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  • Articles  (62)
  • Amino Acid Sequence  (62)
  • 2005-2009  (62)
  • 1935-1939
  • 2008  (62)
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  • Articles  (62)
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  • 2005-2009  (62)
  • 1935-1939
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  • 1
    Publication Date: 2008-07-16
    Description: The bacterium Proteus mirabilis is capable of movement on solid surfaces by a type of motility called swarming. Boundaries form between swarming colonies of different P. mirabilis strains but not between colonies of a single strain. A fundamental requirement for boundary formation is the ability to discriminate between self and nonself. We have isolated mutants that form boundaries with their parent. The mutations map within a six-gene locus that we term ids for identification of self. Five of the genes in the ids locus are required for recognition of the parent strain as self. Three of the ids genes are interchangeable between strains, and two encode specific molecular identifiers.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567286/" 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/PMC2567286/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gibbs, Karine A -- Urbanowski, Mark L -- Greenberg, E Peter -- AI55396/AI/NIAID NIH HHS/ -- T32 AI055396-04/AI/NIAID NIH HHS/ -- T32 AI055396-05/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2008 Jul 11;321(5886):256-9. doi: 10.1126/science.1160033.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, School of 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/18621670" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/genetics/physiology ; *Genes, Bacterial ; Genetic Complementation Test ; Genome, Bacterial ; Molecular Sequence Data ; Movement ; Multigene Family ; Mutagenesis, Insertional ; Mutation ; Proteus mirabilis/*genetics/*physiology ; Sequence Analysis, DNA ; Species Specificity
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  • 2
    Publication Date: 2008-11-29
    Description: Altered abundance of several intrinsically unstructured proteins (IUPs) has been associated with perturbed cellular signaling that may lead to pathological conditions such as cancer. Therefore, it is important to understand how cells precisely regulate the availability of IUPs. We observed that regulation of transcript clearance, proteolytic degradation, and translational rate contribute to controlling the abundance of IUPs, some of which are present in low amounts and for short periods of time. Abundant phosphorylation and low stochasticity in transcription and translation indicate that the availability of IUPs can be finely tuned. Fidelity in signaling may require that most IUPs be available in appropriate amounts and not present longer than needed.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803065/" 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/PMC2803065/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gsponer, Jorg -- Futschik, Matthias E -- Teichmann, Sarah A -- Babu, M Madan -- G0600158/Medical Research Council/United Kingdom -- MC_U105161047/Medical Research Council/United Kingdom -- MC_U105185859/Medical Research Council/United Kingdom -- U.1051.04.027.00001.01 (85859)/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Nov 28;322(5906):1365-8. doi: 10.1126/science.1163581.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK. jgsponer@mrc-lmb.cam.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19039133" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Cycle ; Computational Biology ; Genes, Fungal ; Humans ; Phosphorylation ; Protein Biosynthesis ; Protein Conformation ; Protein Kinases/metabolism ; Proteome/chemistry ; RNA, Fungal/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Saccharomyces cerevisiae/chemistry/cytology/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism ; Schizosaccharomyces pombe Proteins/chemistry/metabolism ; Signal Transduction ; Transcription, Genetic
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  • 3
    Publication Date: 2008-01-26
    Description: Differential cytosine methylation of repeats and genes is important for coordination of genome stability and proper gene expression. Through genetic screen of mutants showing ectopic cytosine methylation in a genic region, we identified a jmjC-domain gene, IBM1 (increase in bonsai methylation 1), in Arabidopsis thaliana. In addition to the ectopic cytosine methylation, the ibm1 mutations induced a variety of developmental phenotypes, which depend on methylation of histone H3 at lysine 9. Paradoxically, the developmental phenotypes of the ibm1 were enhanced by the mutation in the chromatin-remodeling gene DDM1 (decrease in DNA methylation 1), which is necessary for keeping methylation and silencing of repeated heterochromatin loci. Our results demonstrate the importance of chromatin remodeling and histone modifications in the differential epigenetic control of repeats and genes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Saze, Hidetoshi -- Shiraishi, Akiko -- Miura, Asuka -- Kakutani, Tetsuji -- New York, N.Y. -- Science. 2008 Jan 25;319(5862):462-5. doi: 10.1126/science.1150987.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Integrated Genetics, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan. hsaze@lab.nig.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18218897" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/*genetics/growth & development/metabolism ; Arabidopsis Proteins/chemistry/genetics/metabolism/*physiology ; Chromatin Assembly and Disassembly ; Cytosine/metabolism ; *DNA Methylation ; DNA-Binding Proteins/chemistry/genetics/*physiology ; Epigenesis, Genetic ; Gene Silencing ; Genes, Plant ; Heterochromatin/metabolism ; Histones/metabolism ; Jumonji Domain-Containing Histone Demethylases ; Long Interspersed Nucleotide Elements ; Methylation ; Molecular Sequence Data ; Mutation ; Transcription Factors/genetics/physiology
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  • 4
    Publication Date: 2008-04-19
    Description: Toll-like receptor 3 (TLR3) recognizes double-stranded RNA (dsRNA), a molecular signature of most viruses, and triggers inflammatory responses that prevent viral spread. TLR3 ectodomains (ECDs) dimerize on oligonucleotides of at least 40 to 50 base pairs in length, the minimal length required for signal transduction. To establish the molecular basis for ligand binding and signaling, we determined the crystal structure of a complex between two mouse TLR3-ECDs and dsRNA at 3.4 angstrom resolution. Each TLR3-ECD binds dsRNA at two sites located at opposite ends of the TLR3 horseshoe, and an intermolecular contact between the two TLR3-ECD C-terminal domains coordinates and stabilizes the dimer. This juxtaposition could mediate downstream signaling by dimerizing the cytoplasmic Toll interleukin-1 receptor (TIR) domains. The overall shape of the TLR3-ECD does not change upon binding to dsRNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761030/" 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/PMC2761030/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Lin -- Botos, Istvan -- Wang, Yan -- Leonard, Joshua N -- Shiloach, Joseph -- Segal, David M -- Davies, David R -- Z01 BC009254-33/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Apr 18;320(5874):379-81. doi: 10.1126/science.1155406.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18420935" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; Humans ; Ligands ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/genetics/metabolism ; NF-kappa B/metabolism ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Tertiary ; RNA, Double-Stranded/*chemistry/*metabolism ; *Signal Transduction ; Toll-Like Receptor 3/*chemistry/genetics/*metabolism
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  • 5
    Publication Date: 2008-01-05
    Description: We used authentication tests developed for ancient DNA to evaluate claims by Asara et al. (Reports, 13 April 2007, p. 280) of collagen peptide sequences recovered from mastodon and Tyrannosaurus rex fossils. Although the mastodon samples pass these tests, absence of amino acid composition data, lack of evidence for peptide deamidation, and association of alpha1(I) collagen sequences with amphibians rather than birds suggest that T. rex does not.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694913/" 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/PMC2694913/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buckley, Mike -- Walker, Angela -- Ho, Simon Y W -- Yang, Yue -- Smith, Colin -- Ashton, Peter -- Oates, Jane Thomas -- Cappellini, Enrico -- Koon, Hannah -- Penkman, Kirsty -- Elsworth, Ben -- Ashford, Dave -- Solazzo, Caroline -- Andrews, Phillip -- Strahler, John -- Shapiro, Beth -- Ostrom, Peggy -- Gandhi, Hasand -- Miller, Webb -- Raney, Brian -- Zylber, Maria Ines -- Gilbert, M Thomas P -- Prigodich, Richard V -- Ryan, Michael -- Rijsdijk, Kenneth F -- Janoo, Anwar -- Collins, Matthew J -- 076905/Wellcome Trust/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2008 Jan 4;319(5859):33; author reply 33. doi: 10.1126/science.1147046.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO10 5YW, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18174420" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bone and Bones/*chemistry ; Collagen/*chemistry ; *Dinosaurs ; *Elephants ; *Fossils ; Mass Spectrometry ; Phylogeny
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  • 6
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2008-02-16
    Description: Cadherin-mediated cell adhesion and signaling is essential for metazoan development and yet is absent from all other multicellular organisms. We found cadherin genes at numbers similar to those observed in complex metazoans in one of the closest single-celled relatives of metazoans, the choanoflagellate Monosiga brevicollis. Because the evolution of metazoans from a single-celled ancestor required novel cell adhesion and signaling mechanisms, the discovery of diverse cadherins in choanoflagellates suggests that cadherins may have contributed to metazoan origins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Abedin, Monika -- King, Nicole -- New York, N.Y. -- Science. 2008 Feb 15;319(5865):946-8. doi: 10.1126/science.1151084.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology and Center for Integrative Genomics, University of California at Berkeley, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18276888" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/metabolism ; Amino Acid Sequence ; Animals ; Base Sequence ; *Biological Evolution ; Cadherins/*chemistry/*genetics/physiology ; Cell Adhesion ; Ciona intestinalis/chemistry ; Cnidaria/chemistry ; Drosophila melanogaster/chemistry ; Eukaryota/*chemistry ; Eukaryotic Cells/*chemistry/physiology ; Mice ; Molecular Sequence Data ; Protein Structure, Tertiary ; Repetitive Sequences, Amino Acid ; Signal Transduction ; Tyrosine/metabolism ; src Homology Domains
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  • 7
    Publication Date: 2008-04-12
    Description: The toxicity of ionizing radiation is associated with massive apoptosis in radiosensitive organs. Here, we investigate whether a drug that activates a signaling mechanism used by tumor cells to suppress apoptosis can protect healthy cells from the harmful effects of radiation. We studied CBLB502, a polypeptide drug derived from Salmonella flagellin that binds to Toll-like receptor 5 (TLR5) and activates nuclear factor-kappaB signaling. A single injection of CBLB502 before lethal total-body irradiation protected mice from both gastrointestinal and hematopoietic acute radiation syndromes and resulted in improved survival. CBLB502 injected after irradiation also enhanced survival, but at lower radiation doses. It is noteworthy that the drug did not decrease tumor radiosensitivity in mouse models. CBLB502 also showed radioprotective activity in lethally irradiated rhesus monkeys. Thus, TLR5 agonists could potentially improve the therapeutic index of cancer radiotherapy and serve as biological protectants in radiation emergencies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4322935/" 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/PMC4322935/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burdelya, Lyudmila G -- Krivokrysenko, Vadim I -- Tallant, Thomas C -- Strom, Evguenia -- Gleiberman, Anatoly S -- Gupta, Damodar -- Kurnasov, Oleg V -- Fort, Farrel L -- Osterman, Andrei L -- Didonato, Joseph A -- Feinstein, Elena -- Gudkov, Andrei V -- AI066497/AI/NIAID NIH HHS/ -- CA75179/CA/NCI NIH HHS/ -- CA84406/CA/NCI NIH HHS/ -- R01 CA084406/CA/NCI NIH HHS/ -- R01 CA084406-01A1/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2008 Apr 11;320(5873):226-30. doi: 10.1126/science.1154986.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18403709" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Apoptosis/drug effects/radiation effects ; Chemotherapy, Adjuvant ; Flagellin/chemistry/pharmacology ; Gamma Rays ; Hematopoietic System/drug effects/radiation effects ; Intestine, Small/cytology/drug effects/radiation effects ; Macaca mulatta ; Mice ; Mice, Inbred ICR ; Molecular Sequence Data ; NF-kappa B/*metabolism ; Neoplasms, Experimental/drug therapy/radiotherapy ; Peptides/administration & dosage/chemistry/*pharmacology/toxicity ; Radiation Dosage ; Radiation Injuries, Experimental/*prevention & control ; Radiation Tolerance/*drug effects ; Radiation-Protective Agents/administration & ; dosage/chemistry/*pharmacology/toxicity ; Salmonella enterica ; Signal Transduction ; Toll-Like Receptor 5/*agonists/metabolism ; Whole-Body Irradiation
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  • 8
    Publication Date: 2008-11-01
    Description: Nuclear pore complexes (NPCs) facilitate nucleocytoplasmic transport. These massive assemblies comprise an eightfold symmetric scaffold of architectural proteins and central-channel phenylalanine-glycine-repeat proteins forming the transport barrier. We determined the nucleoporin 85 (Nup85)*Seh1 structure, a module in the heptameric Nup84 complex, at 3.5 angstroms resolution. Structural, biochemical, and genetic analyses position the Nup84 complex in two peripheral NPC rings. We establish a conserved tripartite element, the ancestral coatomer element ACE1, that reoccurs in several nucleoporins and vesicle coat proteins, providing structural evidence of coevolution from a common ancestor. We identified interactions that define the organization of the Nup84 complex on the basis of comparison with vesicle coats and confirmed the sites by mutagenesis. We propose that the NPC scaffold, like vesicle coats, is composed of polygons with vertices and edges forming a membrane-proximal lattice that provides docking sites for additional nucleoporins.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680690/" 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/PMC2680690/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brohawn, Stephen G -- Leksa, Nina C -- Spear, Eric D -- Rajashankar, Kanagalaghatta R -- Schwartz, Thomas U -- GM68762/GM/NIGMS NIH HHS/ -- GM77537/GM/NIGMS NIH HHS/ -- R01 GM077537/GM/NIGMS NIH HHS/ -- R01 GM077537-02/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Nov 28;322(5906):1369-73. doi: 10.1126/science.1165886. Epub 2008 Oct 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18974315" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Coated Vesicles/*chemistry ; Crystallography, X-Ray ; Dimerization ; Evolution, Molecular ; Membrane Proteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis ; Nuclear Pore/*chemistry ; Nuclear Pore Complex Proteins/*chemistry/genetics/metabolism ; Nuclear Proteins/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/metabolism ; Vesicular Transport Proteins/*chemistry
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  • 9
    Publication Date: 2008-11-15
    Description: Hybridization between species can lead to introgression of genes from one species to another, providing a potential mechanism for preserving and recombining key traits during evolution. To determine the molecular basis of such transfers, we analyzed a natural polymorphism for flower-head development in Senecio. We show that the polymorphism arose by introgression of a cluster of regulatory genes, the RAY locus, from the diploid species S. squalidus into the tetraploid S. vulgaris. The RAY genes are expressed in the peripheral regions of the inflorescence meristem, where they promote flower asymmetry and lead to an increase in the rate of outcrossing. Our results highlight how key morphological and ecological traits controlled by regulatory genes may be gained, lost, and regained during evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Minsung -- Cui, Min-Long -- Cubas, Pilar -- Gillies, Amanda -- Lee, Karen -- Chapman, Mark A -- Abbott, Richard J -- Coen, Enrico -- BB-D017742/Biotechnology and Biological Sciences Research Council/United Kingdom -- G10929/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Nov 14;322(5904):1116-9. doi: 10.1126/science.1164371.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19008450" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Biological Evolution ; Crosses, Genetic ; Flowers/anatomy & histology/*genetics/growth & development ; *Gene Transfer, Horizontal ; *Genes, Plant ; *Genes, Regulator ; Genotype ; Haplotypes ; *Hybridization, Genetic ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Polymorphism, Genetic ; Selection, Genetic ; Senecio/*genetics/growth & development ; Sequence Analysis, DNA
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  • 10
    Publication Date: 2008-10-04
    Description: A commonly used strategy by microorganisms to survive multiple stresses involves a signal transduction cascade that increases the expression of stress-responsive genes. Stress signals can be integrated by a multiprotein signaling hub that responds to various signals to effect a single outcome. We obtained a medium-resolution cryo-electron microscopy reconstruction of the 1.8-megadalton "stressosome" from Bacillus subtilis. Fitting known crystal structures of components into this reconstruction gave a pseudoatomic structure, which had a virus capsid-like core with sensory extensions. We suggest that the different sensory extensions respond to different signals, whereas the conserved domains in the core integrate the varied signals. The architecture of the stressosome provides the potential for cooperativity, suggesting that the response could be tuned dependent on the magnitude of chemophysical insult.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Marles-Wright, Jon -- Grant, Tim -- Delumeau, Olivier -- van Duinen, Gijs -- Firbank, Susan J -- Lewis, Peter J -- Murray, James W -- Newman, Joseph A -- Quin, Maureen B -- Race, Paul R -- Rohou, Alexis -- Tichelaar, Willem -- van Heel, Marin -- Lewis, Richard J -- BB/D000521/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/F001533/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Oct 3;322(5898):92-6. doi: 10.1126/science.1159572.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18832644" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacillus subtilis/*chemistry/metabolism/ultrastructure ; Bacterial Proteins/*chemistry/metabolism/ultrastructure ; Cryoelectron Microscopy ; Crystallography, X-Ray ; Image Processing, Computer-Assisted ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Multiprotein Complexes/*chemistry/metabolism/ultrastructure ; Phosphoproteins/*chemistry/metabolism/ultrastructure ; Phosphorylation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases/*chemistry/metabolism/ultrastructure ; Sigma Factor/metabolism ; *Signal Transduction
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  • 11
    Publication Date: 2008-12-17
    Description: Dynein motors move various cargos along microtubules within the cytoplasm and power the beating of cilia and flagella. An unusual feature of dynein is that its microtubule-binding domain (MTBD) is separated from its ring-shaped AAA+ adenosine triphosphatase (ATPase) domain by a 15-nanometer coiled-coil stalk. We report the crystal structure of the mouse cytoplasmic dynein MTBD and a portion of the coiled coil, which supports a mechanism by which the ATPase domain and MTBD may communicate through a shift in the heptad registry of the coiled coil. Surprisingly, functional data suggest that the MTBD, and not the ATPase domain, is the main determinant of the direction of dynein motility.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2663340/" 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/PMC2663340/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carter, Andrew P -- Garbarino, Joan E -- Wilson-Kubalek, Elizabeth M -- Shipley, Wesley E -- Cho, Carol -- Milligan, Ronald A -- Vale, Ronald D -- Gibbons, I R -- GM30401-29/GM/NIGMS NIH HHS/ -- GM52468/GM/NIGMS NIH HHS/ -- P01 AR042895/AR/NIAMS NIH HHS/ -- P01 AR042895-15/AR/NIAMS NIH HHS/ -- P01-AR42895/AR/NIAMS NIH HHS/ -- P41 RR-17573/RR/NCRR NIH HHS/ -- R01 GM097312/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Dec 12;322(5908):1691-5. doi: 10.1126/science.1164424.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19074350" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Dyneins/*chemistry/*metabolism ; Hydrophobic and Hydrophilic Interactions ; Image Processing, Computer-Assisted ; Mice ; Microscopy, Electron ; Microtubules/*metabolism/ultrastructure ; Models, Molecular ; Molecular Sequence Data ; Movement ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism
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  • 12
    Publication Date: 2008-03-29
    Description: Schizophrenia is a devastating neurodevelopmental disorder whose genetic influences remain elusive. We hypothesize that individually rare structural variants contribute to the illness. Microdeletions and microduplications 〉100 kilobases were identified by microarray comparative genomic hybridization of genomic DNA from 150 individuals with schizophrenia and 268 ancestry-matched controls. All variants were validated by high-resolution platforms. Novel deletions and duplications of genes were present in 5% of controls versus 15% of cases and 20% of young-onset cases, both highly significant differences. The association was independently replicated in patients with childhood-onset schizophrenia as compared with their parents. Mutations in cases disrupted genes disproportionately from signaling networks controlling neurodevelopment, including neuregulin and glutamate pathways. These results suggest that multiple, individually rare mutations altering genes in neurodevelopmental pathways contribute to schizophrenia.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Walsh, Tom -- McClellan, Jon M -- McCarthy, Shane E -- Addington, Anjene M -- Pierce, Sarah B -- Cooper, Greg M -- Nord, Alex S -- Kusenda, Mary -- Malhotra, Dheeraj -- Bhandari, Abhishek -- Stray, Sunday M -- Rippey, Caitlin F -- Roccanova, Patricia -- Makarov, Vlad -- Lakshmi, B -- Findling, Robert L -- Sikich, Linmarie -- Stromberg, Thomas -- Merriman, Barry -- Gogtay, Nitin -- Butler, Philip -- Eckstrand, Kristen -- Noory, Laila -- Gochman, Peter -- Long, Robert -- Chen, Zugen -- Davis, Sean -- Baker, Carl -- Eichler, Evan E -- Meltzer, Paul S -- Nelson, Stanley F -- Singleton, Andrew B -- Lee, Ming K -- Rapoport, Judith L -- King, Mary-Claire -- Sebat, Jonathan -- HD043569/HD/NICHD NIH HHS/ -- M01 RR000046/RR/NCRR NIH HHS/ -- MH061355/MH/NIMH NIH HHS/ -- MH061464/MH/NIMH NIH HHS/ -- MH061528/MH/NIMH NIH HHS/ -- NS052108/NS/NINDS NIH HHS/ -- R01 HD043569/HD/NICHD NIH HHS/ -- RR000046/RR/NCRR NIH HHS/ -- RR025014/RR/NCRR NIH HHS/ -- U01 MH061355/MH/NIMH NIH HHS/ -- U01 MH061464/MH/NIMH NIH HHS/ -- U01 MH061528/MH/NIMH NIH HHS/ -- U24 NS052108/NS/NINDS NIH HHS/ -- UL1 RR025014/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Apr 25;320(5875):539-43. doi: 10.1126/science.1155174. Epub 2008 Mar 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of 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/18369103" target="_blank"〉PubMed〈/a〉
    Keywords: Adolescent ; Adult ; Age of Onset ; Amino Acid Sequence ; Brain/cytology/*growth & development/metabolism ; Case-Control Studies ; Child ; Excitatory Amino Acid Transporter 1/chemistry/genetics/physiology ; Female ; *Gene Deletion ; *Gene Duplication ; Genetic Predisposition to Disease ; Genome, Human ; Humans ; Male ; Molecular Sequence Data ; *Mutation ; Neurons/cytology/physiology ; Oligonucleotide Array Sequence Analysis ; Polymorphism, Single Nucleotide ; Receptor, Epidermal Growth Factor/chemistry/genetics/physiology ; Receptor, ErbB-4 ; Schizophrenia/*genetics/physiopathology ; Signal Transduction
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  • 13
    Publication Date: 2008-05-24
    Description: Viruses shape microbial community structure and function by altering the fitness of their hosts and by promoting genetic exchange. The complexity of most natural ecosystems has precluded detailed studies of virus-host interactions. We reconstructed virus and host bacterial and archaeal genome sequences from community genomic data from two natural acidophilic biofilms. Viruses were matched to their hosts by analyzing spacer sequences that occur among clustered regularly interspaced short palindromic repeats (CRISPRs) that are a hallmark of virus resistance. Virus population genomic analyses provided evidence that extensive recombination shuffles sequence motifs sufficiently to evade CRISPR spacers. Only the most recently acquired spacers match coexisting viruses, which suggests that community stability is achieved by rapid but compensatory shifts in host resistance levels and virus population structure.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Andersson, Anders F -- Banfield, Jillian F -- New York, N.Y. -- Science. 2008 May 23;320(5879):1047-50. doi: 10.1126/science.1157358.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Departments of Earth and Planetary Science and Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18497291" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Archaea/*genetics/physiology/*virology ; Archaeal Viruses/genetics/*physiology ; Bacteria/*genetics/*virology ; Bacterial Physiological Phenomena ; Bacteriophages/genetics/*physiology ; Base Sequence ; Biofilms ; DNA, Intergenic ; Ecosystem ; Genome, Archaeal ; Genome, Bacterial ; Genome, Viral ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Oligodeoxyribonucleotides ; Recombination, Genetic ; *Repetitive Sequences, Nucleic Acid ; Thermoplasmales/genetics/physiology/virology ; Viral Proteins/chemistry/genetics/physiology
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  • 14
    Publication Date: 2008-07-19
    Description: Sleep is an essential process conserved from flies to humans. The importance of sleep is underscored by its tight homeostatic control. Through a forward genetic screen, we identified a gene, sleepless, required for sleep in Drosophila. The sleepless gene encodes a brain-enriched, glycosylphosphatidylinositol-anchored protein. Loss of SLEEPLESS protein caused an extreme (〉80%) reduction in sleep; a moderate reduction in SLEEPLESS had minimal effects on baseline sleep but markedly reduced the amount of recovery sleep after sleep deprivation. Genetic and molecular analyses revealed that quiver, a mutation that impairs Shaker-dependent potassium current, is an allele of sleepless. Consistent with this finding, Shaker protein levels were reduced in sleepless mutants. We propose that SLEEPLESS is a signaling molecule that connects sleep drive to lowered membrane excitability.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771549/" 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/PMC2771549/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koh, Kyunghee -- Joiner, William J -- Wu, Mark N -- Yue, Zhifeng -- Smith, Corinne J -- Sehgal, Amita -- AG017628/AG/NIA NIH HHS/ -- P01 AG017628/AG/NIA NIH HHS/ -- P01 AG017628-070004/AG/NIA NIH HHS/ -- R01 NS072431/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Jul 18;321(5887):372-6. doi: 10.1126/science.1155942.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Neuroscience, University of Pennsylvania, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18635795" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Animals, Genetically Modified ; Behavior, Animal ; Brain/metabolism ; Cell Membrane/metabolism ; DNA Transposable Elements ; Drosophila Proteins/chemistry/*genetics/*physiology ; Drosophila melanogaster/genetics/*physiology ; Female ; *Genes, Insect ; Glycosylphosphatidylinositols ; Homeostasis ; Longevity ; Male ; Membrane Proteins/chemistry/*genetics/*physiology ; *Models, Animal ; Molecular Sequence Data ; Mutation ; Phenotype ; Shaker Superfamily of Potassium Channels/physiology ; Signal Transduction ; *Sleep/genetics/physiology ; Sleep Deprivation ; Transgenes
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  • 15
    Publication Date: 2008-03-01
    Description: Amyotrophic lateral sclerosis (ALS) is a fatal motor neuron disorder characterized pathologically by ubiquitinated TAR DNA binding protein (TDP-43) inclusions. The function of TDP-43 in the nervous system is uncertain, and a mechanistic role in neurodegeneration remains speculative. We identified neighboring mutations in a highly conserved region of TARDBP in sporadic and familial ALS cases. TARDBPM337V segregated with disease within one kindred and a genome-wide scan confirmed that linkage was restricted to chromosome 1p36, which contains the TARDBP locus. Mutant forms of TDP-43 fragmented in vitro more readily than wild type and, in vivo, caused neural apoptosis and developmental delay in the chick embryo. Our evidence suggests a pathophysiological link between TDP-43 and ALS.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sreedharan, Jemeen -- Blair, Ian P -- Tripathi, Vineeta B -- Hu, Xun -- Vance, Caroline -- Rogelj, Boris -- Ackerley, Steven -- Durnall, Jennifer C -- Williams, Kelly L -- Buratti, Emanuele -- Baralle, Francisco -- de Belleroche, Jacqueline -- Mitchell, J Douglas -- Leigh, P Nigel -- Al-Chalabi, Ammar -- Miller, Christopher C -- Nicholson, Garth -- Shaw, Christopher E -- G0500289/Medical Research Council/United Kingdom -- G0501573/Medical Research Council/United Kingdom -- G0600974/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2008 Mar 21;319(5870):1668-72. doi: 10.1126/science.1154584. Epub 2008 Feb 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Clinical Neuroscience, King's College London, Medical Research Council (MRC) Centre for Neurodegeneration Research, and Institute of Psychiatry, London, SE5 8AF, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18309045" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Amino Acid Sequence ; Amino Acid Substitution ; Amyotrophic Lateral Sclerosis/*genetics ; Animals ; Apoptosis ; CHO Cells ; Chick Embryo ; Chromosomes, Human, Pair 1/genetics ; Cricetinae ; Cricetulus ; DNA-Binding Proteins/chemistry/*genetics/physiology ; Embryonic Development ; Female ; Humans ; Male ; Microsatellite Repeats ; Middle Aged ; Molecular Sequence Data ; Mutant Proteins/chemistry/physiology ; *Mutation, Missense ; Neurons/cytology/physiology
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  • 16
    Publication Date: 2008-07-16
    Description: Secretory and membrane proteins carry amino-terminal signal sequences that, in cotranslational targeting, are recognized by the signal recognition particle protein SRP54 without sequence specificity. The most abundant membrane proteins on Earth are the light-harvesting chlorophyll a/b binding proteins (LHCPs). They are synthesized in the cytoplasm, imported into the chloroplast, and posttranslationally targeted to the thylakoid membrane by cpSRP, a heterodimer formed by cpSRP54 and cpSRP43. We present the 1.5 angstrom crystal structure of cpSRP43 characterized by a unique arrangement of chromodomains and ankyrin repeats. The overall shape and charge distribution of cpSRP43 resembles the SRP RNA, which is absent in chloroplasts. The complex with the internal signal sequence of LHCPs reveals that cpSRP43 specifically recognizes a DPLG peptide motif. We describe how cpSPR43 adapts the universally conserved SRP system to posttranslational targeting and insertion of the LHCP family of membrane proteins.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stengel, Katharina F -- Holdermann, Iris -- Cain, Peter -- Robinson, Colin -- Wild, Klemens -- Sinning, Irmgard -- New York, N.Y. -- Science. 2008 Jul 11;321(5886):253-6. doi: 10.1126/science.1158640.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemie-Zentrum der Universitat Heidelberg, INF328, D-69120 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18621669" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Ankyrin Repeat ; Arabidopsis/chemistry/*metabolism ; Arabidopsis Proteins/*chemistry/metabolism ; Calorimetry ; Chloroplast Proteins ; Crystallography, X-Ray ; Dimerization ; Hydrophobic and Hydrophilic Interactions ; Light-Harvesting Protein Complexes/chemistry/*metabolism ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits ; RNA, Plant/chemistry/metabolism ; Signal Recognition Particle/*chemistry/*metabolism ; Thylakoids/metabolism
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  • 17
    Publication Date: 2008-07-05
    Description: Membrane transporters that use energy stored in sodium gradients to drive nutrients into cells constitute a major class of proteins. We report the crystal structure of a member of the solute sodium symporters (SSS), the Vibrio parahaemolyticus sodium/galactose symporter (vSGLT). The approximately 3.0 angstrom structure contains 14 transmembrane (TM) helices in an inward-facing conformation with a core structure of inverted repeats of 5 TM helices (TM2 to TM6 and TM7 to TM11). Galactose is bound in the center of the core, occluded from the outside solutions by hydrophobic residues. Surprisingly, the architecture of the core is similar to that of the leucine transporter (LeuT) from a different gene family. Modeling the outward-facing conformation based on the LeuT structure, in conjunction with biophysical data, provides insight into structural rearrangements for active transport.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3654663/" 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/PMC3654663/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Faham, Salem -- Watanabe, Akira -- Besserer, Gabriel Mercado -- Cascio, Duilio -- Specht, Alexandre -- Hirayama, Bruce A -- Wright, Ernest M -- Abramson, Jeff -- DK19567/DK/NIDDK NIH HHS/ -- DK44602/DK/NIDDK NIH HHS/ -- GM07844/GM/NIGMS NIH HHS/ -- R01 GM078844/GM/NIGMS NIH HHS/ -- R01 GM078844-01/GM/NIGMS NIH HHS/ -- R01 GM078844-02/GM/NIGMS NIH HHS/ -- R01 GM078844-03/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Aug 8;321(5890):810-4. doi: 10.1126/science.1160406. Epub 2008 Jul 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1751, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18599740" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Biological Transport ; Crystallography, X-Ray ; Dimerization ; Galactose/chemistry/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers/chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Sodium/chemistry/*metabolism ; Sodium-Glucose Transport Proteins/*chemistry/metabolism ; Vibrio parahaemolyticus/*chemistry/metabolism
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  • 18
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2008-01-26
    Description: The statistical methods applied to the analysis of genomic data do not account for uncertainty in the sequence alignment. Indeed, the alignment is treated as an observation, and all of the subsequent inferences depend on the alignment being correct. This may not have been too problematic for many phylogenetic studies, in which the gene is carefully chosen for, among other things, ease of alignment. However, in a comparative genomics study, the same statistical methods are applied repeatedly on thousands of genes, many of which will be difficult to align. Using genomic data from seven yeast species, we show that uncertainty in the alignment can lead to several problems, including different alignment methods resulting in different conclusions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wong, Karen M -- Suchard, Marc A -- Huelsenbeck, John P -- GM-069801/GM/NIGMS NIH HHS/ -- R01 GM069801/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Jan 25;319(5862):473-6. doi: 10.1126/science.1151532.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Section of Ecology, Behavior and Evolution, University of California, San Diego, La Jolla, CA 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18218900" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Base Sequence ; Computational Biology ; Evolution, Molecular ; *Genome, Fungal ; *Genomics ; Models, Statistical ; Monte Carlo Method ; Open Reading Frames ; Phylogeny ; Saccharomyces/*genetics ; Selection, Genetic ; Sequence Alignment/*methods ; Software ; Uncertainty
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  • 19
    Publication Date: 2008-03-15
    Description: Edible fruits, such as that of the tomato plant and other vegetable crops, are markedly diverse in shape and size. SUN, one of the major genes controlling the elongated fruit shape of tomato, was positionally cloned and found to encode a member of the IQ67 domain-containing family. We show that the locus arose as a result of an unusual 24.7-kilobase gene duplication event mediated by the long terminal repeat retrotransposon Rider. This event resulted in a new genomic context that increased SUN expression relative to that of the ancestral copy, culminating in an elongated fruit shape. Our discovery demonstrates that retrotransposons may be a major driving force in genome evolution and gene duplication, resulting in phenotypic change in plants.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Xiao, Han -- Jiang, Ning -- Schaffner, Erin -- Stockinger, Eric J -- van der Knaap, Esther -- New York, N.Y. -- Science. 2008 Mar 14;319(5869):1527-30. doi: 10.1126/science.1153040.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Horticulture and Crop Science, Ohio State University/Ohio Agricultural Research and Development Center, Wooster, OH 44691, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18339939" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Evolution, Molecular ; Fruit/*anatomy & histology ; *Gene Duplication ; Gene Expression Regulation, Plant ; *Genes, Plant ; Genome, Plant ; Lycopersicon esculentum/*anatomy & histology/*genetics ; Molecular Sequence Data ; Phenotype ; Plant Proteins/chemistry/genetics/metabolism ; *Retroelements ; Terminal Repeat Sequences ; Transcription, Genetic ; Transformation, Genetic
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  • 20
    Publication Date: 2008-04-12
    Description: Initiation of actin polymerization in cells requires nucleation factors. Here we describe an actin-binding protein, leiomodin, that acted as a strong filament nucleator in muscle cells. Leiomodin shared two actin-binding sites with the filament pointed end-capping protein tropomodulin: a flexible N-terminal region and a leucine-rich repeat domain. Leiomodin also contained a C-terminal extension of 150 residues. The smallest fragment with strong nucleation activity included the leucine-rich repeat and C-terminal extension. The N-terminal region enhanced the nucleation activity threefold and recruited tropomyosin, which weakly stimulated nucleation and mediated localization of leiomodin to the middle of muscle sarcomeres. Knocking down leiomodin severely compromised sarcomere assembly in cultured muscle cells, which suggests a role for leiomodin in the nucleation of tropomyosin-decorated filaments in muscles.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2845909/" 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/PMC2845909/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chereau, David -- Boczkowska, Malgorzata -- Skwarek-Maruszewska, Aneta -- Fujiwara, Ikuko -- Hayes, David B -- Rebowski, Grzegorz -- Lappalainen, Pekka -- Pollard, Thomas D -- Dominguez, Roberto -- GM026338/GM/NIGMS NIH HHS/ -- GM073791/GM/NIGMS NIH HHS/ -- HL086655/HL/NHLBI NIH HHS/ -- P01 HL086655/HL/NHLBI NIH HHS/ -- P01 HL086655-01A10004/HL/NHLBI NIH HHS/ -- R01 GM073791/GM/NIGMS NIH HHS/ -- R01 GM073791-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Apr 11;320(5873):239-43. doi: 10.1126/science.1155313.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Boston Biomedical Research Institute, Watertown, MA 02472, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18403713" target="_blank"〉PubMed〈/a〉
    Keywords: Actin Cytoskeleton/*metabolism ; Actins/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Cells, Cultured ; Cytoskeletal Proteins/chemistry/*metabolism ; Humans ; Microfilament Proteins/chemistry/*metabolism ; Molecular Sequence Data ; Muscle Proteins/chemistry/*metabolism ; Myocytes, Cardiac/*metabolism ; Protein Structure, Tertiary ; RNA Interference ; Rabbits ; Rats ; Sarcomeres/*metabolism ; Tropomodulin/chemistry ; Tropomyosin/chemistry/metabolism
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  • 21
    Publication Date: 2008-03-08
    Description: Antigenically variable M proteins are major virulence factors and immunogens of the human pathogen group A Streptococcus (GAS). Here, we report the approximately 3 angstrom resolution structure of a GAS M1 fragment containing the regions responsible for eliciting type-specific, protective immunity and for binding fibrinogen, which promotes M1 proinflammatory and antiphagocytic functions. The structure revealed substantial irregularities and instabilities throughout the coiled coil of the M1 fragment. Similar structural irregularities occur in myosin and tropomyosin, explaining the patterns of cross-reactivity seen in autoimmune sequelae of GAS infection. Sequence idealization of a large segment of the M1 coiled coil enhanced stability but diminished fibrinogen binding, proinflammatory effects, and antibody cross-reactivity, whereas it left protective immunogenicity undiminished. Idealized M proteins appear to have promise as vaccine immunogens.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2288698/" 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/PMC2288698/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McNamara, Case -- Zinkernagel, Annelies S -- Macheboeuf, Pauline -- Cunningham, Madeleine W -- Nizet, Victor -- Ghosh, Partho -- R01 AI048694/AI/NIAID NIH HHS/ -- R01 AI052453/AI/NIAID NIH HHS/ -- R01 AI052453-08/AI/NIAID NIH HHS/ -- R21 AI071167/AI/NIAID NIH HHS/ -- R21 AI071167-01A1/AI/NIAID NIH HHS/ -- T32 GM008326/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Mar 7;319(5868):1405-8. doi: 10.1126/science.1154470.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18323455" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Antibodies, Bacterial/immunology ; Antigens, Bacterial/*chemistry/genetics/immunology/metabolism ; Bacterial Outer Membrane Proteins/*chemistry/genetics/immunology/metabolism ; Carrier Proteins/*chemistry/genetics/immunology/metabolism ; Circular Dichroism ; Cross Reactions ; Crystallography, X-Ray ; Dimerization ; Fibrinogen/metabolism ; Humans ; Mice ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry ; Protein Conformation ; Protein Structure, Secondary ; Repetitive Sequences, Amino Acid ; Streptococcal Infections/immunology/microbiology ; Streptococcus pyogenes/*chemistry/immunology/*pathogenicity ; Virulence
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  • 22
    Publication Date: 2008-07-19
    Description: The atypical cadherin Fat acts as a receptor for a signaling pathway that regulates growth, gene expression, and planar cell polarity. Genetic studies in Drosophila identified the four-jointed gene as a regulator of Fat signaling. We show that four-jointed encodes a protein kinase that phosphorylates serine or threonine residues within extracellular cadherin domains of Fat and its transmembrane ligand, Dachsous. Four-jointed functions in the Golgi and is the first molecularly defined kinase that phosphorylates protein domains destined to be extracellular. An acidic sequence motif (Asp-Asn-Glu) within Four-jointed was essential for its kinase activity in vitro and for its biological activity in vivo. Our results indicate that Four-jointed regulates Fat signaling by phosphorylating cadherin domains of Fat and Dachsous as they transit through the Golgi.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2562711/" 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/PMC2562711/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ishikawa, Hiroyuki O -- Takeuchi, Hideyuki -- Haltiwanger, Robert S -- Irvine, Kenneth D -- CA123071/CA/NCI NIH HHS/ -- GM061126/GM/NIGMS NIH HHS/ -- GM078620/GM/NIGMS NIH HHS/ -- R01 CA123071/CA/NCI NIH HHS/ -- R01 CA123071-02/CA/NCI NIH HHS/ -- R01 GM061126/GM/NIGMS NIH HHS/ -- R01 GM061126-08/GM/NIGMS NIH HHS/ -- R01 GM078620/GM/NIGMS NIH HHS/ -- R01 GM078620-02/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Jul 18;321(5887):401-4. doi: 10.1126/science.1158159.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18635802" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cadherins/chemistry/*metabolism ; Cell Adhesion Molecules/chemistry/*metabolism ; Cell Line ; Drosophila Proteins/chemistry/genetics/*metabolism ; Drosophila melanogaster ; Electrophoretic Mobility Shift Assay ; Glycosylation ; Golgi Apparatus/enzymology/*metabolism ; Kinetics ; Membrane Glycoproteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Phosphorylation ; Protein Kinases/chemistry/genetics/*metabolism ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Serine/metabolism ; Signal Transduction ; Threonine/metabolism
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  • 23
    Publication Date: 2008-07-26
    Description: Duane's retraction syndrome (DRS) is a complex congenital eye movement disorder caused by aberrant innervation of the extraocular muscles by axons of brainstem motor neurons. Studying families with a variant form of the disorder (DURS2-DRS), we have identified causative heterozygous missense mutations in CHN1, a gene on chromosome 2q31 that encodes alpha2-chimaerin, a Rac guanosine triphosphatase-activating protein (RacGAP) signaling protein previously implicated in the pathfinding of corticospinal axons in mice. We found that these are gain-of-function mutations that increase alpha2-chimaerin RacGAP activity in vitro. Several of the mutations appeared to enhance alpha2-chimaerin translocation to the cell membrane or enhance its ability to self-associate. Expression of mutant alpha2-chimaerin constructs in chick embryos resulted in failure of oculomotor axons to innervate their target extraocular muscles. We conclude that alpha2-chimaerin has a critical developmental function in ocular motor axon pathfinding.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2593867/" 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/PMC2593867/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miyake, Noriko -- Chilton, John -- Psatha, Maria -- Cheng, Long -- Andrews, Caroline -- Chan, Wai-Man -- Law, Krystal -- Crosier, Moira -- Lindsay, Susan -- Cheung, Michelle -- Allen, James -- Gutowski, Nick J -- Ellard, Sian -- Young, Elizabeth -- Iannaccone, Alessandro -- Appukuttan, Binoy -- Stout, J Timothy -- Christiansen, Stephen -- Ciccarelli, Maria Laura -- Baldi, Alfonso -- Campioni, Mara -- Zenteno, Juan C -- Davenport, Dominic -- Mariani, Laura E -- Sahin, Mustafa -- Guthrie, Sarah -- Engle, Elizabeth C -- G9900837/Medical Research Council/United Kingdom -- G9900989/Medical Research Council/United Kingdom -- R01 EY015298/EY/NEI NIH HHS/ -- R01 EY015298-01/EY/NEI NIH HHS/ -- R01 EY015298-02/EY/NEI NIH HHS/ -- R01 EY015298-03/EY/NEI NIH HHS/ -- R01 EY015298-04/EY/NEI NIH HHS/ -- R01 EY015298-05/EY/NEI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Aug 8;321(5890):839-43. doi: 10.1126/science.1156121. Epub 2008 Jul 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine (Genetics), Children's Hospital Boston, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18653847" target="_blank"〉PubMed〈/a〉
    Keywords: Abducens Nerve/abnormalities ; Amino Acid Sequence ; Animals ; Axons/physiology ; Cell Line ; Cell Membrane/metabolism ; Chick Embryo ; Chimerin 1/chemistry/*genetics/*metabolism ; Duane Retraction Syndrome/*genetics ; Female ; Gene Expression Profiling ; Heterozygote ; Humans ; Male ; Molecular Sequence Data ; *Mutation, Missense ; Oculomotor Muscles/embryology/innervation/metabolism ; Oculomotor Nerve/abnormalities/embryology ; Pedigree
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  • 24
    Publication Date: 2008-06-07
    Description: Telomeres are specialized chromatin structures that protect chromosomal ends. Protection of telomeres 1 (Pot1) binds to the telomeric G-rich overhang, thereby protecting telomeres and regulating telomerase. Mammalian POT1 and TPP1 interact and constitute part of the six-protein shelterin complex. Here we report that Tpz1, the TPP1 homolog in fission yeast, forms a complex with Pot1. Tpz1 binds to Ccq1 and the previously undiscovered protein Poz1 (Pot1-associated in Schizosaccharomyces pombe), which protect telomeres redundantly and regulate telomerase in positive and negative manners, respectively. Thus, the Pot1-Tpz1 complex accomplishes its functions by recruiting effector molecules Ccq1 and Poz1. Moreover, Poz1 bridges Pot1-Tpz1 and Taz1-Rap1, thereby connecting the single-stranded and double-stranded telomeric DNA regions. Such molecular architectures are similar to those of mammalian shelterin, indicating that the overall DNA-protein architecture is conserved across evolution.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miyoshi, Tomoichiro -- Kanoh, Junko -- Saito, Motoki -- Ishikawa, Fuyuki -- New York, N.Y. -- Science. 2008 Jun 6;320(5881):1341-4. doi: 10.1126/science.1154819.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18535244" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Carrier Proteins/chemistry/genetics/*metabolism ; Chromatin Immunoprecipitation ; DNA, Fungal/metabolism ; Immunoprecipitation ; Molecular Sequence Data ; Mutation ; Protein Binding ; Protein Structure, Tertiary ; Schizosaccharomyces/genetics/*metabolism ; Schizosaccharomyces pombe Proteins/chemistry/genetics/*metabolism ; Telomerase/metabolism ; Telomere/metabolism/*physiology/ultrastructure ; Telomere-Binding Proteins/chemistry/genetics/*metabolism ; Two-Hybrid System Techniques
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  • 25
    Publication Date: 2008-02-16
    Description: F1-adenosine triphosphatase (ATPase) is an ATP-driven rotary molecular motor in which the central gamma subunit rotates inside a cylinder made of three alpha and three beta subunits alternately arranged. The rotor shaft, an antiparallel alpha-helical coiled coil of the amino and carboxyl termini of the gamma subunit, deeply penetrates the central cavity of the stator cylinder. We truncated the shaft step by step until the remaining rotor head would be outside the cavity and simply sat on the concave entrance of the stator orifice. All truncation mutants rotated in the correct direction, implying torque generation, although the average rotary speeds were low and short mutants exhibited moments of irregular motion. Neither a fixed pivot nor a rigid axle was needed for rotation of F1-ATPase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Furuike, Shou -- Hossain, Mohammad Delawar -- Maki, Yasushi -- Adachi, Kengo -- Suzuki, Toshiharu -- Kohori, Ayako -- Itoh, Hiroyasu -- Yoshida, Masasuke -- Kinosita, Kazuhiko Jr -- New York, N.Y. -- Science. 2008 Feb 15;319(5865):955-8. doi: 10.1126/science.1151343.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physics, Faculty of Science and Engineering, Waseda University, Shinjuku-ku, Tokyo 169-8555, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18276891" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Hydrolysis ; Microspheres ; Molecular Motor Proteins/*chemistry/metabolism ; Molecular Sequence Data ; Mutant Proteins/chemistry ; Mutation ; Protein Conformation ; Protein Subunits/chemistry/metabolism ; Proton-Translocating ATPases/*chemistry/genetics/*metabolism ; Rotation ; Torque
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  • 26
    Publication Date: 2008-04-19
    Description: It has been widely assumed that the atomic structure of the flagellar filament from Salmonella typhimurium serves as a model for all bacterial flagellar filaments given the sequence conservation in the coiled-coil regions responsible for polymerization. On the basis of electron microscopic images, we show that the flagellar filaments from Campylobacter jejuni have seven protofilaments rather than the 11 in S. typhimurium. The vertebrate Toll-like receptor 5 (TLR5) recognizes a region of bacterial flagellin that is involved in subunit-subunit assembly in Salmonella and many other pathogenic bacteria, and this short region has diverged in Campylobacter and related bacteria, such as Helicobacter pylori, which are not recognized by TLR5. The driving force in the change of quaternary structure between Salmonella and Campylobacter may have been the evasion of TLR5.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Galkin, Vitold E -- Yu, Xiong -- Bielnicki, Jakub -- Heuser, John -- Ewing, Cheryl P -- Guerry, Patricia -- Egelman, Edward H -- AI043559/AI/NIAID NIH HHS/ -- EB001567/EB/NIBIB NIH HHS/ -- New York, N.Y. -- Science. 2008 Apr 18;320(5874):382-5. doi: 10.1126/science.1155307.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Genetics, Box 800733, University of Virginia, Charlottesville, VA 22908-0733, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18420936" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Campylobacter jejuni/chemistry/genetics/*ultrastructure ; Cryoelectron Microscopy ; Evolution, Molecular ; Flagella/*chemistry/*ultrastructure ; Flagellin/*chemistry/genetics/immunology/metabolism ; Image Processing, Computer-Assisted ; Molecular Sequence Data ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Salmonella typhimurium/chemistry/*ultrastructure ; Toll-Like Receptor 5/immunology/metabolism
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  • 27
    Publication Date: 2008-07-16
    Description: The crystal structure of the high-affinity Escherichia coli MetNI methionine uptake transporter, a member of the adenosine triphosphate (ATP)-binding cassette (ABC) family, has been solved to 3.7 angstrom resolution. The overall architecture of MetNI reveals two copies of the adenosine triphosphatase (ATPase) MetN in complex with two copies of the transmembrane domain MetI, with the transporter adopting an inward-facing conformation exhibiting widely separated nucleotide binding domains. Each MetI subunit is organized around a core of five transmembrane helices that correspond to a subset of the helices observed in the larger membrane-spanning subunits of the molybdate (ModBC) and maltose (MalFGK) ABC transporters. In addition to the conserved nucleotide binding domain of the ABC family, MetN contains a carboxyl-terminal extension with a ferredoxin-like fold previously assigned to a conserved family of regulatory ligand-binding domains. These domains separate the nucleotide binding domains and would interfere with their association required for ATP binding and hydrolysis. Methionine binds to the dimerized carboxyl-terminal domain and is shown to inhibit ATPase activity. These observations are consistent with an allosteric regulatory mechanism operating at the level of transport activity, where increased intracellular levels of the transported ligand stabilize an inward-facing, ATPase-inactive state of MetNI to inhibit further ligand translocation into the cell.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527972/" 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/PMC2527972/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kadaba, Neena S -- Kaiser, Jens T -- Johnson, Eric -- Lee, Allen -- Rees, Douglas C -- GM45162/GM/NIGMS NIH HHS/ -- R37 GM045162/GM/NIGMS NIH HHS/ -- R37 GM045162-18/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Jul 11;321(5886):250-3. doi: 10.1126/science.1157987.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Division of Chemistry and Chemical Engineering, Mail Code 114-96, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18621668" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry/metabolism ; Adenosine Triphosphatases/*chemistry/*metabolism ; Allosteric Regulation ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Dimerization ; Escherichia coli Proteins/*chemistry/*metabolism ; Membrane Transport Proteins/*chemistry/*metabolism ; Methionine/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism
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  • 28
    Publication Date: 2008-06-21
    Description: Biofilms are multicellular aggregates of sessile bacteria encased by an extracellular matrix and are important medically as a source of drug-resistant microbes. In Bacillus subtilis, we found that an operon required for biofilm matrix biosynthesis also encoded an inhibitor of motility, EpsE. EpsE arrested flagellar rotation in a manner similar to that of a clutch, by disengaging motor force-generating elements in cells embedded in the biofilm matrix. The clutch is a simple, rapid, and potentially reversible form of motility control.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Blair, Kris M -- Turner, Linda -- Winkelman, Jared T -- Berg, Howard C -- Kearns, Daniel B -- AI065540/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2008 Jun 20;320(5883):1636-8. doi: 10.1126/science.1157877.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Indiana University, Bloomington, IN 47405, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18566286" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacillus subtilis/genetics/*physiology ; Bacterial Proteins/chemistry/genetics/metabolism/*physiology ; Biofilms/*growth & development ; Flagella/*physiology ; Genes, Bacterial ; Molecular Motor Proteins/genetics/*physiology ; Molecular Sequence Data ; Movement ; Mutation ; Operon ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism
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  • 29
    Publication Date: 2008-12-20
    Description: Diversity in leaf shape is produced by alterations of the margin: for example, deep dissection leads to leaflet formation and less-pronounced incision results in serrations or lobes. By combining gene silencing and mutant analyses in four distantly related eudicot species, we show that reducing the function of NAM/CUC boundary genes (NO APICAL MERISTEM and CUP-SHAPED COTYLEDON) leads to a suppression of all marginal outgrowths and to fewer and fused leaflets. We propose that NAM/CUC genes promote formation of a boundary domain that delimits leaflets. This domain has a dual role promoting leaflet separation locally and leaflet formation at distance. In this manner, boundaries of compound leaves resemble boundaries functioning during animal development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Blein, Thomas -- Pulido, Amada -- Vialette-Guiraud, Aurelie -- Nikovics, Krisztina -- Morin, Halima -- Hay, Angela -- Johansen, Ida Elisabeth -- Tsiantis, Miltos -- Laufs, Patrick -- Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Dec 19;322(5909):1835-9. doi: 10.1126/science.1166168.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratoire de Biologie Cellulaire, Institut Jean Pierre Bourgin, Institut National de la Recherche Agronomique (INRA), 78026 Versailles Cedex, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19095941" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Aquilegia/genetics/growth & development/metabolism ; Cardamine/genetics/growth & development/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Plant ; Gene Silencing ; *Genes, Plant ; Lycopersicon esculentum/genetics/growth & development/metabolism ; Molecular Sequence Data ; Peas/genetics/growth & development ; Phylogeny ; Plant Leaves/genetics/*growth & development/metabolism ; Plant Proteins/genetics/metabolism ; Plants, Genetically Modified ; Solanum tuberosum/genetics/growth & development/metabolism ; Transcription Factors/chemistry/*genetics/metabolism
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  • 30
    Publication Date: 2008-03-08
    Description: Diffuse large B cell lymphoma (DLBCL) is the most common form of non-Hodgkin's lymphoma. In the least curable (ABC) subtype of DLBCL, survival of the malignant cells is dependent on constitutive activation of the nuclear factor-kappaB (NF-kappaB) signaling pathway. In normal B cells, antigen receptor-induced NF-kappaB activation requires CARD11, a cytoplasmic scaffolding protein. To determine whether CARD11 contributes to tumorigenesis, we sequenced the CARD11 gene in human DLBCL tumors. We detected missense mutations in 7 of 73 ABC DLBCL biopsies (9.6%), all within exons encoding the coiled-coil domain. Experimental introduction of CARD11 coiled-coil domain mutants into lymphoma cell lines resulted in constitutive NF-kappaB activation and enhanced NF-kappaB activity upon antigen receptor stimulation. These results demonstrate that CARD11 is a bona fide oncogenein DLBCL, providing a genetic rationale for the development of pharmacological inhibitors of the CARD11 pathway for DLBCL therapy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lenz, Georg -- Davis, R Eric -- Ngo, Vu N -- Lam, Lloyd -- George, Thaddeus C -- Wright, George W -- Dave, Sandeep S -- Zhao, Hong -- Xu, Weihong -- Rosenwald, Andreas -- Ott, German -- Muller-Hermelink, Hans Konrad -- Gascoyne, Randy D -- Connors, Joseph M -- Rimsza, Lisa M -- Campo, Elias -- Jaffe, Elaine S -- Delabie, Jan -- Smeland, Erlend B -- Fisher, Richard I -- Chan, Wing C -- Staudt, Louis M -- UO1-CA84967/CA/NCI NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Mar 21;319(5870):1676-9. doi: 10.1126/science.1153629. Epub 2008 Mar 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Metabolism Branch, Division of Cancer Treatment and Diagnosis, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18323416" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Apoptosis Regulatory Proteins/chemistry/*genetics/metabolism ; CARD Signaling Adaptor Proteins/chemistry/*genetics/metabolism ; Cell Line, Tumor ; Cytoplasm/metabolism ; Guanylate Cyclase/chemistry/*genetics/metabolism ; Humans ; I-kappa B Kinase/metabolism ; Jurkat Cells ; Lymphoma, Large B-Cell, Diffuse/*genetics ; Molecular Sequence Data ; *Mutation, Missense ; NF-kappa B ; *Oncogenes ; Protein Structure, Tertiary ; Receptors, Antigen, B-Cell/physiology ; Sequence Analysis, DNA
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  • 31
    Publication Date: 2008-11-29
    Description: The Vibrio parahaemolyticus type III effector VopS is implicated in cell rounding and the collapse of the actin cytoskeleton by inhibiting Rho guanosine triphosphatases (GTPases). We found that VopS could act to covalently modify a conserved threonine residue on Rho, Rac, and Cdc42 with adenosine 5'-monophosphate (AMP). The resulting AMPylation prevented the interaction of Rho GTPases with downstream effectors, thereby inhibiting actin assembly in the infected cell. Eukaryotic proteins were also directly modified with AMP, potentially expanding the repertoire of posttranslational modifications for molecular signaling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yarbrough, Melanie L -- Li, Yan -- Kinch, Lisa N -- Grishin, Nick V -- Ball, Haydn L -- Orth, Kim -- R01-AI056404/AI/NIAID NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Jan 9;323(5911):269-72. doi: 10.1126/science.1166382. Epub 2008 Nov 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, University of Texas (UT) Southwestern Medical Center, Dallas, TX 75390, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19039103" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Monophosphate/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/*metabolism ; Binding Sites ; Cell Shape ; HeLa Cells ; Humans ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Phosphorylation ; Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Signal Transduction ; Threonine/chemistry/metabolism ; Vibrio parahaemolyticus/*metabolism/pathogenicity ; cdc42 GTP-Binding Protein/antagonists & inhibitors/chemistry/*metabolism ; rac GTP-Binding Proteins/antagonists & inhibitors/chemistry/*metabolism ; rho GTP-Binding Proteins/antagonists & inhibitors/chemistry/*metabolism
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  • 32
    Publication Date: 2008-12-17
    Description: Speciation genes restrict gene flow between the incipient species and related taxa. Three decades ago, we mapped a mammalian speciation gene, hybrid sterility 1 (Hst1), in the intersubspecific hybrids of house mouse. Here, we identify this gene as Prdm9, encoding a histone H3 lysine 4 trimethyltransferase. We rescued infertility in male hybrids with bacterial artificial chromosomes carrying Prdm9 from a strain with the "fertility" Hst1(f) allele. Sterile hybrids display down-regulated microrchidia 2B (Morc2b) and fail to compartmentalize gammaH2AX into the pachynema sex (XY) body. These defects, seen also in Prdm9-null mutants, are rescued by the Prdm9 transgene. Identification of a vertebrate hybrid sterility gene reveals a role for epigenetics in speciation and opens a window to a hybrid sterility gene network.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mihola, Ondrej -- Trachtulec, Zdenek -- Vlcek, Cestmir -- Schimenti, John C -- Forejt, Jiri -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Jan 16;323(5912):373-5. doi: 10.1126/science.1163601. Epub 2008 Dec 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 142 20 Prague, Czech Republic.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19074312" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Chromosome Mapping ; Chromosomes, Artificial, Bacterial ; Crosses, Genetic ; Epigenesis, Genetic ; Female ; Gene Expression Regulation ; *Genetic Speciation ; Histone-Lysine N-Methyltransferase/chemistry/*genetics/*metabolism ; Histones/metabolism ; Hybridization, Genetic ; Infertility, Male/*genetics ; Male ; *Meiosis ; Methylation ; Mice ; Mice, Inbred C3H ; Mice, Transgenic ; Molecular Sequence Data ; Ovary/enzymology ; Testis/enzymology
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  • 33
    Publication Date: 2008-07-26
    Description: Brassinosteroids (BRs) bind to the extracellular domain of the receptor kinase BRI1 to activate a signal transduction cascade that regulates nuclear gene expression and plant development. Many components of the BR signaling pathway have been identified and studied in detail. However, the substrate of BRI1 kinase that transduces the signal to downstream components remains unknown. Proteomic studies of plasma membrane proteins lead to the identification of three homologous BR-signaling kinases (BSK1, BSK2, and BSK3). The BSKs are phosphorylated by BRI1 in vitro and interact with BRI1 in vivo. Genetic and transgenic studies demonstrate that the BSKs represent a small family of kinases that activate BR signaling downstream of BRI1. These results demonstrate that BSKs are the substrates of BRI1 kinase that activate downstream BR signal transduction.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2730546/" 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/PMC2730546/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tang, Wenqiang -- Kim, Tae-Wuk -- Oses-Prieto, Juan A -- Sun, Yu -- Deng, Zhiping -- Zhu, Shengwei -- Wang, Ruiju -- Burlingame, Alma L -- Wang, Zhi-Yong -- R01 GM066258/GM/NIGMS NIH HHS/ -- R01 GM066258-07/GM/NIGMS NIH HHS/ -- R01GM066258/GM/NIGMS NIH HHS/ -- RR012961/RR/NCRR NIH HHS/ -- RR01614/RR/NCRR NIH HHS/ -- RR019934/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 2008 Jul 25;321(5888):557-60. doi: 10.1126/science.1156973.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Biology, Carnegie Institution of Washington, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18653891" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/enzymology/genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Brassinosteroids ; Cell Membrane/metabolism ; Cholestanols/metabolism/pharmacology ; Molecular Sequence Data ; Mutagenesis, Insertional ; Phosphorylation ; Plants, Genetically Modified ; Protein Kinases/chemistry/genetics/*metabolism ; Protein Structure, Tertiary ; Protein-Serine-Threonine Kinases ; Proteomics ; Recombinant Fusion Proteins/metabolism ; *Signal Transduction ; Steroids, Heterocyclic/metabolism/pharmacology
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  • 34
    Publication Date: 2008-06-28
    Description: Nonribosomal peptide synthetases (NRPSs) are modular multidomain enzymes that act as an assembly line to catalyze the biosynthesis of complex natural products. The crystal structure of the 144-kilodalton Bacillus subtilis termination module SrfA-C was solved at 2.6 angstrom resolution. The adenylation and condensation domains of SrfA-C associate closely to form a catalytic platform, with their active sites on the same side of the platform. The peptidyl carrier protein domain is flexibly tethered to this platform and thus can move with its substrate-loaded 4'-phosphopantetheine arm between the active site of the adenylation domain and the donor side of the condensation domain. The SrfA-C crystal structure has implications for the rational redesign of NRPSs as a means of producing novel bioactive peptides.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tanovic, Alan -- Samel, Stefan A -- Essen, Lars-Oliver -- Marahiel, Mohamed A -- New York, N.Y. -- Science. 2008 Aug 1;321(5889):659-63. doi: 10.1126/science.1159850. Epub 2008 Jun 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein-Strasse, D35032 Marburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18583577" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacillus subtilis/*enzymology ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Models, Molecular ; Molecular Sequence Data ; Peptide Synthases/*chemistry/metabolism ; Protein Conformation ; Protein Engineering ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry/metabolism
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  • 35
    Publication Date: 2008-11-15
    Description: Archaea are prokaryotic organisms that lack endomembrane structures. However, a number of hyperthermophilic members of the Kingdom Crenarchaea, including members of the Sulfolobus genus, encode homologs of the eukaryotic endosomal sorting system components Vps4 and ESCRT-III (endosomal sorting complex required for transport-III). We found that Sulfolobus ESCRT-III and Vps4 homologs underwent regulation of their expression during the cell cycle. The proteins interacted and we established the structural basis of this interaction. Furthermore, these proteins specifically localized to the mid-cell during cell division. Overexpression of a catalytically inactive mutant Vps4 in Sulfolobus resulted in the accumulation of enlarged cells, indicative of failed cell division. Thus, the archaeal ESCRT system plays a key role in cell division.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4121953/" 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/PMC4121953/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Samson, Rachel Y -- Obita, Takayuki -- Freund, Stefan M -- Williams, Roger L -- Bell, Stephen D -- 083639/Z/07/Z/Wellcome Trust/United Kingdom -- MC_U105184308/Medical Research Council/United Kingdom -- Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Dec 12;322(5908):1710-3. doi: 10.1126/science.1165322. Epub 2008 Nov 13.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Cancer Cell Unit, Hills Road, Cambridge CB2 0XZ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19008417" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry/*metabolism ; Amino Acid Sequence ; Archaeal Proteins/chemistry/*metabolism ; Biological Evolution ; Cell Cycle ; *Cell Division ; Crystallography, X-Ray ; Molecular Sequence Data ; Peptides/chemistry/metabolism ; Protein Structure, Tertiary ; Sequence Alignment ; Sulfolobus/*cytology/genetics/*metabolism ; Sulfolobus acidocaldarius/*cytology/genetics/*metabolism ; Vesicular Transport Proteins/chemistry/metabolism
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  • 36
    Publication Date: 2008-08-09
    Description: Andromonoecy is a widespread sexual system in angiosperms characterized by plants carrying both male and bisexual flowers. In melon, this sexual form is controlled by the identity of the alleles at the andromonoecious (a) locus. Cloning of the a gene reveals that andromonoecy results from a mutation in the active site of 1-aminocyclopropane-1-carboxylic acid synthase. Expression of the active enzyme inhibits the development of the male organs and is not required for carpel development. A causal single-nucleotide polymorphism associated with andromonoecy was identified, which suggests that the a allele has been under recent positive selection and may be linked to the evolution of this sexual system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boualem, Adnane -- Fergany, Mohamed -- Fernandez, Ronan -- Troadec, Christelle -- Martin, Antoine -- Morin, Halima -- Sari, Marie-Agnes -- Collin, Fabrice -- Flowers, Jonathan M -- Pitrat, Michel -- Purugganan, Michael D -- Dogimont, Catherine -- Bendahmane, Abdelhafid -- New York, N.Y. -- Science. 2008 Aug 8;321(5890):836-8. doi: 10.1126/science.1159023.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉INRA (Institut National de la Recherche Agronomique)-CNRS, UMR1165, Unite de Recherche en Genomique Vegetale, 2 rue Gaston Cremieux, F-91057 Evry, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18687965" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Binding Sites ; Biological Evolution ; Crosses, Genetic ; Cucumis melo/*enzymology/genetics/*physiology ; Flowers/genetics/growth & development/*physiology ; Genes, Plant ; Haplotypes ; Lyases/chemistry/*genetics/metabolism ; Molecular Sequence Data ; *Mutation ; Phylogeny ; *Polymorphism, Single Nucleotide ; Reverse Transcriptase Polymerase Chain Reaction ; Selection, Genetic ; Sequence Analysis, DNA
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  • 37
    Publication Date: 2008-08-16
    Description: Prokaryotes acquire virus resistance by integrating short fragments of viral nucleic acid into clusters of regularly interspaced short palindromic repeats (CRISPRs). Here we show how virus-derived sequences contained in CRISPRs are used by CRISPR-associated (Cas) proteins from the host to mediate an antiviral response that counteracts infection. After transcription of the CRISPR, a complex of Cas proteins termed Cascade cleaves a CRISPR RNA precursor in each repeat and retains the cleavage products containing the virus-derived sequence. Assisted by the helicase Cas3, these mature CRISPR RNAs then serve as small guide RNAs that enable Cascade to interfere with virus proliferation. Our results demonstrate that the formation of mature guide RNAs by the CRISPR RNA endonuclease subunit of Cascade is a mechanistic requirement for antiviral defense.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brouns, Stan J J -- Jore, Matthijs M -- Lundgren, Magnus -- Westra, Edze R -- Slijkhuis, Rik J H -- Snijders, Ambrosius P L -- Dickman, Mark J -- Makarova, Kira S -- Koonin, Eugene V -- van der Oost, John -- New York, N.Y. -- Science. 2008 Aug 15;321(5891):960-4. doi: 10.1126/science.1159689.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18703739" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacteriophage lambda/*genetics/*growth & development ; Base Sequence ; DNA, Intergenic ; DNA, Viral/metabolism ; Escherichia coli/genetics/metabolism ; Escherichia coli K12/*genetics/metabolism/*virology ; Escherichia coli Proteins/chemistry/genetics/*metabolism ; Genes, Bacterial ; Molecular Sequence Data ; RNA Precursors/metabolism ; RNA, Bacterial/*genetics/metabolism ; RNA, Guide/genetics/metabolism ; *Repetitive Sequences, Nucleic Acid ; Transcription, Genetic ; Viral Plaque Assay
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  • 38
    Publication Date: 2008-07-26
    Description: Chromosome segregation, transcriptional regulation, and repair of DNA double-strand breaks require the cohesin protein complex. Cohesin holds the replicated chromosomes (sister chromatids) together to mediate sister chromatid cohesion. The mechanism of how cohesion is established is unknown. We found that in budding yeast, the head domain of the Smc3p subunit of cohesin is acetylated by the Eco1p acetyltransferase at two evolutionarily conserved residues, promoting the chromatin-bound cohesin to tether sister chromatids. Smc3p acetylation is induced in S phase after the chromatin loading of cohesin and is suppressed in G(1) and G(2)/M. Smc3 head acetylation and its cell cycle regulation provide important insights into the biology and mechanism of cohesion establishment.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Unal, Elcin -- Heidinger-Pauli, Jill M -- Kim, Woong -- Guacci, Vincent -- Onn, Itay -- Gygi, Steven P -- Koshland, Douglas E -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2008 Jul 25;321(5888):566-9. doi: 10.1126/science.1157880.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Embryology, Carnegie Institution, 3520 San Martin Drive, Baltimore, MD 21218, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18653894" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Acetyltransferases/genetics/*metabolism ; Amino Acid Sequence ; Amino Acid Substitution ; Cell Cycle Proteins/chemistry/genetics/*metabolism ; Cell Division ; Chondroitin Sulfate Proteoglycans/chemistry/genetics/*metabolism ; Chromatids/*physiology ; Chromatin/metabolism ; Chromosomal Proteins, Non-Histone/chemistry/genetics/*metabolism ; Chromosomes, Fungal/*physiology ; G1 Phase ; G2 Phase ; Immunoprecipitation ; Lysine/metabolism ; Molecular Sequence Data ; Mutation ; Nuclear Proteins/genetics/*metabolism ; Protein Structure, Tertiary ; S Phase ; Saccharomyces cerevisiae/genetics/growth & development/*physiology ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism
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  • 39
    Publication Date: 2008-02-16
    Description: Staphylococcus aureus produces hospital- and community-acquired infections, with methicillin-resistant S. aureus posing a serious public health threat. The golden carotenoid pigment of S. aureus, staphyloxanthin, promotes resistance to reactive oxygen species and host neutrophil-based killing, and early enzymatic steps in staphyloxanthin production resemble those for cholesterol biosynthesis. We determined the crystal structures of S. aureus dehydrosqualene synthase (CrtM) at 1.58 angstrom resolution, finding structural similarity to human squalene synthase (SQS). We screened nine SQS inhibitors and determined the structures of three, bound to CrtM. One, previously tested for cholesterol-lowering activity in humans, blocked staphyloxanthin biosynthesis in vitro (median inhibitory concentration approximately 100 nM), resulting in colorless bacteria with increased susceptibility to killing by human blood and to innate immune clearance in a mouse infection model. This finding represents proof of principle for a virulence factor-based therapy against S. aureus.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2747771/" 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/PMC2747771/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Chia-I -- Liu, George Y -- Song, Yongcheng -- Yin, Fenglin -- Hensler, Mary E -- Jeng, Wen-Yih -- Nizet, Victor -- Wang, Andrew H-J -- Oldfield, Eric -- AI07482/AI/NIAID NIH HHS/ -- GM073216/GM/NIGMS NIH HHS/ -- GM65307/GM/NIGMS NIH HHS/ -- HD051796/HD/NICHD NIH HHS/ -- R01 GM065307/GM/NIGMS NIH HHS/ -- R01 GM065307-07/GM/NIGMS NIH HHS/ -- R01 GM073216/GM/NIGMS NIH HHS/ -- R01 GM073216-29/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Mar 7;319(5868):1391-4. doi: 10.1126/science.1153018. Epub 2008 Feb 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biological Chemistry, Academia Sinica, Nankang, Taipei 11529, Taiwan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18276850" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Anti-Bacterial Agents/chemical synthesis/chemistry/*pharmacology/therapeutic use ; Bacterial Proteins/*antagonists & inhibitors/chemistry/isolation & ; purification/metabolism ; Cell Line ; Cell Proliferation/drug effects ; Cholesterol/biosynthesis ; Crystallography, X-Ray ; Enzyme Inhibitors/chemical synthesis/metabolism/*pharmacology ; Farnesyl-Diphosphate Farnesyltransferase/*antagonists & ; inhibitors/chemistry/isolation & purification/metabolism ; Humans ; Mice ; Molecular Sequence Data ; Organothiophosphorus Compounds/chemical ; synthesis/metabolism/*pharmacology/therapeutic use ; Polyisoprenyl Phosphates/chemistry/metabolism ; Protein Structure, Secondary ; Sesquiterpenes/chemistry/metabolism ; Staphylococcal Infections/*drug therapy/microbiology ; Staphylococcus aureus/drug effects/growth & development/metabolism/*pathogenicity ; Virulence/drug effects ; Xanthophylls/biosynthesis
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  • 40
    Publication Date: 2008-11-08
    Description: Cryptochromes (CRY) are photolyase-like blue-light receptors that mediate light responses in plants and animals. How plant cryptochromes act in response to blue light is not well understood. We report here the identification and characterization of the Arabidopsis CIB1 (cryptochrome-interacting basic-helix-loop-helix) protein. CIB1 interacts with CRY2 (cryptochrome 2) in a blue light-specific manner in yeast and Arabidopsis cells, and it acts together with additional CIB1-related proteins to promote CRY2-dependent floral initiation. CIB1 binds to G box (CACGTG) in vitro with a higher affinity than its interaction with other E-box elements (CANNTG). However, CIB1 stimulates FT messenger RNA expression, and it interacts with chromatin DNA of the FT gene that possesses various E-box elements except G box. We propose that the blue light-dependent interaction of cryptochrome(s) with CIB1 and CIB1-related proteins represents an early photoreceptor signaling mechanism in plants.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Hongtao -- Yu, Xuhong -- Li, Kunwu -- Klejnot, John -- Yang, Hongyun -- Lisiero, Dominique -- Lin, Chentao -- GM56265/GM/NIGMS NIH HHS/ -- R01 GM056265/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Dec 5;322(5907):1535-9. doi: 10.1126/science.1163927. Epub 2008 Nov 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18988809" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/genetics/growth & development/*physiology ; Arabidopsis Proteins/chemistry/*genetics/*metabolism ; Basic Helix-Loop-Helix Transcription Factors/chemistry/genetics/*metabolism ; Cell Nucleus/metabolism ; Chromatin Immunoprecipitation ; Cryptochromes ; DNA-Binding Proteins/genetics/metabolism ; Flowers/*growth & development ; Gene Expression Regulation, Plant ; Light ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Plants, Genetically Modified ; Promoter Regions, Genetic ; Protein Binding ; RNA, Messenger/genetics/metabolism ; RNA, Plant/genetics/metabolism ; Signal Transduction ; Transcription Factors/genetics/metabolism ; *Transcription, Genetic ; Two-Hybrid System Techniques
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  • 41
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2008-11-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Uversky, Vladimir N -- Dunker, A Keith -- GM071714-01A2/GM/NIGMS NIH HHS/ -- R01 LM007688-01A1/LM/NLM NIH HHS/ -- New York, N.Y. -- Science. 2008 Nov 28;322(5906):1340-1. doi: 10.1126/science.1167453.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Intrinsically Disordered Protein Research, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. vuversky@iupui.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19039128" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Computational Biology ; Escherichia coli Proteins/chemistry/metabolism ; Evolution, Molecular ; Humans ; Protein Conformation ; Protein Structure, Secondary ; Proteins/*chemistry/*metabolism ; Proteome/chemistry ; RNA, Fungal/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism ; Schizosaccharomyces pombe Proteins/chemistry/metabolism
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  • 42
    Publication Date: 2008-05-03
    Description: The protozoan parasite Trypanosoma brucei is lysed by apolipoprotein L-I, a component of human high-density lipoprotein (HDL) particles that are also characterized by the presence of haptoglobin-related protein. We report that this process is mediated by a parasite glycoprotein receptor, which binds the haptoglobin-hemoglobin complex with high affinity for the uptake and incorporation of heme into intracellular hemoproteins. In mice, this receptor was required for optimal parasite growth and the resistance of parasites to the oxidative burst by host macrophages. In humans, the trypanosome receptor also recognized the complex between hemoglobin and haptoglobin-related protein, which explains its ability to capture trypanolytic HDLs. Thus, in humans the presence of haptoglobin-related protein has diverted the function of the trypanosome haptoglobin-hemoglobin receptor to elicit innate host immunity against the parasite.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vanhollebeke, Benoit -- De Muylder, Geraldine -- Nielsen, Marianne J -- Pays, Annette -- Tebabi, Patricia -- Dieu, Marc -- Raes, Martine -- Moestrup, Soren K -- Pays, Etienne -- New York, N.Y. -- Science. 2008 May 2;320(5876):677-81. doi: 10.1126/science.1156296.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Molecular Parasitology, Institute for Molecular Biology and Medicine, Universite Libre de Bruxelles, 12 rue des Profs Jeener et Brachet, B6041 Gosselies, Belgium.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18451305" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Haptoglobins/metabolism ; Hemoglobins/metabolism ; Humans ; Immunity, Innate ; Lipoproteins, HDL/metabolism ; Mice ; Mice, Inbred Strains ; Molecular Sequence Data ; Receptors, Cell Surface/*immunology/metabolism ; Trypanosoma brucei brucei/*immunology
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  • 43
    Publication Date: 2008-04-26
    Description: We report a molecular phylogeny for a nonavian dinosaur, extending our knowledge of trait evolution within nonavian dinosaurs into the macromolecular level of biological organization. Fragments of collagen alpha1(I) and alpha2(I) proteins extracted from fossil bones of Tyrannosaurus rex and Mammut americanum (mastodon) were analyzed with a variety of phylogenetic methods. Despite missing sequence data, the mastodon groups with elephant and the T. rex groups with birds, consistent with predictions based on genetic and morphological data for mastodon and on morphological data for T. rex. Our findings suggest that molecular data from long-extinct organisms may have the potential for resolving relationships at critical areas in the vertebrate evolutionary tree that have, so far, been phylogenetically intractable.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Organ, Chris L -- Schweitzer, Mary H -- Zheng, Wenxia -- Freimark, Lisa M -- Cantley, Lewis C -- Asara, John M -- F32 GM075490/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Apr 25;320(5875):499. doi: 10.1126/science.1154284.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18436782" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bayes Theorem ; Biological Evolution ; Birds/classification/genetics ; Bone and Bones ; Collagen Type I/*chemistry/genetics ; Dinosaurs/anatomy & histology/*classification/*genetics ; Elephants/anatomy & histology/*classification/*genetics ; Fossils ; Likelihood Functions ; Molecular Sequence Data ; *Phylogeny ; Sequence Alignment
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  • 44
    Publication Date: 2008-07-19
    Description: Golgi-resident glycosyltransferases are a family of enzymes that sequentially modify glycoproteins in a subcompartment-specific manner. These type II integral membrane proteins are characterized by a short cytoplasmically exposed amino-terminal tail and a luminal enzymatic domain. The cytoplasmic tails play a role in the localization of glycosyltransferases, and coat protein complex I (COPI) vesicle-mediated retrograde transport is also involved in their Golgi localization. However, the tails of these enzymes lack known COPI-binding motifs. Here, we found that Vps74p bound to a pentameric motif present in the cytoplasmic tails of the majority of yeast Golgi-localized glycosyltransferases, as well as to COPI. We propose that Vps74p maintains the steady-state localization of Golgi glycosyltransferases dynamically, by promoting their incorporation into COPI-coated vesicles.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tu, Linna -- Tai, William C S -- Chen, Lu -- Banfield, David K -- New York, N.Y. -- Science. 2008 Jul 18;321(5887):404-7. doi: 10.1126/science.1159411.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, Special Administrative Region (SAR) of the People's Republic of China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18635803" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; COP-Coated Vesicles/metabolism ; Carrier Proteins/*metabolism ; Coat Protein Complex I/metabolism ; Endoplasmic Reticulum/metabolism ; Glycosyltransferases/chemistry/*metabolism ; Golgi Apparatus/*metabolism ; Molecular Sequence Data ; Protein Transport ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/*metabolism ; Saccharomyces cerevisiae Proteins/*metabolism
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  • 45
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    Unknown
    American Association for the Advancement of Science (AAAS)
    Publication Date: 2008-09-06
    Description: Mammalian fatty acid synthase is a large multienzyme that catalyzes all steps of fatty acid synthesis. We have determined its crystal structure at 3.2 angstrom resolution covering five catalytic domains, whereas the flexibly tethered terminal acyl carrier protein and thioesterase domains remain unresolved. The structure reveals a complex architecture of alternating linkers and enzymatic domains. Substrate shuttling is facilitated by flexible tethering of the acyl carrier protein domain and by the limited contact between the condensing and modifying portions of the multienzyme, which are mainly connected by linkers rather than direct interaction. The structure identifies two additional nonenzymatic domains: (i) a pseudo-ketoreductase and (ii) a peripheral pseudo-methyltransferase that is probably a remnant of an ancestral methyltransferase domain maintained in some related polyketide synthases. The structural comparison of mammalian fatty acid synthase with modular polyketide synthases shows how their segmental construction allows the variation of domain composition to achieve diverse product synthesis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maier, Timm -- Leibundgut, Marc -- Ban, Nenad -- New York, N.Y. -- Science. 2008 Sep 5;321(5894):1315-22. doi: 10.1126/science.1161269.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, 8092 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18772430" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Carrier Protein/chemistry/metabolism ; Amino Acid Sequence ; Animals ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Dimerization ; Evolution, Molecular ; Fatty Acid Synthase, Type I/*chemistry ; Fatty Acids/biosynthesis ; Methyltransferases/chemistry ; Models, Molecular ; Molecular Sequence Data ; NADP/chemistry/metabolism ; Polyketide Synthases/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Swine/*metabolism
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  • 46
    Publication Date: 2008-09-06
    Description: Calcium-dependent chloride channels are required for normal electrolyte and fluid secretion, olfactory perception, and neuronal and smooth muscle excitability. The molecular identity of these membrane proteins is still unclear. Treatment of bronchial epithelial cells with interleukin-4 (IL-4) causes increased calcium-dependent chloride channel activity, presumably by regulating expression of the corresponding genes. We performed a global gene expression analysis to identify membrane proteins that are regulated by IL-4. Transfection of epithelial cells with specific small interfering RNA against each of these proteins shows that TMEM16A, a member of a family of putative plasma membrane proteins with unknown function, is associated with calcium-dependent chloride current, as measured with halide-sensitive fluorescent proteins, short-circuit current, and patch-clamp techniques. Our results indicate that TMEM16A is an intrinsic constituent of the calcium-dependent chloride channel. Identification of a previously unknown family of membrane proteins associated with chloride channel function will improve our understanding of chloride transport physiopathology and allow for the development of pharmacological tools useful for basic research and drug development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Caputo, Antonella -- Caci, Emanuela -- Ferrera, Loretta -- Pedemonte, Nicoletta -- Barsanti, Cristina -- Sondo, Elvira -- Pfeffer, Ulrich -- Ravazzolo, Roberto -- Zegarra-Moran, Olga -- Galietta, Luis J V -- GGP05103/Telethon/Italy -- New York, N.Y. -- Science. 2008 Oct 24;322(5901):590-4. doi: 10.1126/science.1163518. Epub 2008 Sep 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratorio di Genetica Molecolare, Istituto Giannina Gaslini, Genova 16148, Italy.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18772398" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing ; Amino Acid Sequence ; Animals ; Bronchi/cytology/*metabolism ; Calcium/*metabolism ; Cell Line ; Cell Membrane/*metabolism ; Cells, Cultured ; Chloride Channels/*metabolism ; Chlorides/*metabolism ; Epithelial Cells/metabolism ; Humans ; Interleukin-4/metabolism ; Membrane Proteins/chemistry/genetics/*metabolism ; Molecular Sequence Data ; Neoplasm Proteins/chemistry/genetics/*metabolism ; Oligonucleotide Array Sequence Analysis ; Patch-Clamp Techniques ; RNA, Small Interfering ; Respiratory Mucosa/cytology/metabolism ; Transfection
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  • 47
    Publication Date: 2008-09-27
    Description: Variable lymphocyte receptors (VLRs) rather than antibodies play the primary role in recognition of antigens in the adaptive immune system of jawless vertebrates. Combinatorial assembly of leucine-rich repeat (LRR) gene segments achieves the required repertoire for antigen recognition. We have determined a crystal structure for a VLR-antigen complex, VLR RBC36 in complex with the H-antigen trisaccharide from human blood type O erythrocytes, at 1.67 angstrom resolution. RBC36 binds the H-trisaccharide on the concave surface of the LRR modules of the solenoid structure where three key hydrophilic residues, multiple van der Waals interactions, and the highly variable insert of the carboxyl-terminal LRR module determine antigen recognition and specificity. The concave surface assembled from the most highly variable regions of the LRRs, along with diversity in the sequence and length of the highly variable insert, can account for the recognition of diverse antigens by VLRs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581502/" 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/PMC2581502/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Han, Byung Woo -- Herrin, Brantley R -- Cooper, Max D -- Wilson, Ian A -- AI072435/AI/NIAID NIH HHS/ -- AI42266/AI/NIAID NIH HHS/ -- R37 AI042266/AI/NIAID NIH HHS/ -- R37 AI042266-11/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2008 Sep 26;321(5897):1834-7. doi: 10.1126/science.1162484.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18818359" target="_blank"〉PubMed〈/a〉
    Keywords: ABO Blood-Group System/chemistry/*immunology/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Binding Sites ; Crystallography, X-Ray ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lampreys/*immunology ; Lymphocytes/*immunology ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Receptors, Antigen/*chemistry/*immunology/metabolism ; Trisaccharides/chemistry/*immunology/metabolism
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  • 48
    Publication Date: 2008-09-20
    Description: FtsZ is an essential bacterial guanosine triphosphatase and homolog of mammalian beta-tubulin that polymerizes and assembles into a ring to initiate cell division. We have created a class of small synthetic antibacterials, exemplified by PC190723, which inhibits FtsZ and prevents cell division. PC190723 has potent and selective in vitro bactericidal activity against staphylococci, including methicillin- and multi-drug-resistant Staphylococcus aureus. The putative inhibitor-binding site of PC190723 was mapped to a region of FtsZ that is analogous to the Taxol-binding site of tubulin. PC190723 was efficacious in an in vivo model of infection, curing mice infected with a lethal dose of S. aureus. The data validate FtsZ as a target for antibacterial intervention and identify PC190723 as suitable for optimization into a new anti-staphylococcal therapy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Haydon, David J -- Stokes, Neil R -- Ure, Rebecca -- Galbraith, Greta -- Bennett, James M -- Brown, David R -- Baker, Patrick J -- Barynin, Vladimir V -- Rice, David W -- Sedelnikova, Sveta E -- Heal, Jonathan R -- Sheridan, Joseph M -- Aiwale, Sachin T -- Chauhan, Pramod K -- Srivastava, Anil -- Taneja, Amit -- Collins, Ian -- Errington, Jeff -- Czaplewski, Lloyd G -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2008 Sep 19;321(5896):1673-5. doi: 10.1126/science.1159961.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Prolysis, Begbroke Science Park, Oxfordshire OX5 1PF, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18801997" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Anti-Bacterial Agents/*pharmacology/therapeutic use ; Bacillus subtilis/chemistry/*drug effects/genetics ; Bacterial Proteins/*antagonists & inhibitors/chemistry/genetics/metabolism ; Binding Sites ; Cell Division/drug effects ; Crystallography, X-Ray ; Cytoskeletal Proteins/*antagonists & inhibitors/chemistry/genetics/metabolism ; Drug Resistance, Bacterial/genetics ; Drug Resistance, Multiple, Bacterial ; Ligands ; Methicillin Resistance ; Mice ; Microbial Sensitivity Tests ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Conformation ; Pyridines/chemistry/metabolism/*pharmacology/therapeutic use ; Staphylococcal Infections/*drug therapy ; Staphylococcus aureus/chemistry/*drug effects ; Thiazoles/chemistry/metabolism/*pharmacology/therapeutic use ; Tubulin/chemistry/metabolism
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  • 49
    Publication Date: 2008-09-13
    Description: Mexican and Peruvian hairless dogs and Chinese crested dogs are characterized by missing hair and teeth, a phenotype termed canine ectodermal dysplasia (CED). CED is inherited as a monogenic autosomal semidominant trait. With genomewide association analysis we mapped the CED mutation to a 102-kilo-base pair interval on chromosome 17. The associated interval contains a previously uncharacterized member of the forkhead box transcription factor family (FOXI3), which is specifically expressed in developing hair and teeth. Mutation analysis revealed a frameshift mutation within the FOXI3 coding sequence in hairless dogs. Thus, we have identified FOXI3 as a regulator of ectodermal development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Drogemuller, Cord -- Karlsson, Elinor K -- Hytonen, Marjo K -- Perloski, Michele -- Dolf, Gaudenz -- Sainio, Kirsi -- Lohi, Hannes -- Lindblad-Toh, Kerstin -- Leeb, Tosso -- New York, N.Y. -- Science. 2008 Sep 12;321(5895):1462. doi: 10.1126/science.1162525.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Berne, 3001 Berne, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18787161" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Chromosome Mapping ; Dog Diseases/*genetics ; Dogs/*genetics ; Ectoderm/*embryology/metabolism ; Ectodermal Dysplasia/genetics/*veterinary ; Ectodysplasins/metabolism ; Female ; Forkhead Transcription Factors/chemistry/*genetics/physiology ; *Frameshift Mutation ; Gene Duplication ; Hair/embryology/metabolism ; Haplotypes ; Male ; Mice ; Molecular Sequence Data ; Mutant Proteins/chemistry/genetics/physiology ; Pedigree ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA ; Signal Transduction ; Tooth/embryology/metabolism ; Vibrissae/embryology/metabolism
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  • 50
    Publication Date: 2008-03-22
    Description: Hermaphroditic organisms avoid inbreeding by a system of self-incompatibility (SI). A primitive chordate (ascidian) Ciona intestinalis is an example of such an organism, but the molecular mechanism underlying its SI system is not known. Here, we show that the SI system is governed by two gene loci that act cooperatively. Each locus contains a tightly linked pair of polycystin 1-related receptor (s-Themis) and fibrinogen-like ligand (v-Themis) genes, the latter of which is located in the first intron of s-Themis but transcribed in the opposite direction. These genes may encode male- and female-side self-recognition molecules. The SI system of C. intestinalis has a similar framework to that of flowering plants but utilizing different molecules.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Harada, Yoshito -- Takagaki, Yuhei -- Sunagawa, Masahiko -- Saito, Takako -- Yamada, Lixy -- Taniguchi, Hisaaki -- Shoguchi, Eiichi -- Sawada, Hitoshi -- New York, N.Y. -- Science. 2008 Apr 25;320(5875):548-50. doi: 10.1126/science.1152488. Epub 2008 Mar 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Sugashima Marine Biological Laboratory, Graduate School of Science, Nagoya University, Sugashima, Toba 517-0004, Japan. yharada@bio.nagoya-u.ac.jp〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18356489" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Ciona intestinalis/*genetics/*physiology ; Disorders of Sex Development ; Female ; Fertility ; Fertilization ; *Genes ; Male ; Molecular Sequence Data ; Ovum/metabolism/physiology ; Spermatozoa/physiology ; *TRPP Cation Channels/chemistry
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  • 51
    Publication Date: 2008-03-15
    Description: Prion and nonprion forms of proteins are believed to differ solely in their three-dimensional structure, which is therefore of paramount importance for the prion function. However, no atomic-resolution structure of the fibrillar state that is likely infectious has been reported to date. We present a structural model based on solid-state nuclear magnetic resonance restraints for amyloid fibrils from the prion-forming domain (residues 218 to 289) of the HET-s protein from the filamentous fungus Podospora anserina. On the basis of 134 intra- and intermolecular experimental distance restraints, we find that HET-s(218-289) forms a left-handed beta solenoid, with each molecule forming two helical windings, a compact hydrophobic core, at least 23 hydrogen bonds, three salt bridges, and two asparagine ladders. The structure is likely to have broad implications for understanding the infectious amyloid state.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wasmer, Christian -- Lange, Adam -- Van Melckebeke, Helene -- Siemer, Ansgar B -- Riek, Roland -- Meier, Beat H -- New York, N.Y. -- Science. 2008 Mar 14;319(5869):1523-6. doi: 10.1126/science.1151839.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18339938" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amyloid/*chemistry ; Fungal Proteins/*chemistry ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Peptides/chemistry ; Podospora/*chemistry ; Prions/*chemistry ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary
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  • 52
    Publication Date: 2008-08-30
    Description: The voltage-dependent anion channel (VDAC) mediates trafficking of small molecules and ions across the eukaryotic outer mitochondrial membrane. VDAC also interacts with antiapoptotic proteins from the Bcl-2 family, and this interaction inhibits release of apoptogenic proteins from the mitochondrion. We present the nuclear magnetic resonance (NMR) solution structure of recombinant human VDAC-1 reconstituted in detergent micelles. It forms a 19-stranded beta barrel with the first and last strand parallel. The hydrophobic outside perimeter of the barrel is covered by detergent molecules in a beltlike fashion. In the presence of cholesterol, recombinant VDAC-1 can form voltage-gated channels in phospholipid bilayers similar to those of the native protein. NMR measurements revealed the binding sites of VDAC-1 for the Bcl-2 protein Bcl-x(L), for reduced beta-nicotinamide adenine dinucleotide, and for cholesterol. Bcl-x(L) interacts with the VDAC barrel laterally at strands 17 and 18.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2579273/" 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/PMC2579273/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hiller, Sebastian -- Garces, Robert G -- Malia, Thomas J -- Orekhov, Vladislav Y -- Colombini, Marco -- Wagner, Gerhard -- EB002026/EB/NIBIB NIH HHS/ -- GM066360/GM/NIGMS NIH HHS/ -- GM075879/GM/NIGMS NIH HHS/ -- GM47467/GM/NIGMS NIH HHS/ -- P01 GM047467/GM/NIGMS NIH HHS/ -- P01 GM047467-11/GM/NIGMS NIH HHS/ -- P01 GM047467-12/GM/NIGMS NIH HHS/ -- P01 GM047467-12S2/GM/NIGMS NIH HHS/ -- P01 GM047467-13/GM/NIGMS NIH HHS/ -- P01 GM047467-14/GM/NIGMS NIH HHS/ -- P01 GM047467-14S1/GM/NIGMS NIH HHS/ -- P01 GM047467-15/GM/NIGMS NIH HHS/ -- P01 GM047467-16/GM/NIGMS NIH HHS/ -- P01 GM047467-17/GM/NIGMS NIH HHS/ -- P41 EB002026/EB/NIBIB NIH HHS/ -- P41 EB002026-28/EB/NIBIB NIH HHS/ -- P41 EB002026-29/EB/NIBIB NIH HHS/ -- P41 EB002026-30/EB/NIBIB NIH HHS/ -- P41 EB002026-31/EB/NIBIB NIH HHS/ -- P41 EB002026-32/EB/NIBIB NIH HHS/ -- P41 EB002026-33/EB/NIBIB NIH HHS/ -- P41 GM066360/GM/NIGMS NIH HHS/ -- P41 GM066360-01/GM/NIGMS NIH HHS/ -- P41 GM066360-02/GM/NIGMS NIH HHS/ -- P41 GM066360-03/GM/NIGMS NIH HHS/ -- P41 GM066360-04/GM/NIGMS NIH HHS/ -- P41 GM066360-05/GM/NIGMS NIH HHS/ -- R01 GM075879/GM/NIGMS NIH HHS/ -- R01 GM075879-01/GM/NIGMS NIH HHS/ -- R01 GM075879-02/GM/NIGMS NIH HHS/ -- R01 GM075879-03/GM/NIGMS NIH HHS/ -- R01 GM075879-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Aug 29;321(5893):1206-10. doi: 10.1126/science.1161302.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18755977" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Cholesterol/metabolism ; Detergents ; Dimethylamines ; Humans ; Hydrophobic and Hydrophilic Interactions ; Ion Channel Gating ; Lipid Bilayers ; Micelles ; Molecular Sequence Data ; NAD/metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombinant Proteins/chemistry/metabolism ; Static Electricity ; Voltage-Dependent Anion Channel 1/*chemistry/*metabolism ; bcl-X Protein/metabolism
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  • 53
    Publication Date: 2008-09-13
    Description: There is substantial interest in the development of drugs that limit the extent of ischemia-induced cardiac damage caused by myocardial infarction or by certain surgical procedures. Here, using an unbiased proteomic search, we identified mitochondrial aldehyde dehydrogenase 2 (ALDH2) as an enzyme whose activation correlates with reduced ischemic heart damage in rodent models. A high-throughput screen yielded a small-molecule activator of ALDH2 (Alda-1) that, when administered to rats before an ischemic event, reduced infarct size by 60%, most likely through its inhibitory effect on the formation of cytotoxic aldehydes. In vitro, Alda-1 was a particularly effective activator of ALDH2*2, an inactive mutant form of the enzyme that is found in 40% of East Asian populations. Thus, pharmacologic enhancement of ALDH2 activity may be useful for patients with wild-type or mutant ALDH2 who are subjected to cardiac ischemia, such as during coronary bypass surgery.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2741612/" 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/PMC2741612/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Che-Hong -- Budas, Grant R -- Churchill, Eric N -- Disatnik, Marie-Helene -- Hurley, Thomas D -- Mochly-Rosen, Daria -- AA11147/AA/NIAAA NIH HHS/ -- R01 AA011147/AA/NIAAA NIH HHS/ -- R01 AA011147-08/AA/NIAAA NIH HHS/ -- R01 AA011147-09/AA/NIAAA NIH HHS/ -- R01 AA011147-10/AA/NIAAA NIH HHS/ -- R01 AA011147-11/AA/NIAAA NIH HHS/ -- R01 AA011147-12/AA/NIAAA NIH HHS/ -- New York, N.Y. -- Science. 2008 Sep 12;321(5895):1493-5. doi: 10.1126/science.1158554.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305-5174, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18787169" target="_blank"〉PubMed〈/a〉
    Keywords: Aldehyde Dehydrogenase/antagonists & inhibitors/*metabolism ; Aldehydes/metabolism ; Amino Acid Sequence ; Animals ; Benzamides/*pharmacology ; Benzodioxoles/*pharmacology ; Cardiotonic Agents/*pharmacology ; Cyanamide/pharmacology ; Enzyme Activation ; Ethanol/pharmacology ; Ischemic Preconditioning, Myocardial ; Mitochondrial Proteins/agonists/antagonists & inhibitors/*metabolism ; Molecular Sequence Data ; Myocardial Infarction/enzymology/pathology/*prevention & control ; Myocardial Reperfusion Injury/*enzymology ; Myocardium/*enzymology/pathology ; Nitroglycerin/pharmacology ; Phosphorylation ; Protein Kinase C-epsilon/metabolism ; Proteomics ; Rats ; Rats, Wistar
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  • 54
    Publication Date: 2008-01-19
    Description: Mammalian telomeres are protected by a six-protein complex: shelterin. Shelterin contains two closely related proteins (TRF1 and TRF2), which recruit various proteins to telomeres. We dissect the interactions of TRF1 and TRF2 with their shared binding partner (TIN2) and other shelterin accessory factors. TRF1 recognizes TIN2 using a conserved molecular surface in its TRF homology (TRFH) domain. However, this same surface does not act as a TIN2 binding site in TRF2, and TIN2 binding to TRF2 is mediated by a region outside the TRFH domain. Instead, the TRFH docking site of TRF2 binds a shelterin accessory factor (Apollo), which does not interact with the TRFH domain of TRF1. Conversely, the TRFH domain of TRF1, but not of TRF2, interacts with another shelterin-associated factor: PinX1.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Yong -- Yang, Yuting -- van Overbeek, Megan -- Donigian, Jill R -- Baciu, Paul -- de Lange, Titia -- Lei, Ming -- New York, N.Y. -- Science. 2008 Feb 22;319(5866):1092-6. doi: 10.1126/science.1151804. Epub 2008 Jan 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18202258" target="_blank"〉PubMed〈/a〉
    Keywords: *Amino Acid Motifs ; Amino Acid Sequence ; Crystallography, X-Ray ; Dimerization ; Humans ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Inhibitor of Apoptosis Proteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Nuclear Proteins/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; TATA Box Binding Protein-Like Proteins/*chemistry/genetics/*metabolism ; Telomere-Binding Proteins/chemistry/genetics/*metabolism ; Telomeric Repeat Binding Protein 1/*chemistry/*metabolism ; Telomeric Repeat Binding Protein 2 ; Tumor Suppressor Proteins/chemistry/metabolism
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  • 55
    Publication Date: 2008-11-08
    Description: A major barrier to regenerating axons after injury in the mammalian central nervous system is an unfavorable milieu. Three proteins found in myelin--Nogo, MAG, and OMgp--inhibit axon regeneration in vitro and bind to the glycosylphosphatidylinositol-anchored Nogo receptor (NgR). However, genetic deletion of NgR has only a modest disinhibitory effect, suggesting that other binding receptors for these molecules probably exist. With the use of expression cloning, we have found that paired immunoglobulin-like receptor B (PirB), which has been implicated in nervous system plasticity, is a high-affinity receptor for Nogo, MAG, and OMgp. Interfering with PirB activity, either with antibodies or genetically, partially rescues neurite inhibition by Nogo66, MAG, OMgp, and myelin in cultured neurons. Blocking both PirB and NgR activities leads to near-complete release from myelin inhibition. Our results implicate PirB in mediating regeneration block, identify PirB as a potential target for axon regeneration therapies, and provide an explanation for the similar enhancements of visual system plasticity in PirB and NgR knockout mice.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Atwal, Jasvinder K -- Pinkston-Gosse, Julie -- Syken, Josh -- Stawicki, Scott -- Wu, Yan -- Shatz, Carla -- Tessier-Lavigne, Marc -- New York, N.Y. -- Science. 2008 Nov 7;322(5903):967-70. doi: 10.1126/science.1161151.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Neurodegeneration Labs and Research Drug Discovery, Genentech, 1 DNA Way, South San Francisco, CA 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18988857" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Axons/*physiology ; Cells, Cultured ; Cerebellum/cytology ; GPI-Linked Proteins ; Ganglia, Spinal/cytology ; Growth Cones/physiology ; Mice ; Molecular Sequence Data ; Myelin Proteins/*metabolism ; Myelin-Associated Glycoprotein/metabolism ; Myelin-Oligodendrocyte Glycoprotein ; *Nerve Regeneration ; Neurites/physiology ; Neurons/*cytology/*metabolism ; Receptors, Cell Surface/metabolism ; Receptors, Immunologic/genetics/*metabolism ; Sensory Receptor Cells/cytology/metabolism
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  • 56
    Publication Date: 2008-03-01
    Description: The tubular structure of the endoplasmic reticulum (ER) appears to be generated by integral membrane proteins, the reticulons and a protein family consisting of DP1 in mammals and Yop1p in yeast. Here, individual members of these families were found to be sufficient to generate membrane tubules. When we purified yeast Yop1p and incorporated it into proteoliposomes, narrow tubules (approximately 15 to 17 nanometers in diameter) were generated. Tubule formation occurred with different lipids; required essentially only the central portion of the protein, including its two long hydrophobic segments; and was prevented by mutations that affected tubule formation in vivo. Tubules were also formed by reconstituted purified yeast Rtn1p. Tubules made in vitro were narrower than normal ER tubules, due to a higher concentration of tubule-inducing proteins. The shape and oligomerization of the "morphogenic" proteins could explain the formation of the tubular ER.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hu, Junjie -- Shibata, Yoko -- Voss, Christiane -- Shemesh, Tom -- Li, Zongli -- Coughlin, Margaret -- Kozlov, Michael M -- Rapoport, Tom A -- Prinz, William A -- Howard Hughes Medical Institute/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2008 Feb 29;319(5867):1247-50. doi: 10.1126/science.1153634.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and Department of Cell Biology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18309084" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Biopolymers/chemistry/metabolism ; COS Cells ; Cercopithecus aethiops ; Endoplasmic Reticulum/*chemistry/metabolism/*ultrastructure ; Hydrophobic and Hydrophilic Interactions ; Intracellular Membranes/chemistry/ultrastructure ; Lipid Bilayers ; Membrane Lipids/chemistry ; Membrane Proteins/*chemistry/*metabolism ; Membrane Transport Proteins/*chemistry/*metabolism ; Microscopy, Electron ; Models, Biological ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Proteolipids/chemistry ; Saccharomyces cerevisiae Proteins/*chemistry/genetics/*metabolism
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  • 57
    Publication Date: 2008-04-26
    Description: We have assembled a proteome map for Arabidopsis thaliana from high-density, organ-specific proteome catalogs that we generated for different organs, developmental stages, and undifferentiated cultured cells. We matched 86,456 unique peptides to 13,029 proteins and provide expression evidence for 57 gene models that are not represented in the TAIR7 protein database. Analysis of the proteome identified organ-specific biomarkers and allowed us to compile an organ-specific set of proteotypic peptides for 4105 proteins to facilitate targeted quantitative proteomics surveys. Quantitative information for the identified proteins was used to establish correlations between transcript and protein accumulation in different plant organs. The Arabidopsis proteome map provides information about genome activity and proteome assembly and is available as a resource for plant systems biology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baerenfaller, Katja -- Grossmann, Jonas -- Grobei, Monica A -- Hull, Roger -- Hirsch-Hoffmann, Matthias -- Yalovsky, Shaul -- Zimmermann, Philip -- Grossniklaus, Ueli -- Gruissem, Wilhelm -- Baginsky, Sacha -- New York, N.Y. -- Science. 2008 May 16;320(5878):938-41. doi: 10.1126/science.1157956. Epub 2008 Apr 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Plant Sciences, ETH (Swiss Federal Institute of Technology) Zurich, Universitatstrasse 2, 8092 Zurich, Switzerland. kbaerenfaller@ethz.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18436743" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Arabidopsis/*chemistry/cytology/*genetics/physiology ; Arabidopsis Proteins/*analysis/chemistry/genetics ; Base Sequence ; Biomarkers/analysis ; Cells, Cultured ; Computational Biology ; Databases, Genetic ; Flowers/chemistry/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Genome, Plant ; Models, Genetic ; Molecular Sequence Data ; Peptides/analysis/chemistry ; Plant Roots/chemistry/genetics ; Proteome/*analysis ; *Proteomics ; Seeds/chemistry/genetics ; Transcription, Genetic
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  • 58
    Publication Date: 2008-10-18
    Description: The nucleobase-cation-symport-1 (NCS1) transporters are essential components of salvage pathways for nucleobases and related metabolites. Here, we report the 2.85-angstrom resolution structure of the NCS1 benzyl-hydantoin transporter, Mhp1, from Microbacterium liquefaciens. Mhp1 contains 12 transmembrane helices, 10 of which are arranged in two inverted repeats of five helices. The structures of the outward-facing open and substrate-bound occluded conformations were solved, showing how the outward-facing cavity closes upon binding of substrate. Comparisons with the leucine transporter LeuT(Aa) and the galactose transporter vSGLT reveal that the outward- and inward-facing cavities are symmetrically arranged on opposite sides of the membrane. The reciprocal opening and closing of these cavities is synchronized by the inverted repeat helices 3 and 8, providing the structural basis of the alternating access model for membrane transport.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885439/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885439/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weyand, Simone -- Shimamura, Tatsuro -- Yajima, Shunsuke -- Suzuki, Shun'ichi -- Mirza, Osman -- Krusong, Kuakarun -- Carpenter, Elisabeth P -- Rutherford, Nicholas G -- Hadden, Jonathan M -- O'Reilly, John -- Ma, Pikyee -- Saidijam, Massoud -- Patching, Simon G -- Hope, Ryan J -- Norbertczak, Halina T -- Roach, Peter C J -- Iwata, So -- Henderson, Peter J F -- Cameron, Alexander D -- 062164/Z/00/Z/Wellcome Trust/United Kingdom -- 079209/Wellcome Trust/United Kingdom -- B17935/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/C51725/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G020043/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2008 Oct 31;322(5902):709-13. doi: 10.1126/science.1164440. Epub 2008 Oct 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Membrane Protein Laboratory, Diamond Light Source Limited, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18927357" target="_blank"〉PubMed〈/a〉
    Keywords: Actinomycetales/*chemistry/metabolism ; Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Cations/chemistry/metabolism ; Cell Membrane/chemistry/metabolism ; Crystallography, X-Ray ; Hydantoins/chemistry/metabolism ; Ion Transport ; Models, Molecular ; Molecular Sequence Data ; Nucleobase Transport Proteins/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Sodium/metabolism ; Symporters/*chemistry/metabolism
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  • 59
    Publication Date: 2008-11-15
    Description: Stomata, epidermal structures that modulate gas exchange between plants and the atmosphere, play critical roles in primary productivity and the global climate. Positively acting transcription factors and negatively acting mitogen-activated protein kinase (MAPK) signaling control stomatal development in Arabidopsis; however, it is not known how the opposing activities of these regulators are integrated. We found that a unique domain in a basic helix-loop-helix (bHLH) stomatal initiating factor, SPEECHLESS, renders it a MAPK phosphorylation target in vitro and modulates its function in vivo. MAPK cascades modulate a diverse set of activities including development, cell proliferation, and response to external stresses. The coupling of MAPK signaling to SPEECHLESS activity provides cell type specificity for MAPK output while allowing the integration of multiple developmental and environmental signals into the production and spacing of stomata.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lampard, Gregory R -- Macalister, Cora A -- Bergmann, Dominique C -- New York, N.Y. -- Science. 2008 Nov 14;322(5904):1113-6. doi: 10.1126/science.1162263.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Stanford University, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19008449" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/genetics/growth & development/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Basic Helix-Loop-Helix Transcription Factors/chemistry/genetics/*metabolism ; Cell Division ; *MAP Kinase Signaling System ; Mitogen-Activated Protein Kinases/*metabolism ; Molecular Sequence Data ; Mutation ; Phosphorylation ; Plant Epidermis/cytology/metabolism ; Plant Leaves/growth & development/metabolism ; Plant Stomata/cytology/*growth & development ; Protein Structure, Tertiary
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  • 60
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2008-01-26
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rokas, Antonis -- New York, N.Y. -- Science. 2008 Jan 25;319(5862):416-7. doi: 10.1126/science.1153156.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Sciences, Vanderbilt University, VU Station B 35-1634, Nashville, TN 37235, USA. antonis.rokas@vanderbilt.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18218881" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Base Sequence ; Bias (Epidemiology) ; Computational Biology ; Evolution, Molecular ; *Genome, Fungal ; *Genomics ; Phylogeny ; Saccharomyces/*genetics ; Sequence Alignment/*methods/standards ; Software ; Uncertainty
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  • 61
    Publication Date: 2008-05-31
    Description: Transport across cellular membranes is an essential process that is catalyzed by diverse membrane transport proteins. The turnover rates of certain transporters are inhibited by their substrates in a process termed trans-inhibition, whose structural basis is poorly understood. We present the crystal structure of a molybdate/tungstate ABC transporter (ModBC) from Methanosarcina acetivorans in a trans-inhibited state. The regulatory domains of the nucleotide-binding subunits are in close contact and provide two oxyanion binding pockets at the shared interface. By specifically binding to these pockets, molybdate or tungstate prevent adenosine triphosphatase activity and lock the transporter in an inward-facing conformation, with the catalytic motifs of the nucleotide-binding domains separated. This allosteric effect prevents the transporter from switching between the inward-facing and the outward-facing states, thus interfering with the alternating access and release mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gerber, Sabina -- Comellas-Bigler, Mireia -- Goetz, Birke A -- Locher, Kaspar P -- New York, N.Y. -- Science. 2008 Jul 11;321(5886):246-50. doi: 10.1126/science.1156213. Epub 2008 May 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Molecular Biology and Biophysics, ETH Zurich, HPK D14.3, 8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18511655" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*antagonists & inhibitors/*chemistry/metabolism ; Adenosine Triphosphatases/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Archaeal Proteins/antagonists & inhibitors/*chemistry/metabolism ; Binding Sites ; Catalytic Domain ; Crystallography, X-Ray ; Methanosarcina/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Molybdenum/*metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Tungsten Compounds/*metabolism
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  • 62
    Publication Date: 2008-12-20
    Description: Perforin-like proteins are expressed by many bacterial and protozoan pathogens, yet little is known about their function or mode of action. Here, we describe Toxoplasma perforin-like protein 1 (TgPLP1), a secreted perforin-like protein of the intracellular protozoan pathogen Toxoplasma gondii that displays structural features necessary for pore formation. After intracellular growth, TgPLP1-deficient parasites failed to exit normally, resulting in entrapment within host cells. We show that this defect is due to an inability to rapidly permeabilize the parasitophorous vacuole membrane and host plasma membrane during exit. TgPLP1 ablation had little effect on growth in culture but resulted in a reduction greater than five orders of magnitude of acute virulence in mice. Perforin-like proteins from other intracellular pathogens may play a similar role in microbial egress and virulence.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2662845/" 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/PMC2662845/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kafsack, Bjorn F C -- Pena, Janethe D O -- Coppens, Isabelle -- Ravindran, Sandeep -- Boothroyd, John C -- Carruthers, Vern B -- R01 AI021423/AI/NIAID NIH HHS/ -- R01 AI046675/AI/NIAID NIH HHS/ -- R01 AI046675-06/AI/NIAID NIH HHS/ -- R01 AI046675-07/AI/NIAID NIH HHS/ -- R01 AI046675-08/AI/NIAID NIH HHS/ -- R01 AI046675-09/AI/NIAID NIH HHS/ -- R01 AI46675/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2009 Jan 23;323(5913):530-3. doi: 10.1126/science.1165740. Epub 2008 Dec 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19095897" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Calcimycin/pharmacology ; Cell Membrane/*metabolism ; Cell Membrane Permeability ; Cells, Cultured ; Host-Parasite Interactions ; Humans ; Intracellular Membranes/*metabolism ; Ionophores/pharmacology ; Models, Molecular ; Molecular Sequence Data ; Perforin/chemistry/genetics/*metabolism ; Permeability ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protozoan Proteins/chemistry/genetics/*metabolism ; Toxoplasma/genetics/growth & development/*metabolism/pathogenicity ; Vacuoles/*metabolism/*parasitology
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