; Biological Evolution ; Calcification, Physiologic ; Carbon Dioxide ; *Ecosystem ; Environment ; *Extinction, Biological ; *Fossils ; Geologic Sediments ; New Jersey ; Oceans and Seas ; Pacific Ocean ; *Phytoplankton/classification ; *Plankton/classification ; Rivers ; Temperature
    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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