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  • Articles  (49)
  • Models, Molecular
  • 2005-2009  (47)
  • 1975-1979  (2)
  • 2006  (47)
  • 1978  (2)
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  • Articles  (49)
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  • 2005-2009  (47)
  • 1975-1979  (2)
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  • 1
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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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  • 2
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    An inward-facing conformation of a putative metal-chelate-type ABC transporter (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-12-13
    Description: The crystal structure of a putative metal-chelate-type adenosine triphosphate (ATP)-binding cassette (ABC) transporter encoded by genes HI1470 and HI1471 of Haemophilus influenzae has been solved at 2.4 angstrom resolution. The permeation pathway exhibits an inward-facing conformation, in contrast to the outward-facing state previously observed for the homologous vitamin B12 importer BtuCD. Although the structures of both HI1470/1 and BtuCD have been solved in nucleotide-free states, the pairs of ABC subunits in these two structures differ by a translational shift in the plane of the membrane that coincides with a repositioning of the membrane-spanning subunits. The differences observed between these ABC transporters involve relatively modest rearrangements and may serve as structural models for inward- and outward-facing conformations relevant to the alternating access mechanism of substrate translocation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pinkett, H W -- Lee, A T -- Lum, P -- Locher, K P -- Rees, D C -- GM45162/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Jan 19;315(5810):373-7. Epub 2006 Dec 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, MC 114-96, California Institute of Technology (Caltech), Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17158291" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry ; Bacterial Proteins/*chemistry ; Catalytic Domain ; Crystallography, X-Ray ; Dimerization ; Haemophilus influenzae/*chemistry ; Metals/metabolism ; Models, Molecular ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry
    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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  • 3
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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)
    Details
    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
    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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    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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  • 5
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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
    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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  • 6
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    The dynamic energy landscape of dihydrofolate reductase catalysis (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    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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  • 7
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    Structure of the 70S ribosome complexed with mRNA and tRNA (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-09
    Description: The crystal structure of the bacterial 70S ribosome refined to 2.8 angstrom resolution reveals atomic details of its interactions with messenger RNA (mRNA) and transfer RNA (tRNA). A metal ion stabilizes a kink in the mRNA that demarcates the boundary between A and P sites, which is potentially important to prevent slippage of mRNA. Metal ions also stabilize the intersubunit interface. The interactions of E-site tRNA with the 50S subunit have both similarities and differences compared to those in the archaeal ribosome. The structure also rationalizes much biochemical and genetic data on translation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Selmer, Maria -- Dunham, Christine M -- Murphy, Frank V 4th -- Weixlbaumer, Albert -- Petry, Sabine -- Kelley, Ann C -- Weir, John R -- Ramakrishnan, V -- GM67624/GM/NIGMS NIH HHS/ -- MC_U105184332/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2006 Sep 29;313(5795):1935-42. Epub 2006 Sep 7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16959973" target="_blank"〉PubMed〈/a〉
    Keywords: Anticodon ; Bacterial Proteins/*chemistry/metabolism ; Codon ; Crystallization ; Crystallography, X-Ray ; Magnesium/metabolism ; Models, Molecular ; Nucleic Acid Conformation ; Peptidyl Transferases/chemistry/metabolism ; Protein Biosynthesis ; Protein Conformation ; RNA, Bacterial/chemistry/metabolism ; RNA, Messenger/chemistry/*metabolism ; RNA, Transfer/chemistry/*metabolism ; RNA, Transfer, Met/chemistry/metabolism ; RNA, Transfer, Phe/chemistry/metabolism ; Ribosomal Proteins/*chemistry/metabolism ; Ribosomes/*chemistry/metabolism/*ultrastructure ; Thermus thermophilus/*chemistry/ultrastructure
    Print ISSN: 0036-8075
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  • 8
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    Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-02
    Description: The AcrA/AcrB/TolC complex spans the inner and outer membranes of Escherichia coli and serves as its major drug-resistance pump. Driven by the proton motive force, it mediates the efflux of bile salts, detergents, organic solvents, and many structurally unrelated antibiotics. Here, we report a crystallographic structure of trimeric AcrB determined at 2.9 and 3.0 angstrom resolution in space groups that allow asymmetry of the monomers. This structure reveals three different monomer conformations representing consecutive states in a transport cycle. The structural data imply an alternating access mechanism and a novel peristaltic mode of drug transport by this type of transporter.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seeger, Markus A -- Schiefner, Andre -- Eicher, Thomas -- Verrey, Francois -- Diederichs, Kay -- Pos, Klaas M -- New York, N.Y. -- Science. 2006 Sep 1;313(5791):1295-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Physiology and Zurich Centre for Integrative Human Physiology (ZIHP), University of Zurich, Winterthurerstrasse 190, Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16946072" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Transport ; Crystallization ; Crystallography, X-Ray ; Diffusion ; Drug Resistance, Multiple, Bacterial ; Escherichia coli/*chemistry/drug effects ; Escherichia coli Proteins/*chemistry/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Membrane Transport Proteins/*chemistry/metabolism ; Models, Molecular ; Multidrug Resistance-Associated Proteins/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protons
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  • 9
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    Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-08-26
    Description: In higher eukaryotes, a multiprotein exon junction complex is deposited on spliced messenger RNAs. The complex is organized around a stable core, which serves as a binding platform for numerous factors that influence messenger RNA function. Here, we present the crystal structure of a tetrameric exon junction core complex containing the DEAD-box adenosine triphosphatase (ATPase) eukaryotic initiation factor 4AIII (eIF4AIII) bound to an ATP analog, MAGOH, Y14, a fragment of MLN51, and a polyuracil mRNA mimic. eIF4AIII interacts with the phosphate-ribose backbone of six consecutive nucleotides and prevents part of the bound RNA from being double stranded. The MAGOH and Y14 subunits lock eIF4AIII in a prehydrolysis state, and activation of the ATPase probably requires only modest conformational changes in eIF4AIII motif I.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Andersen, Christian B F -- Ballut, Lionel -- Johansen, Jesper S -- Chamieh, Hala -- Nielsen, Klaus H -- Oliveira, Cristiano L P -- Pedersen, Jan Skov -- Seraphin, Bertrand -- Le Hir, Herve -- Andersen, Gregers Rom -- New York, N.Y. -- Science. 2006 Sep 29;313(5795):1968-72. Epub 2006 Aug 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, University of Aarhus, DK-8000 Aarhus, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16931718" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/analogs & derivatives/metabolism ; Adenylyl Imidodiphosphate/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Crystallography, X-Ray ; DEAD-box RNA Helicases ; Dimerization ; Drosophila Proteins/chemistry/metabolism ; Eukaryotic Initiation Factor-4A/*chemistry/metabolism ; *Exons ; Humans ; Hydrogen Bonding ; Hydrolysis ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Neoplasm Proteins/*chemistry/metabolism ; Nuclear Proteins/*chemistry/metabolism ; Nucleic Acid Conformation ; Poly U/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA Helicases/chemistry/metabolism ; RNA, Messenger/*chemistry/metabolism ; RNA-Binding Proteins/*chemistry/metabolism
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  • 10
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    Immunology. Sugar determines antibody activity (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-08-05
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burton, Dennis R -- Dwek, Raymond A -- New York, N.Y. -- Science. 2006 Aug 4;313(5787):627-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology, Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA. burton@scripps.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16888131" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arthritis, Rheumatoid/immunology ; Glycosylation ; Humans ; Immunoglobulin Fc Fragments/chemistry/*immunology ; Immunoglobulin G/chemistry/*immunology/metabolism ; Immunoglobulin M/chemistry/immunology ; Immunoglobulins, Intravenous/chemistry/immunology/therapeutic use ; Inflammation/*immunology/therapy ; Mannose-Binding Lectin/metabolism ; Mice ; Models, Molecular ; Oligosaccharides/*analysis ; Receptors, Fc/*immunology/metabolism ; Sialic Acids/*analysis
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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