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  • Amino Acid Sequence  (424)
  • American Association for the Advancement of Science (AAAS)  (424)
  • Periodicals Archive Online (PAO)
  • Springer Nature
  • 2005-2009  (331)
  • 1980-1984  (93)
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  • 1
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    An antigen produced by splicing of noncontiguous peptides in the reverse order (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-09-09
    Description: CD8-positive T lymphocytes recognize peptides that are usually derived from the degradation of cellular proteins and are presented by class I molecules of the major histocompatibility complex. Here we describe a human minor histocompatibility antigen created by a polymorphism in the SP110 nuclear phosphoprotein gene. The antigenic peptide comprises two noncontiguous SP110 peptide segments spliced together in reverse order to that in which they occur in the predicted SP110 protein. The antigenic peptide could be produced in vitro by incubation of precursor peptides with highly purified 20S proteasomes. Cutting and splicing probably occur within the proteasome by transpeptidation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Warren, Edus H -- Vigneron, Nathalie J -- Gavin, Marc A -- Coulie, Pierre G -- Stroobant, Vincent -- Dalet, Alexandre -- Tykodi, Scott S -- Xuereb, Suzanne M -- Mito, Jeffrey K -- Riddell, Stanley R -- Van den Eynde, Benoit J -- CA106512/CA/NCI NIH HHS/ -- CA18029/CA/NCI NIH HHS/ -- P01 CA018029/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2006 Sep 8;313(5792):1444-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Program in Immunology, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16960008" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Motifs ; Amino Acid Sequence ; Amino Acid Substitution ; *Antigen Presentation ; B-Lymphocytes/immunology ; Cell Line, Transformed ; Cytotoxicity, Immunologic ; Electroporation ; HLA-A Antigens/immunology ; Humans ; Interferon-gamma/metabolism ; Male ; Middle Aged ; Minor Histocompatibility Antigens/genetics/*immunology/*metabolism ; Molecular Sequence Data ; Nuclear Proteins/chemistry/genetics/*immunology/*metabolism ; Peptide Fragments/metabolism ; Polymorphism, Single Nucleotide ; Proteasome Endopeptidase Complex/metabolism ; *Protein Splicing ; T-Lymphocytes, Cytotoxic/*immunology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
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    Two Dobzhansky-Muller genes interact to cause hybrid lethality in Drosophila (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-25
    Description: The Dobzhansky-Muller model proposes that hybrid incompatibilities are caused by the interaction between genes that have functionally diverged in the respective hybridizing species. Here, we show that Lethal hybrid rescue (Lhr) has functionally diverged in Drosophila simulans and interacts with Hybrid male rescue (Hmr), which has functionally diverged in D. melanogaster, to cause lethality in F1 hybrid males. LHR localizes to heterochromatic regions of the genome and has diverged extensively in sequence between these species in a manner consistent with positive selection. Rapidly evolving heterochromatic DNA sequences may be driving the evolution of this incompatibility gene.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brideau, Nicholas J -- Flores, Heather A -- Wang, Jun -- Maheshwari, Shamoni -- Wang, Xu -- Barbash, Daniel A -- R01 GM074737-01/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 24;314(5803):1292-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17124320" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Chromosomal Proteins, Non-Histone/metabolism ; Chromosome Mapping ; Crosses, Genetic ; Drosophila/*genetics/physiology ; Drosophila Proteins/chemistry/*genetics/metabolism ; Drosophila melanogaster/*genetics/physiology ; *Evolution, Molecular ; Female ; *Genes, Insect ; Genetic Speciation ; *Hybridization, Genetic ; Male ; Molecular Sequence Data ; Selection, Genetic ; Transformation, Genetic ; Transgenes
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
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    Structure and mechanism of the lantibiotic cyclase involved in nisin biosynthesis (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-11
    Description: Nisin is a posttranslationally modified antimicrobial peptide that is widely used as a food preservative. It contains five cyclic thioethers of varying sizes that are installed by a single enzyme, NisC. Reported here are the in vitro reconstitution of the cyclization process and the x-ray crystal structure of the NisC enzyme. The structure reveals similarities in fold and substrate activation with mammalian farnesyl transferases, suggesting that human homologs of NisC posttranslationally modify a cysteine of a protein substrate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Bo -- Yu, John Paul J -- Brunzelle, Joseph S -- Moll, Gert N -- van der Donk, Wilfred A -- Nair, Satish K -- GM58822/GM/NIGMS NIH HHS/ -- R01 GM079038/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Mar 10;311(5766):1464-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16527981" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Anti-Bacterial Agents/*biosynthesis/chemistry ; Carbon-Sulfur Lyases/chemistry/genetics/*metabolism ; Crystallography, X-Ray ; Farnesyltranstransferase/chemistry ; Humans ; Lactococcus lactis/*enzymology ; Models, Molecular ; Molecular Sequence Data ; Nisin/*biosynthesis/chemistry ; Protein Conformation ; Protein Processing, Post-Translational ; Sequence Homology, Amino Acid ; Structure-Activity Relationship
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Rice domestication by reducing shattering (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-11
    Description: Crop domestication frequently began with the selection of plants that did not naturally shed ripe fruits or seeds. The reduction in grain shattering that led to cereal domestication involved genetic loci of large effect. The molecular basis of this key domestication transition, however, remains unknown. Here we show that human selection of an amino acid substitution in the predicted DNA binding domain encoded by a gene of previously unknown function was primarily responsible for the reduction of grain shattering in rice domestication. The substitution undermined the gene function necessary for the normal development of an abscission layer that controls the separation of a grain from the pedicel.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Changbao -- Zhou, Ailing -- Sang, Tao -- New York, N.Y. -- Science. 2006 Mar 31;311(5769):1936-9. Epub 2006 Mar 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16527928" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; Amino Acid Substitution ; Biological Evolution ; Chromosome Mapping ; Computational Biology ; Crops, Agricultural/*genetics/growth & development ; Flowers/growth & development ; Gene Expression ; Genes, Plant ; Genotype ; Molecular Sequence Data ; Mutation ; Oryza/cytology/*genetics/growth & development ; Phenotype ; Plant Proteins/chemistry/*genetics ; Plants, Genetically Modified ; Quantitative Trait Loci ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, DNA ; Transcription Factors/chemistry/*genetics ; Transformation, Genetic
    Print ISSN: 0036-8075
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  • 5
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    Structure of the vesicular stomatitis virus nucleoprotein-RNA complex (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-06-17
    Description: Vesicular stomatitis virus is a negative-stranded RNA virus. Its nucleoprotein (N) binds the viral genomic RNA and is involved in multiple functions including transcription, replication, and assembly. We have determined a 2.9 angstrom structure of a complex containing 10 molecules of the N protein and 90 bases of RNA. The RNA is tightly sequestered in a cavity at the interface between two lobes of the N protein. This serves to protect the RNA in the absence of polynucleotide synthesis. For the RNA to be accessed, some conformational change in the N protein should be necessary.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Green, Todd J -- Zhang, Xin -- Wertz, Gail W -- Luo, Ming -- AI050066/AI/NIAID NIH HHS/ -- R37 AI012464/AI/NIAID NIH HHS/ -- R37 AI012464-28/AI/NIAID NIH HHS/ -- R37 AI012464-29/AI/NIAID NIH HHS/ -- R37 AI012464-30/AI/NIAID NIH HHS/ -- R37 AI012464-31/AI/NIAID NIH HHS/ -- R37AI012464/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2006 Jul 21;313(5785):357-60. Epub 2006 Jun 15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, School of Medicine, University of Alabama at Birmingham, 1025 18th Street South, Birmingham, AL 35294, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16778022" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Crystallography, X-Ray ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; Nucleocapsid Proteins/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Viral/*chemistry/metabolism ; Ribonucleoproteins/*chemistry ; Sequence Alignment ; Vesicular stomatitis Indiana virus/*chemistry
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  • 6
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    Ammonia channel couples glutaminase with transamidase reactions in GatCAB (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-01
    Description: The formation of glutaminyl transfer RNA (Gln-tRNA(Gln)) differs among the three domains of life. Most bacteria employ an indirect pathway to produce Gln-tRNA(Gln) by a heterotrimeric glutamine amidotransferase CAB (GatCAB) that acts on the misacylated Glu-tRNA(Gln). Here, we describe a series of crystal structures of intact GatCAB from Staphylococcus aureus in the apo form and in the complexes with glutamine, asparagine, Mn2+, and adenosine triphosphate analog. Two identified catalytic centers for the glutaminase and transamidase reactions are markedly distant but connected by a hydrophilic ammonia channel 30 A in length. Further, we show that the first U-A base pair in the acceptor stem and the D loop of tRNA(Gln) serve as identity elements essential for discrimination by GatCAB and propose a complete model for the overall concerted reactions to synthesize Gln-tRNA(Gln).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Nakamura, Akiyoshi -- Yao, Min -- Chimnaronk, Sarin -- Sakai, Naoki -- Tanaka, Isao -- New York, N.Y. -- Science. 2006 Jun 30;312(5782):1954-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Faculty of Advanced Life Sciences, Hokkaido University, Sapporo 060-0810, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16809541" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Diphosphate/metabolism ; Amino Acid Sequence ; Aminoacyltransferases/metabolism ; Ammonia/*metabolism ; Apoenzymes/chemistry/metabolism ; Asparagine/metabolism ; Base Pairing ; Catalytic Domain ; Crystallography, X-Ray ; Glutaminase/metabolism ; Glutamine/*chemistry/metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Magnesium/metabolism ; Manganese/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits ; RNA, Bacterial/chemistry/metabolism ; RNA, Transfer, Amino Acyl/chemistry/*metabolism ; RNA, Transfer, Gln/*chemistry/metabolism ; Staphylococcus aureus/*enzymology/genetics/metabolism
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  • 7
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    Human hair growth deficiency is linked to a genetic defect in the phospholipase gene LIPH (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-11
    Description: The molecular mechanisms controlling human hair growth and scalp hair loss are poorly understood. By screening about 350,000 individuals in two populations from the Volga-Ural region of Russia, we identified a gene mutation in families who show an inherited form of hair loss and a hair growth defect. Affected individuals were homozygous for a deletion in the LIPH gene on chromosome 3q27, caused by short interspersed nuclear element-retrotransposon-mediated recombination. The LIPH gene is expressed in hair follicles and encodes a phospholipase called lipase H (alternatively known as membrane-associated phosphatidic acid-selective phospholipase A1alpha), an enzyme that regulates the production of bioactive lipids. These results suggest that lipase H participates in hair growth and development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kazantseva, Anastasiya -- Goltsov, Andrey -- Zinchenko, Rena -- Grigorenko, Anastasia P -- Abrukova, Anna V -- Moliaka, Yuri K -- Kirillov, Alexander G -- Guo, Zhiru -- Lyle, Stephen -- Ginter, Evgeny K -- Rogaev, Evgeny I -- K08-AR02179/AR/NIAMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 10;314(5801):982-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Brudnick Neuropsychiatric Research Institute, Department of Psychiatry, University of Massachusetts Medical School, 303 Belmont Street, Worcester, MA 01604, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095700" target="_blank"〉PubMed〈/a〉
    Keywords: Alu Elements ; Amino Acid Sequence ; Base Sequence ; Chromosomes, Human, Pair 3/genetics ; Exons ; Female ; Gene Deletion ; Gene Expression ; Genetic Markers ; Hair/*growth & development ; Hair Follicle/enzymology ; Heterozygote ; Homozygote ; Humans ; Hypotrichosis/*genetics ; Lipase/chemistry/*genetics/metabolism ; Lipid Metabolism ; Lod Score ; Male ; Molecular Sequence Data ; Pedigree ; Protein Structure, Tertiary ; Recombination, Genetic ; Retroelements ; Russia ; Tandem Repeat Sequences
    Print ISSN: 0036-8075
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  • 8
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    Tequila, a neurotrypsin ortholog, regulates long-term memory formation in Drosophila (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-08-12
    Description: Mutations in the human neurotrypsin gene are associated with autosomal recessive mental retardation. To further understand the pathophysiological consequences of the lack of this serine protease, we studied Tequila (Teq), the Drosophila neurotrypsin ortholog, using associative memory as a behavioral readout. We found that teq inactivation resulted in a long-term memory (LTM)-specific defect. After LTM conditioning of wild-type flies, teq expression transiently increased in the mushroom bodies. Moreover, specific inhibition of teq expression in adult mushroom bodies resulted in a reversible LTM defect. Hence, the Teq pathway is essential for information processing in Drosophila.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Didelot, Gerard -- Molinari, Florence -- Tchenio, Paul -- Comas, Daniel -- Milhiet, Elodie -- Munnich, Arnold -- Colleaux, Laurence -- Preat, Thomas -- New York, N.Y. -- Science. 2006 Aug 11;313(5788):851-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genes et Dynamique des Systemes de Memoire, UMR CNRS 7637, Ecole Superieure de Physique et de Chimie Industrielles, 10 Rue Vauquelin 75005 Paris, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16902143" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Animals, Genetically Modified ; Conditioning, Classical ; Drosophila Proteins/chemistry/genetics/*physiology ; Drosophila melanogaster/genetics/*physiology ; Gene Expression ; Gene Expression Regulation ; Humans ; Learning ; *Memory ; Mifepristone/pharmacology ; Models, Animal ; Molecular Sequence Data ; Mushroom Bodies/anatomy & histology/physiology ; Mutation ; Odors ; RNA Interference ; RNA, Messenger/genetics/metabolism ; Serine Endopeptidases/chemistry/genetics/*physiology
    Print ISSN: 0036-8075
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  • 9
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    Engineering cooperativity in biomotor-protein assemblies (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-11
    Description: A biosynthetic approach was developed to control and probe cooperativity in multiunit biomotor assemblies by linking molecular motors to artificial protein scaffolds. This approach provides precise control over spatial and elastic coupling between motors. Cooperative interactions between monomeric kinesin-1 motors attached to protein scaffolds enhance hydrolysis activity and microtubule gliding velocity. However, these interactions are not influenced by changes in the elastic properties of the scaffold, distinguishing multimotor transport from that powered by unorganized monomeric motors. These results highlight the role of supramolecular architecture in determining mechanisms of collective transport.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Diehl, Michael R -- Zhang, Kechun -- Lee, Heun Jin -- Tirrell, David A -- New York, N.Y. -- Science. 2006 Mar 10;311(5766):1468-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA. diehl@rice.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16527982" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry ; Amino Acid Sequence ; Elasticity ; Elastin/chemistry ; Hydrolysis ; Kinesin/chemistry ; Microtubules/physiology ; Models, Biological ; Molecular Motor Proteins/*physiology ; Molecular Sequence Data ; Protein Engineering ; Protein Structure, Tertiary ; Proteins/chemistry/*physiology ; Recombinant Proteins/chemistry ; Structure-Activity Relationship
    Print ISSN: 0036-8075
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  • 10
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    Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-10-07
    Description: For characterization of sequence and posttranslational modifications, molecular and fragment ion mass data from ionizing and dissociating a protein in the mass spectrometer are far more specific than are masses of peptides from the protein's digestion. We extend the approximately 500-residue, approximately 50-kilodalton (kD) dissociation limitation of this top-down methodology by using electrospray additives, heated vaporization, and separate noncovalent and covalent bond dissociation. This process can cleave 287 interresidue bonds in the termini of a 1314-residue (144-kD) protein, specify previously unidentified disulfide bonds between 8 of 27 cysteines in a 1714-residue (200-kD) protein, and correct sequence predictions in two proteins, one with 2153 residues (229 kD).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Han, Xuemei -- Jin, Mi -- Breuker, Kathrin -- McLafferty, Fred W -- GM16609/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Oct 6;314(5796):109-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17023655" target="_blank"〉PubMed〈/a〉
    Keywords: Acyltransferases/chemistry ; Amino Acid Sequence ; Carbon-Nitrogen Ligases with Glutamine as Amide-N-Donor/chemistry ; Chemistry, Physical ; Complement C4/chemistry ; Cysteine/chemistry ; Humans ; Mass Spectrometry/*methods ; Molecular Weight ; Peptide Fragments/chemistry ; Physicochemical Phenomena ; Protein Conformation ; Protein Folding ; Protein Processing, Post-Translational ; Proteins/*chemistry ; Proteomics ; Spectrometry, Mass, Electrospray Ionization/*methods
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  • 11
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    A bacterial protein enhances the release and efficacy of liposomal cancer drugs (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-25
    Description: Clostridium novyi-NT is an anaerobic bacterium that can infect hypoxic regions within experimental tumors. Because C. novyi-NT lyses red blood cells, we hypothesized that its membrane-disrupting properties could be exploited to enhance the release of liposome-encapsulated drugs within tumors. Here, we show that treatment of mice bearing large, established tumors with C. novyi-NT plus a single dose of liposomal doxorubicin often led to eradication of the tumors. The bacterial factor responsible for the enhanced drug release was identified as a previously unrecognized protein termed liposomase. This protein could potentially be incorporated into diverse experimental approaches for the specific delivery of chemotherapeutic agents to tumors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cheong, Ian -- Huang, Xin -- Bettegowda, Chetan -- Diaz, Luis A Jr -- Kinzler, Kenneth W -- Zhou, Shibin -- Vogelstein, Bert -- CA062924/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2006 Nov 24;314(5803):1308-11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute and the Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins Kimmel Comprehensive Cancer Center, Baltimore, MD 21231, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17124324" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antineoplastic Agents/*administration & dosage/pharmacokinetics/therapeutic use ; Bacterial Proteins/chemistry/genetics/*metabolism ; Base Sequence ; Camptothecin/administration & dosage/analogs & ; derivatives/pharmacokinetics/therapeutic use ; Cell Line, Tumor ; Cloning, Molecular ; Clostridium/*chemistry/genetics ; Colorectal Neoplasms/*drug therapy ; Doxorubicin/*administration & dosage/pharmacokinetics/therapeutic use ; Drug Carriers ; Humans ; Lipase/chemistry/genetics/*metabolism ; Lipid Bilayers/chemistry ; Liposomes/chemistry/*metabolism ; Mice ; Molecular Sequence Data ; Mutation ; Neoplasm Transplantation ; Protein Structure, Tertiary
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  • 12
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    Structural basis for double-stranded RNA processing by Dicer (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-01-18
    Description: The specialized ribonuclease Dicer initiates RNA interference by cleaving double-stranded RNA (dsRNA) substrates into small fragments about 25 nucleotides in length. In the crystal structure of an intact Dicer enzyme, the PAZ domain, a module that binds the end of dsRNA, is separated from the two catalytic ribonuclease III (RNase III) domains by a flat, positively charged surface. The 65 angstrom distance between the PAZ and RNase III domains matches the length spanned by 25 base pairs of RNA. Thus, Dicer itself is a molecular ruler that recognizes dsRNA and cleaves a specified distance from the helical end.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Macrae, Ian J -- Zhou, Kaihong -- Li, Fei -- Repic, Adrian -- Brooks, Angela N -- Cande, W Zacheus -- Adams, Paul D -- Doudna, Jennifer A -- New York, N.Y. -- Science. 2006 Jan 13;311(5758):195-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16410517" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Conserved Sequence ; Crystallography, X-Ray ; Giardia lamblia/enzymology ; Humans ; Lanthanoid Series Elements/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Tertiary ; RNA Interference ; RNA, Double-Stranded/*metabolism ; RNA, Protozoan/metabolism ; Recombinant Fusion Proteins/genetics/metabolism ; Ribonuclease III/*chemistry/metabolism ; Schizosaccharomyces/genetics ; Structure-Activity Relationship
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  • 13
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    Structure of tracheal cytotoxin in complex with a heterodimeric pattern-recognition receptor (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-03-25
    Description: Tracheal cytotoxin (TCT), a naturally occurring fragment of Gram-negative peptidoglycan, is a potent elicitor of innate immune responses in Drosophila. It induces the heterodimerization of its recognition receptors, the peptidoglycan recognition proteins (PGRPs) LCa and LCx, which activates the immune deficiency pathway. The crystal structure at 2.1 angstrom resolution of TCT in complex with the ectodomains of PGRP-LCa and PGRP-LCx shows that TCT is bound to and presented by the LCx ectodomain for recognition by the LCa ectodomain; the latter lacks a canonical peptidoglycan-docking groove conserved in other PGRPs. The interface, revealed in atomic detail, between TCT and the receptor complex highlights the importance of the anhydro-containing disaccharide in bridging the two ectodomains together and the critical role of diaminopimelic acid as the specificity determinant for PGRP interaction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Chung-I -- Chelliah, Yogarany -- Borek, Dominika -- Mengin-Lecreulx, Dominique -- Deisenhofer, Johann -- New York, N.Y. -- Science. 2006 Mar 24;311(5768):1761-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, 6001 Forest Park Road, Dallas, TX 75390-9050, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16556841" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Carrier Proteins/*chemistry/metabolism ; Crystallization ; Crystallography, X-Ray ; Cytotoxins/*chemistry/metabolism ; Drosophila melanogaster ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Peptidoglycan/*chemistry/metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary
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    Virology. Genomic analysis hints at H5N1 pathogenicity (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-01-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Normile, Dennis -- New York, N.Y. -- Science. 2006 Jan 27;311(5760):457.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16439636" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Base Sequence ; Birds ; Databases, Nucleic Acid ; Genetic Variation ; *Genome, Viral ; Humans ; Influenza A Virus, H5N1 Subtype/*genetics/*pathogenicity ; Influenza in Birds/*virology ; Influenza, Human/*virology ; Ligands ; Poultry ; RNA, Viral/genetics ; Viral Nonstructural Proteins/chemistry/*genetics/metabolism ; Virulence/genetics
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  • 15
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    Biochemistry. Loop grafting and the origins of enzyme species (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-01-28
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tawfik, Dan S -- New York, N.Y. -- Science. 2006 Jan 27;311(5760):475-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel. tawfik@weizmann.ac.il〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16439649" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Catalytic Domain ; *Directed Molecular Evolution ; Evolution, Molecular ; *Protein Engineering ; Substrate Specificity ; Thiolester Hydrolases/*chemistry/*metabolism ; beta-Lactamases/chemistry/*metabolism ; beta-Lactams/metabolism
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  • 16
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    Genome of Rice Cluster I archaea--the key methane producers in the rice rhizosphere (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-07-22
    Description: Rice fields are a global source of the greenhouse gas methane, which is produced by methanogenic archaea, and by methanogens of Rice Cluster I (RC-I) in particular. RC-I methanogens are not yet available in pure culture, and the mechanistic reasons for their prevalence in rice fields are unknown. We reconstructed a complete RC-I genome (3.18 megabases) using a metagenomic approach. Sequence analysis demonstrated an aerotolerant, H2/CO2-dependent lifestyle and enzymatic capacities for carbohydrate metabolism and assimilatory sulfate reduction, hitherto unknown among methanogens. These capacities and a unique set of antioxidant enzymes and DNA repair mechanisms as well as oxygen-insensitive enzymes provide RC-I with a selective advantage over other methanogens in its habitats, thereby explaining the prevalence of RC-I methanogens in the rice rhizosphere.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Erkel, Christoph -- Kube, Michael -- Reinhardt, Richard -- Liesack, Werner -- New York, N.Y. -- Science. 2006 Jul 21;313(5785):370-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse, 35043 Marburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16857943" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acids/biosynthesis/metabolism ; Carbohydrate Metabolism ; DNA Repair ; Euryarchaeota/classification/*genetics/metabolism/physiology ; *Genome, Archaeal ; Genomics ; Glycolysis ; Methane/*biosynthesis ; Methanomicrobiales/classification/genetics/metabolism/physiology ; Methanosarcinales/classification/genetics/metabolism/physiology ; Molecular Sequence Data ; Oryza/*microbiology ; Oxidative Stress ; Pyruvic Acid/metabolism ; Sequence Alignment ; Sequence Analysis, DNA ; *Soil Microbiology ; Sulfates/metabolism ; Sulfur/metabolism
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    Crystal structure of a divalent metal ion transporter CorA at 2.9 angstrom resolution (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-07-22
    Description: CorA family members are ubiquitously distributed transporters of divalent metal cations and are considered to be the primary Mg2+ transporter of Bacteria and Archaea. We have determined a 2.9 angstrom resolution structure of CorA from Thermotoga maritima that reveals a pentameric cone-shaped protein. Two potential regulatory metal binding sites are found in the N-terminal domain that bind both Mg2+ and Co2+. The structure of CorA supports an efflux system involving dehydration and rehydration of divalent metal ions potentially mediated by a ring of conserved aspartate residues at the cytoplasmic entrance and a carbonyl funnel at the periplasmic side of the pore.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Eshaghi, Said -- Niegowski, Damian -- Kohl, Andreas -- Martinez Molina, Daniel -- Lesley, Scott A -- Nordlund, Par -- New York, N.Y. -- Science. 2006 Jul 21;313(5785):354-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Biophysics, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-171 77 Stockholm, Sweden. Said.Eshaghi@ki.se〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16857941" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/*chemistry/metabolism ; Binding Sites ; Cation Transport Proteins/*chemistry/metabolism ; Chlorides/analysis/metabolism ; Cobalt/chemistry/*metabolism ; Crystallography, X-Ray ; Hydrophobic and Hydrophilic Interactions ; Magnesium/chemistry/*metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Sequence Alignment ; Thermotoga maritima/*chemistry ; Water/chemistry
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  • 18
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    Anaphase inactivation of the spindle checkpoint (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-07-11
    Description: The spindle checkpoint delays cell cycle progression until microtubules attach each pair of sister chromosomes to opposite poles of the mitotic spindle. Following sister chromatid separation, however, the checkpoint ignores chromosomes whose kinetochores are attached to only one spindle pole, a state that activates the checkpoint prior to metaphase. We demonstrate that, in budding yeast, mutual inhibition between the anaphase-promoting complex (APC) and Mps1, an essential component of the checkpoint, leads to sustained inactivation of the spindle checkpoint. Mps1 protein abundance decreases in anaphase, and Mps1 is a target of the APC. Furthermore, expression of Mps1 in anaphase, or repression of the APC in anaphase, reactivates the spindle checkpoint. This APC-Mps1 feedback circuit allows cells to irreversibly inactivate the checkpoint during anaphase.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Palframan, William J -- Meehl, Janet B -- Jaspersen, Sue L -- Winey, Mark -- Murray, Andrew W -- GM43987/GM/NIGMS NIH HHS/ -- GM51312/GM/NIGMS NIH HHS/ -- R37 GM043987/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 Aug 4;313(5787):680-4. Epub 2006 Jul 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, Biological Laboratories, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16825537" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Anaphase/*physiology ; Anaphase-Promoting Complex-Cyclosome ; Cdc20 Proteins ; Cell Cycle Proteins/metabolism ; Chromosomes, Fungal/physiology ; Feedback, Physiological ; GTP-Binding Proteins/metabolism ; Kinetochores/physiology ; Mad2 Proteins ; Mitosis ; Molecular Sequence Data ; Nuclear Proteins/metabolism ; Phosphorylation ; Protein-Serine-Threonine Kinases/genetics/*metabolism ; Protein-Tyrosine Kinases/genetics/*metabolism ; Recombinant Fusion Proteins/metabolism ; Saccharomyces cerevisiae/*cytology/metabolism ; Saccharomyces cerevisiae Proteins/genetics/*metabolism ; Securin ; Spindle Apparatus/*physiology ; Ubiquitin-Protein Ligase Complexes/*metabolism
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    Nitrogen fixation at 92 degrees C by a hydrothermal vent archaeon (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-12-16
    Description: A methanogenic archaeon isolated from deep-sea hydrothermal vent fluid was found to reduce N(2) to NH(3) at up to 92 degrees C, which is 28 degrees C higher than the current upper temperature limit of biological nitrogen fixation. The 16S ribosomal RNA gene of the hyperthermophilic nitrogen fixer, designated FS406-22, was 99% similar to that of non-nitrogen fixing Methanocaldococcus jannaschii DSM 2661. At its optimal growth temperature of 90 degrees C, FS406-22 incorporated (15)N(2) and expressed nifH messenger RNA. This increase in the temperature limit of nitrogen fixation could reveal a broader range of conditions for life in the subseafloor biosphere and other nitrogen-limited ecosystems than previously estimated.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mehta, Mausmi P -- Baross, John A -- New York, N.Y. -- Science. 2006 Dec 15;314(5806):1783-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Oceanography, University of Washington, Seattle, WA 98195, USA. mausmi@alum.mit.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17170307" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Archaea/classification/genetics/*isolation & purification/*metabolism ; Archaeal Proteins/chemistry/genetics/metabolism ; Base Sequence ; *Ecosystem ; Genes, Archaeal ; Genes, rRNA ; Geologic Sediments/microbiology ; *Hot Temperature ; Molecular Sequence Data ; Nitrogen/metabolism ; *Nitrogen Fixation/genetics ; Nitrogenase/chemistry/*genetics/metabolism ; Operon ; Oxidation-Reduction ; Oxidoreductases/chemistry/genetics/metabolism ; Pacific Ocean ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/*microbiology ; Volcanic Eruptions
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  • 20
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    Structures of the CCR5 N terminus and of a tyrosine-sulfated antibody with HIV-1 gp120 and CD4 (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-09-29
    Description: The CCR5 co-receptor binds to the HIV-1 gp120 envelope glycoprotein and facilitates HIV-1 entry into cells. Its N terminus is tyrosine-sulfated, as are many antibodies that react with the co-receptor binding site on gp120. We applied nuclear magnetic resonance and crystallographic techniques to analyze the structure of the CCR5 N terminus and that of the tyrosine-sulfated antibody 412d in complex with gp120 and CD4. The conformations of tyrosine-sulfated regions of CCR5 (alpha-helix) and 412d (extended loop) are surprisingly different. Nonetheless, a critical sulfotyrosine on CCR5 and on 412d induces similar structural rearrangements in gp120. These results now provide a framework for understanding HIV-1 interactions with the CCR5 N terminus during viral entry and define a conserved site on gp120, whose recognition of sulfotyrosine engenders posttranslational mimicry by the immune system.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2278242/" 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/PMC2278242/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Chih-Chin -- Lam, Son N -- Acharya, Priyamvada -- Tang, Min -- Xiang, Shi-Hua -- Hussan, Syed Shahzad-Ul -- Stanfield, Robyn L -- Robinson, James -- Sodroski, Joseph -- Wilson, Ian A -- Wyatt, Richard -- Bewley, Carole A -- Kwong, Peter D -- P30 AI060354/AI/NIAID NIH HHS/ -- U19 AI067854/AI/NIAID NIH HHS/ -- U19 AI067854-03/AI/NIAID NIH HHS/ -- Z99 AI999999/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 28;317(5846):1930-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institute of Allergy and Infectious 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/17901336" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antigens, CD4/*chemistry/immunology ; Crystallography, X-Ray ; HIV Antibodies/*chemistry/immunology ; HIV Envelope Protein gp120/*chemistry/immunology/metabolism ; HIV-1/metabolism ; Humans ; Models, Molecular ; Molecular Mimicry ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Peptide Fragments/chemistry/metabolism ; Receptors, CCR5/*chemistry/metabolism ; Sulfates/metabolism ; Tyrosine/metabolism ; Virus Internalization
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    Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-04-08
    Description: Biological responses to histone methylation critically depend on the faithful readout and transduction of the methyl-lysine signal by "effector" proteins, yet our understanding of methyl-lysine recognition has so far been limited to the study of histone binding by chromodomain and WD40-repeat proteins. The double tudor domain of JMJD2A, a Jmjc domain-containing histone demethylase, binds methylated histone H3-K4 and H4-K20. We found that the double tudor domain has an interdigitated structure, and the unusual fold is required for its ability to bind methylated histone tails. The cocrystal structure of the JMJD2A double tudor domain with a trimethylated H3-K4 peptide reveals that the trimethyl-K4 is bound in a cage of three aromatic residues, two of which are from the tudor-2 motif, whereas the binding specificity is determined by side-chain interactions involving amino acids from the tudor-1 motif. Our study provides mechanistic insights into recognition of methylated histone tails by tudor domains and reveals the structural intricacy of methyl-lysine recognition by two closely spaced effector domains.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Huang, Ying -- Fang, Jia -- Bedford, Mark T -- Zhang, Yi -- Xu, Rui-Ming -- DK62248/DK/NIDDK NIH HHS/ -- GM 63718/GM/NIGMS NIH HHS/ -- GM68804/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2006 May 5;312(5774):748-51. Epub 2006 Apr 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16601153" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Histones/*chemistry/*metabolism ; Humans ; Hydrogen Bonding ; Jumonji Domain-Containing Histone Demethylases ; Lysine/metabolism ; Methylation ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Oxidoreductases, N-Demethylating ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Static Electricity ; Transcription Factors/*chemistry/genetics/*metabolism
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    Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-08-04
    Description: BtuCD is an adenosine triphosphate-binding cassette (ABC) transporter that translocates vitamin B12 from the periplasmic binding protein BtuF into the cytoplasm of Escherichia coli. The 2.6 angstrom crystal structure of a complex BtuCD-F reveals substantial conformational changes as compared with the previously reported structures of BtuCD and BtuF. The lobes of BtuF are spread apart, and B12 is displaced from the binding pocket. The transmembrane BtuC subunits reveal two distinct conformations, and the translocation pathway is closed to both sides of the membrane. Electron paramagnetic resonance spectra of spin-labeled cysteine mutants reconstituted in proteoliposomes are consistent with the conformation of BtuCD-F that was observed in the crystal structure. A comparison with BtuCD and the homologous HI1470/71 protein suggests that the structure of BtuCD-F may reflect a posttranslocation intermediate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hvorup, Rikki N -- Goetz, Birke A -- Niederer, Martina -- Hollenstein, Kaspar -- Perozo, Eduardo -- Locher, Kaspar P -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1387-90. Epub 2007 Aug 2.〈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/17673622" target="_blank"〉PubMed〈/a〉
    Keywords: ATP-Binding Cassette Transporters/*chemistry ; Amino Acid Sequence ; Crystallography, X-Ray ; Electron Spin Resonance Spectroscopy ; Escherichia coli ; Escherichia coli Proteins/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Periplasmic Binding Proteins/*chemistry ; Protein Binding ; Protein Conformation ; Recombinant Fusion Proteins/chemistry
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    BKCa-Cav channel complexes mediate rapid and localized Ca2+-activated K+ signaling (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-10-28
    Description: Large-conductance calcium- and voltage-activated potassium channels (BKCa) are dually activated by membrane depolarization and elevation of cytosolic calcium ions (Ca2+). Under normal cellular conditions, BKCa channel activation requires Ca2+ concentrations that typically occur in close proximity to Ca2+ sources. We show that BKCa channels affinity-purified from rat brain are assembled into macromolecular complexes with the voltage-gated calcium channels Cav1.2 (L-type), Cav2.1 (P/Q-type), and Cav2.2 (N-type). Heterologously expressed BKCa-Cav complexes reconstitute a functional "Ca2+ nanodomain" where Ca2+ influx through the Cav channel activates BKCa in the physiological voltage range with submillisecond kinetics. Complex formation with distinct Cav channels enables BKCa-mediated membrane hyperpolarization that controls neuronal firing pattern and release of hormones and transmitters in the central nervous system.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berkefeld, Henrike -- Sailer, Claudia A -- Bildl, Wolfgang -- Rohde, Volker -- Thumfart, Jorg-Oliver -- Eble, Silke -- Klugbauer, Norbert -- Reisinger, Ellen -- Bischofberger, Josef -- Oliver, Dominik -- Knaus, Hans-Gunther -- Schulte, Uwe -- Fakler, Bernd -- New York, N.Y. -- Science. 2006 Oct 27;314(5799):615-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Physiology, University of Freiburg, Hermann-Herder-Strasse 7, 79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17068255" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Brain Chemistry ; CHO Cells ; Calcium/*metabolism ; Calcium Channels, L-Type/drug effects/isolation & purification/*metabolism ; Calcium Channels, N-Type/drug effects/isolation & purification/*metabolism ; Calcium Signaling ; Chromaffin Cells/drug effects/metabolism ; Cricetinae ; Cricetulus ; Egtazic Acid/analogs & derivatives/pharmacology ; Large-Conductance Calcium-Activated Potassium Channels/drug effects/isolation & ; purification/*metabolism ; Membrane Potentials/drug effects ; Molecular Sequence Data ; Patch-Clamp Techniques ; Potassium/*metabolism ; Rats ; *Signal Transduction ; Transfection ; Xenopus
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    Protrudin induces neurite formation by directional membrane trafficking (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-04
    Description: Guanosine triphosphatases of the Rab family are key regulators of membrane trafficking, with Rab11 playing a specific role in membrane recycling. We identified a mammalian protein, protrudin, that promoted neurite formation through interaction with the guanosine diphosphate (GDP)-bound form of Rab11. Phosphorylation of protrudin by extracellular signal-regulated kinase (ERK) in response to nerve growth factor promoted protrudin association with Rab11-GDP. Down-regulation of protrudin by RNA interference induced membrane extension in all directions and inhibited neurite formation. Thus, protrudin regulates Rab11-dependent membrane recycling to promote the directional membrane trafficking required for neurite formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shirane, Michiko -- Nakayama, Keiichi I -- New York, N.Y. -- Science. 2006 Nov 3;314(5800):818-21.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, Fukuoka 812-8582, Japan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17082457" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Carrier Proteins/chemistry/genetics/*metabolism ; Cell Adhesion Molecules/metabolism ; Cell Line ; Cell Membrane/*metabolism ; Extracellular Signal-Regulated MAP Kinases/metabolism ; Guanosine Diphosphate/metabolism ; HeLa Cells ; Humans ; MAP Kinase Kinase 1/metabolism ; Membrane Proteins ; Mice ; Mice, Inbred C57BL ; Molecular Sequence Data ; Nerve Growth Factor/pharmacology/physiology ; Neurites/*physiology ; PC12 Cells ; Phosphorylation ; RNA Interference ; Rats ; Recombinant Fusion Proteins/chemistry/metabolism ; Vesicular Transport Proteins ; rab GTP-Binding Proteins/metabolism
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    From the genome to the proteome: uncovering peptides in the Apis brain (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-10-28
    Description: Neuropeptides, critical brain peptides that modulate animal behavior by affecting the activity of almost every neuronal circuit, are inherently difficult to predict directly from a nascent genome sequence because of extensive posttranslational processing. The combination of bioinformatics and proteomics allows unprecedented neuropeptide discovery from an unannotated genome. Within the Apis mellifera genome, we have inferred more than 200 neuropeptides and have confirmed the sequences of 100 peptides. This study lays the groundwork for future molecular studies of Apis neuropeptides with the identification of 36 genes, 33 of which were previously unreported.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hummon, Amanda B -- Richmond, Timothy A -- Verleyen, Peter -- Baggerman, Geert -- Huybrechts, Jurgen -- Ewing, Michael A -- Vierstraete, Evy -- Rodriguez-Zas, Sandra L -- Schoofs, Liliane -- Robinson, Gene E -- Sweedler, Jonathan V -- DC006395/DC/NIDCD NIH HHS/ -- GM068946/GM/NIGMS NIH HHS/ -- NS31609/NS/NINDS NIH HHS/ -- P30 DA01830/DA/NIDA NIH HHS/ -- P30 DA018310/DA/NIDA NIH HHS/ -- R01 GM068946/GM/NIGMS NIH HHS/ -- R01 NS031609/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2006 Oct 27;314(5799):647-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Illinois, Urbana, IL 61801, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17068263" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Bees/*chemistry/*genetics ; Brain Chemistry ; Codon ; Computational Biology ; *Genes, Insect ; Genome, Insect ; Insect Proteins/*chemistry/*genetics ; Mass Spectrometry ; Molecular Sequence Data ; Neuropeptides/*chemistry/*genetics ; Protein Precursors/chemistry/genetics ; Proteome
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    Autophagic fungal cell death is necessary for infection by the rice blast fungus (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-04-29
    Description: Rice blast is caused by the fungus Magnaporthe grisea, which elaborates specialized infection cells called appressoria to penetrate the tough outer cuticle of the rice plant Oryza sativa. We found that the formation of an appressorium required, sequentially, the completion of mitosis, nuclear migration, and death of the conidium (fungal spore) from which the infection originated. Genetic intervention during mitosis prevented both appressorium development and conidium death. Impairment of autophagy, by the targeted mutation of the MgATG8 gene, arrested conidial cell death but rendered the fungus nonpathogenic. Thus, the initiation of rice blast requires autophagic cell death of the conidium.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Veneault-Fourrey, Claire -- Barooah, Madhumita -- Egan, Martin -- Wakley, Gavin -- Talbot, Nicholas J -- New York, N.Y. -- Science. 2006 Apr 28;312(5773):580-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biosciences, University of Exeter, Washington Singer Laboratories, Perry Road, Exeter EX4 4QG, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16645096" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; *Autophagy ; Benomyl/pharmacology ; Cell Nucleus/physiology ; Cell Nucleus Division ; Genes, Fungal ; Hydroxyurea/pharmacology ; Magnaporthe/*cytology/genetics/pathogenicity/*physiology ; Microtubule-Associated Proteins/genetics/physiology ; Mitosis/drug effects ; Molecular Sequence Data ; Morphogenesis ; Mutation ; Oryza/*microbiology ; Plant Diseases/*microbiology ; Spores, Fungal/cytology/*physiology
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    Changes in regulation of a transcription factor lead to autogamy in cultivated tomatoes (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-10-27
    Description: We report the cloning of Style2.1, the major quantitative trait locus responsible for a key floral attribute (style length) associated with the evolution of self-pollination in cultivated tomatoes. The gene encodes a putative transcription factor that regulates cell elongation in developing styles. The transition from cross-pollination to self-pollination was accompanied, not by a change in the STYLE2.1 protein, but rather by a mutation in the Style2.1 promoter that results in a down-regulation of Style2.1 expression during flower development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chen, Kai-Yi -- Cong, Bin -- Wing, Rod -- Vrebalov, Julia -- Tanksley, Steven D -- New York, N.Y. -- Science. 2007 Oct 26;318(5850):643-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17962563" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; Biological Evolution ; Chromosome Mapping ; Cloning, Molecular ; Crosses, Genetic ; Down-Regulation ; Flowers/*anatomy & histology/genetics/growth & development ; Genes, Plant ; Genotype ; Helix-Loop-Helix Motifs ; Lycopersicon esculentum/anatomy & histology/*genetics/*physiology ; Molecular Sequence Data ; Plant Proteins/chemistry/*genetics/metabolism ; Pollen/physiology ; Promoter Regions, Genetic ; Quantitative Trait Loci ; Reproduction ; Sequence Deletion ; Transcription Factors/chemistry/*genetics/metabolism ; Transformation, Genetic
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  • 28
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    JETLAG resets the Drosophila circadian clock by promoting light-induced degradation of TIMELESS (2006)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2006-06-24
    Description: Organisms ranging from bacteria to humans synchronize their internal clocks to daily cycles of light and dark. Photic entrainment of the Drosophila clock is mediated by proteasomal degradation of the clock protein TIMELESS (TIM). We have identified mutations in jetlag-a gene coding for an F-box protein with leucine-rich repeats-that result in reduced light sensitivity of the circadian clock. Mutant flies show rhythmic behavior in constant light, reduced phase shifts in response to light pulses, and reduced light-dependent degradation of TIM. Expression of JET along with the circadian photoreceptor cryptochrome (CRY) in cultured S2R cells confers light-dependent degradation onto TIM, thereby reconstituting the acute response + of the circadian clock to light in a cell culture system. Our results suggest that JET is essential for resetting the clock by transmitting light signals from CRY to TIM.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2767177/" 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/PMC2767177/" 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 -- Zheng, Xiangzhong -- Sehgal, Amita -- NS048471/NS/NINDS NIH HHS/ -- R01 NS048471/NS/NINDS NIH HHS/ -- R01 NS048471-02/NS/NINDS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2006 Jun 23;312(5781):1809-12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Neuroscience, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16794082" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Cells, Cultured ; *Circadian Rhythm ; Cryptochromes ; Drosophila/chemistry/genetics/physiology ; Drosophila Proteins/chemistry/*genetics/*metabolism/*physiology ; Drosophila melanogaster/chemistry/*genetics/*physiology ; Eye Proteins/metabolism ; F-Box Proteins/chemistry/*genetics/*physiology ; Female ; *Light ; Male ; Models, Biological ; Molecular Sequence Data ; Mutation ; Protein Structure, Tertiary ; Receptors, G-Protein-Coupled/metabolism ; Transgenes ; Ubiquitin/metabolism
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    Structure of Nup58/45 suggests flexible nuclear pore diameter by intermolecular sliding (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-03-24
    Description: The nucleoporins Nup58 and Nup45 are part of the central transport channel of the nuclear pore complex, which is thought to have a flexible diameter. In the crystal structure of an alpha-helical region of mammalian Nup58/45, we identified distinct tetramers, each consisting of two antiparallel hairpin dimers. The intradimeric interface is hydrophobic, whereas dimer-dimer association occurs through large hydrophilic residues. These residues are laterally displaced in various tetramer conformations, which suggests an intermolecular sliding by 11 angstroms. We propose that circumferential sliding plays a role in adjusting the diameter of the central transport channel.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Melcak, Ivo -- Hoelz, Andre -- Blobel, Gunter -- R01 GM111461/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Mar 23;315(5819):1729-32.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Cell Biology, Howard Hughes Medical Institute, Rockefeller University, 1230 York Avenue, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17379812" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Membrane Glycoproteins/chemistry ; Molecular Sequence Data ; Nuclear Pore Complex Proteins/*chemistry ; Protein Folding ; Protein Structure, Quaternary ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Rats ; Static Electricity
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    Structure of fungal fatty acid synthase and implications for iterative substrate shuttling (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-04-14
    Description: We report crystal structures of the 2.6-megadalton alpha6beta6 heterododecameric fatty acid synthase from Thermomyces lanuginosus at 3.1 angstrom resolution. The alpha and beta polypeptide chains form the six catalytic domains required for fatty acid synthesis and numerous expansion segments responsible for extensive intersubunit connections. Detailed views of all active sites provide insights into substrate specificities and catalytic mechanisms and reveal their unique characteristics, which are due to the integration into the multienzyme. The mode of acyl carrier protein attachment in the reaction chamber, together with the spatial distribution of active sites, suggests that iterative substrate shuttling is achieved by a relatively restricted circular motion of the carrier domain in the multifunctional enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jenni, Simon -- Leibundgut, Marc -- Boehringer, Daniel -- Frick, Christian -- Mikolasek, Bohdan -- Ban, Nenad -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):254-61.〈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/17431175" target="_blank"〉PubMed〈/a〉
    Keywords: 3-Oxoacyl-(Acyl-Carrier-Protein) Synthase/metabolism ; Acetyltransferases/metabolism ; Acyl Carrier Protein/chemistry/metabolism/ultrastructure ; Acyltransferases/metabolism ; Amino Acid Sequence ; Ascomycota/*enzymology ; Catalytic Domain ; Crystallography, X-Ray ; Enoyl-(Acyl-Carrier-Protein) Reductase (NADH)/metabolism ; Fatty Acid Synthases/*chemistry/metabolism ; Fungal Proteins/*chemistry/metabolism ; Hydro-Lyases/metabolism ; Models, Molecular ; Molecular Sequence Data ; NADP/chemistry ; Protein Conformation ; Protein Subunits/chemistry ; Substrate Specificity
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    Signals from chloroplasts converge to regulate nuclear gene expression (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-03-31
    Description: Plastid-to-nucleus retrograde signaling coordinates nuclear gene expression with chloroplast function and is essential for the photoautotrophic life-style of plants. Three retrograde signals have been described, but little is known of their signaling pathways. We show here that GUN1, a chloroplast-localized pentatricopeptide-repeat protein, and ABI4, an Apetala 2 (AP2)-type transcription factor, are common to all three pathways. ABI4 binds the promoter of a retrograde-regulated gene through a conserved motif found in close proximity to a light-regulatory element. We propose a model in which multiple indicators of aberrant plastid function in Arabidopsis are integrated upstream of GUN1 within plastids, which leads to ABI4-mediated repression of nuclear-encoded genes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Koussevitzky, Shai -- Nott, Ajit -- Mockler, Todd C -- Hong, Fangxin -- Sachetto-Martins, Gilberto -- Surpin, Marci -- Lim, Jason -- Mittler, Ron -- Chory, Joanne -- DRG-1865-05/PHS HHS/ -- F32 GM 18172/GM/NIGMS NIH HHS/ -- F32 GM 69090/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 May 4;316(5825):715-9. Epub 2007 Mar 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17395793" target="_blank"〉PubMed〈/a〉
    Keywords: Abscisic Acid ; Amino Acid Motifs ; Amino Acid Sequence ; Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/chemistry/genetics/*metabolism ; Cell Nucleus/*metabolism/*microbiology ; Chloroplasts/*metabolism ; DNA, Plant/metabolism ; DNA-Binding Proteins/chemistry/genetics/*metabolism ; Electron Transport ; *Gene Expression Regulation, Plant ; Light-Harvesting Protein Complexes/genetics ; Lincomycin/pharmacology ; Models, Biological ; Molecular Sequence Data ; Oligonucleotide Array Sequence Analysis ; Plants, Genetically Modified ; Promoter Regions, Genetic ; Protoporphyrins/metabolism ; Pyridazines/pharmacology ; Signal Transduction ; Transcription Factors/*metabolism
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    Structure of the membrane protein FhaC: a member of the Omp85-TpsB transporter superfamily (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-08-19
    Description: In Gram-negative bacteria and eukaryotic organelles, beta-barrel proteins of the outer membrane protein 85-two-partner secretion B (Omp85-TpsB) superfamily are essential components of protein transport machineries. The TpsB transporter FhaC mediates the secretion of Bordetella pertussis filamentous hemagglutinin (FHA). We report the 3.15 A crystal structure of FhaC. The transporter comprises a 16-stranded beta barrel that is occluded by an N-terminal alpha helix and an extracellular loop and a periplasmic module composed of two aligned polypeptide-transport-associated (POTRA) domains. Functional data reveal that FHA binds to the POTRA 1 domain via its N-terminal domain and likely translocates the adhesin-repeated motifs in an extended hairpin conformation, with folding occurring at the cell surface. General features of the mechanism obtained here are likely to apply throughout the superfamily.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clantin, Bernard -- Delattre, Anne-Sophie -- Rucktooa, Prakash -- Saint, Nathalie -- Meli, Albano C -- Locht, Camille -- Jacob-Dubuisson, Francoise -- Villeret, Vincent -- New York, N.Y. -- Science. 2007 Aug 17;317(5840):957-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉UMR8161 CNRS, Institut de Biologie de Lille, Universite de Lille 1, Universite de Lille 2, 1 rue du Prof. Calmette, F-59021 Lille cedex, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17702945" target="_blank"〉PubMed〈/a〉
    Keywords: Adhesins, Bacterial/chemistry/*metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*chemistry/genetics/*metabolism ; Bordetella pertussis/*chemistry/metabolism ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Hydrophobic and Hydrophilic Interactions ; Lipid Bilayers/chemistry/metabolism ; Membrane Transport Proteins/chemistry/metabolism ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport ; Virulence Factors, Bordetella/chemistry/*metabolism
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    A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-12-15
    Description: The assimilation of carbon dioxide (CO2) into organic material is quantitatively the most important biosynthetic process. We discovered that an autotrophic member of the archaeal order Sulfolobales, Metallosphaera sedula, fixed CO2 with acetyl-coenzyme A (acetyl-CoA)/propionyl-CoA carboxylase as the key carboxylating enzyme. In this system, one acetyl-CoA and two bicarbonate molecules were reductively converted via 3-hydroxypropionate to succinyl-CoA. This intermediate was reduced to 4-hydroxybutyrate and converted into two acetyl-CoA molecules via 4-hydroxybutyryl-CoA dehydratase. The key genes of this pathway were found not only in Metallosphaera but also in Sulfolobus, Archaeoglobus, and Cenarchaeum species. Moreover, the Global Ocean Sampling database contains half as many 4-hydroxybutyryl-CoA dehydratase sequences as compared with those found for another key photosynthetic CO2-fixing enzyme, ribulose-1,5-bisphosphate carboxylase-oxygenase. This indicates the importance of this enzyme in global carbon cycling.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berg, Ivan A -- Kockelkorn, Daniel -- Buckel, Wolfgang -- Fuchs, Georg -- New York, N.Y. -- Science. 2007 Dec 14;318(5857):1782-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Mikrobiologie, Fakultat Biologie, Universitat Freiburg, Schanzlestrasse 1, D-79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18079405" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyl Coenzyme A/metabolism ; Acetyl-CoA Carboxylase/metabolism ; Acyl Coenzyme A/metabolism ; Amino Acid Sequence ; Anaerobiosis ; Archaea/genetics/metabolism ; Autotrophic Processes ; Bicarbonates/metabolism ; Carbon Dioxide/*metabolism ; Genes, Archaeal ; Hydro-Lyases/genetics/metabolism ; Hydroxybutyrates/*metabolism ; Kinetics ; Lactic Acid/*analogs & derivatives/metabolism ; Metabolic Networks and Pathways ; Molecular Sequence Data ; Oxidation-Reduction ; Photosynthesis ; Phylogeny ; Sulfolobaceae/genetics/*metabolism
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    Comment on "A G protein coupled receptor is a plasma membrane receptor for the plant hormone abscisic acid" (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-11-10
    Description: Liu et al. (Reports, 23 March 2007, p. 1712) reported that the Arabidopsis thaliana gene GCR2 encodes a seven-transmembrane, G protein-coupled receptor for abscisic acid. We argue that GCR2 is not likely to be a transmembrane protein nor a G protein-coupled receptor. Instead, GCR2 is most likely a plant homolog of bacterial lanthionine synthetases.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Johnston, Christopher A -- Temple, Brenda R -- Chen, Jin-Gui -- Gao, Yajun -- Moriyama, Etsuko N -- Jones, Alan M -- Siderovski, David P -- Willard, Francis S -- New York, N.Y. -- Science. 2007 Nov 9;318(5852):914; author reply 914.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991845" target="_blank"〉PubMed〈/a〉
    Keywords: Abscisic Acid/*metabolism ; Algorithms ; Amino Acid Sequence ; Arabidopsis/chemistry/*metabolism ; Arabidopsis Proteins/*chemistry/isolation & purification/*metabolism ; GTP-Binding Protein alpha Subunits/metabolism ; Hydro-Lyases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Multienzyme Complexes/*chemistry/metabolism ; Plant Growth Regulators/*metabolism ; Protein Binding ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, G-Protein-Coupled/*chemistry/isolation & purification/*metabolism ; Recombinant Proteins/chemistry/metabolism ; Sequence Alignment
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    The slit receptor EVA-1 coactivates a SAX-3/Robo mediated guidance signal in C. elegans (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-29
    Description: The SAX-3/roundabout (Robo) receptor has SLT-1/Slit-dependent and -independent functions in guiding cell and axon migrations. We identified enhancer of ventral-axon guidance defects of unc-40 mutants (EVA-1) as a Caenorhabditis elegans transmembrane receptor for SLT-1. EVA-1 has two predicted galactose-binding ectodomains, acts cell-autonomously for SLT-1/Slit-dependent axon migration functions of SAX-3/Robo, binds to SLT-1 and SAX-3, colocalizes with SAX-3 on cells, and provides cell specificity to the activation of SAX-3 signaling by SLT-1. Double mutants of eva-1 or slt-1 with sax-3 mutations suggest that SAX-3 can (when slt-1 or eva-1 function is reduced) inhibit a parallel-acting guidance mechanism, which involves UNC-40/deleted in colorectal cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fujisawa, Kazuko -- Wrana, Jeffrey L -- Culotti, Joseph G -- NS41397/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 28;317(5846):1934-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Samuel Lunenfeld Research Institute of Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17901337" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Animals, Genetically Modified ; Axons/*physiology ; Caenorhabditis elegans/cytology/genetics/growth & development/*physiology ; Caenorhabditis elegans Proteins/*chemistry/genetics/*metabolism ; Carrier Proteins/chemistry/genetics/*metabolism ; Cell Line ; Cell Movement ; Cloning, Molecular ; Humans ; Molecular Sequence Data ; Mutation ; Nerve Tissue Proteins/*metabolism ; Nervous System/growth & development/metabolism ; Neurons/physiology ; Protein Structure, Tertiary ; Receptors, Immunologic/*metabolism ; Recombinant Fusion Proteins/metabolism ; Signal Transduction
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    RAP80 targets BRCA1 to specific ubiquitin structures at DNA damage sites (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-05-26
    Description: Mutations affecting the BRCT domains of the breast cancer-associated tumor suppressor BRCA1 disrupt the recruitment of this protein to DNA double-strand breaks (DSBs). The molecular structures at DSBs recognized by BRCA1 are presently unknown. We report the interaction of the BRCA1 BRCT domain with RAP80, a ubiquitin-binding protein. RAP80 targets a complex containing the BRCA1-BARD1 (BRCA1-associated ring domain protein 1) E3 ligase and the deubiquitinating enzyme (DUB) BRCC36 to MDC1-gammaH2AX-dependent lysine(6)- and lysine(63)-linked ubiquitin polymers at DSBs. These events are required for cell cycle checkpoint and repair responses to ionizing radiation, implicating ubiquitin chain recognition and turnover in the BRCA1-mediated repair of DSBs.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2706583/" 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/PMC2706583/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sobhian, Bijan -- Shao, Genze -- Lilli, Dana R -- Culhane, Aedin C -- Moreau, Lisa A -- Xia, Bing -- Livingston, David M -- Greenberg, Roger A -- K08 CA106597/CA/NCI NIH HHS/ -- K08 CA106597-01A2/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2007 May 25;316(5828):1198-202.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Dana-Farber Cancer Institute and Department of Genetics and Department of Medicine, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17525341" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; BRCA1 Protein/*metabolism ; Binding Sites ; Carrier Proteins/*metabolism ; Cell Line ; DNA/*metabolism ; *DNA Breaks, Double-Stranded ; DNA Repair/physiology ; HeLa Cells ; Humans ; Mice ; Molecular Sequence Data ; Nuclear Proteins/*metabolism ; Nucleic Acid Conformation ; Protein Structure, Tertiary ; Tumor Suppressor Proteins/metabolism ; Ubiquitin/*metabolism ; Ubiquitin-Protein Ligases/metabolism
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    Functional divergence of former alleles in an ancient asexual invertebrate (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-10-13
    Description: Theory suggests it should be difficult for asexual organisms to adapt to a changing environment because genetic diversity can only arise from mutations accumulating within direct antecedents and not through sexual exchange. In an asexual microinvertebrate, the bdelloid rotifer, we have observed a mechanism by which such organisms could acquire the diversity needed for adaptation. Gene copies most likely representing former alleles have diverged in function so that the proteins they encode play complementary roles in survival of dry conditions. One protein prevents desiccation-sensitive enzymes from aggregating during drying, whereas its counterpart does not have this activity, but is able to associate with phospholipid bilayers and is potentially involved in maintenance of membrane integrity. The functional divergence of former alleles observed here suggests that adoption of asexual reproduction could itself be an evolutionary mechanism for the generation of diversity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pouchkina-Stantcheva, Natalia N -- McGee, Brian M -- Boschetti, Chiara -- Tolleter, Dimitri -- Chakrabortee, Sohini -- Popova, Antoaneta V -- Meersman, Filip -- Macherel, David -- Hincha, Dirk K -- Tunnacliffe, Alan -- New York, N.Y. -- Science. 2007 Oct 12;318(5848):268-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biotechnology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QT, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17932297" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Biological ; *Alleles ; Amino Acid Sequence ; Animals ; Biological Evolution ; Chromosomes/genetics ; DNA, Complementary ; Dehydration ; Gene Dosage ; *Genes, Helminth ; *Genetic Variation ; Helminth Proteins/chemistry/genetics/*physiology ; Lipid Bilayers ; Molecular Sequence Data ; Protein Structure, Secondary ; *Reproduction, Asexual ; Rotifera/*genetics/*physiology
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    Genome transplantation in bacteria: changing one species to another (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-06-30
    Description: As a step toward propagation of synthetic genomes, we completely replaced the genome of a bacterial cell with one from another species by transplanting a whole genome as naked DNA. Intact genomic DNA from Mycoplasma mycoides large colony (LC), virtually free of protein, was transplanted into Mycoplasma capricolum cells by polyethylene glycol-mediated transformation. Cells selected for tetracycline resistance, carried by the M. mycoides LC chromosome, contain the complete donor genome and are free of detectable recipient genomic sequences. These cells that result from genome transplantation are phenotypically identical to the M. mycoides LC donor strain as judged by several criteria.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lartigue, Carole -- Glass, John I -- Alperovich, Nina -- Pieper, Rembert -- Parmar, Prashanth P -- Hutchison, Clyde A 3rd -- Smith, Hamilton O -- Venter, J Craig -- New York, N.Y. -- Science. 2007 Aug 3;317(5838):632-8. Epub 2007 Jun 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉J. Craig Venter Institute, Rockville, MD 20850, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17600181" target="_blank"〉PubMed〈/a〉
    Keywords: Acetate Kinase/chemistry/genetics ; Amino Acid Sequence ; DNA, Bacterial/*genetics/isolation & purification ; *Genome, Bacterial ; Genotype ; Molecular Sequence Data ; Mycoplasma/chemistry/*genetics ; Mycoplasma mycoides/chemistry/*genetics ; Phenotype ; Polyethylene Glycols ; Proteome/analysis ; Recombination, Genetic ; Sequence Analysis, DNA ; *Transformation, Bacterial
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    Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-07-14
    Description: Many human cancers involve up-regulation of the phosphoinositide 3-kinase PI3Kalpha, with oncogenic mutations identified in both the p110alpha catalytic and the p85alpha regulatory subunits. We used crystallographic and biochemical approaches to gain insight into activating mutations in two noncatalytic p110alpha domains-the adaptor-binding and the helical domains. A structure of the adaptor-binding domain of p110alpha in a complex with the p85alpha inter-Src homology 2 (inter-SH2) domain shows that oncogenic mutations in the adaptor-binding domain are not at the inter-SH2 interface but in a polar surface patch that is a plausible docking site for other domains in the holo p110/p85 complex. We also examined helical domain mutations and found that the Glu545 to Lys545 (E545K) oncogenic mutant disrupts an inhibitory charge-charge interaction with the p85 N-terminal SH2 domain. These studies extend our understanding of the architecture of PI3Ks and provide insight into how two classes of mutations that cause a gain in function can lead to cancer.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Miled, Nabil -- Yan, Ying -- Hon, Wai-Ching -- Perisic, Olga -- Zvelebil, Marketa -- Inbar, Yuval -- Schneidman-Duhovny, Dina -- Wolfson, Haim J -- Backer, Jonathan M -- Williams, Roger L -- GM55692/GM/NIGMS NIH HHS/ -- MC_U105184308/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2007 Jul 13;317(5835):239-42.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17626883" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; *Catalytic Domain ; Cattle ; Cell Line ; Cell Transformation, Neoplastic ; Crystallography, X-Ray ; Dimerization ; Humans ; Models, Molecular ; Molecular Sequence Data ; *Mutation ; Neoplasms/*genetics ; Phosphatidylinositol 3-Kinases/antagonists & ; inhibitors/chemistry/*genetics/*metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; src Homology Domains
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    Protein composition of catalytically active human telomerase from immortal cells (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-03-31
    Description: Telomerase is a ribonucleoprotein enzyme complex that adds 5'-TTAGGG-3' repeats onto the ends of human chromosomes, providing a telomere maintenance mechanism for approximately 90% of human cancers. We have purified human telomerase approximately 10(8)-fold, with the final elution dependent on the enzyme's ability to catalyze nucleotide addition onto a DNA oligonucleotide of telomeric sequence, thereby providing specificity for catalytically active telomerase. Mass spectrometric sequencing of the protein components and molecular size determination indicated an enzyme composition of two molecules each of telomerase reverse transcriptase, telomerase RNA, and dyskerin.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cohen, Scott B -- Graham, Mark E -- Lovrecz, George O -- Bache, Nicolai -- Robinson, Phillip J -- Reddel, Roger R -- New York, N.Y. -- Science. 2007 Mar 30;315(5820):1850-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research Unit, Children's Medical Research Institute, 214 Hawkesbury Road, Westmead NSW 2145, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17395830" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Cycle Proteins/*chemistry/isolation & purification ; Cell Line ; Cell Line, Tumor ; Centrifugation, Density Gradient ; Humans ; Molecular Sequence Data ; Molecular Weight ; Multienzyme Complexes/chemistry ; Nuclear Proteins/*chemistry/isolation & purification ; RNA/*chemistry/isolation & purification ; Tandem Mass Spectrometry ; Telomerase/*chemistry/isolation & purification/metabolism
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    PDZ domain binding selectivity is optimized across the mouse proteome (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-07-21
    Description: PDZ domains have long been thought to cluster into discrete functional classes defined by their peptide-binding preferences. We used protein microarrays and quantitative fluorescence polarization to characterize the binding selectivity of 157 mouse PDZ domains with respect to 217 genome-encoded peptides. We then trained a multidomain selectivity model to predict PDZ domain-peptide interactions across the mouse proteome with an accuracy that exceeds many large-scale, experimental investigations of protein-protein interactions. Contrary to the current paradigm, PDZ domains do not fall into discrete classes; instead, they are evenly distributed throughout selectivity space, which suggests that they have been optimized across the proteome to minimize cross-reactivity. We predict that focusing on families of interaction domains, which facilitates the integration of experimentation and modeling, will play an increasingly important role in future investigations of protein function.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2674608/" 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/PMC2674608/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stiffler, Michael A -- Chen, Jiunn R -- Grantcharova, Viara P -- Lei, Ying -- Fuchs, Daniel -- Allen, John E -- Zaslavskaia, Lioudmila A -- MacBeath, Gavin -- 1 RO1 GM072872-01/GM/NIGMS NIH HHS/ -- 5 T32 GM07598-25/GM/NIGMS NIH HHS/ -- R01 GM072872/GM/NIGMS NIH HHS/ -- R01 GM072872-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Jul 20;317(5836):364-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17641200" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Animals ; Computational Biology ; Computer Simulation ; Fluorescence Polarization ; Mice ; Peptides/*metabolism ; Protein Array Analysis ; Protein Binding ; *Protein Structure, Tertiary ; Proteome/chemistry/*metabolism
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    LeuT-desipramine structure reveals how antidepressants block neurotransmitter reuptake (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-08-11
    Description: Tricyclic antidepressants exert their pharmacological effect-inhibiting the reuptake of serotonin, norepinephrine, and dopamine-by directly blocking neurotransmitter transporters (SERT, NET, and DAT, respectively) in the presynaptic membrane. The drug-binding site and the mechanism of this inhibition are poorly understood. We determined the crystal structure at 2.9 angstroms of the bacterial leucine transporter (LeuT), a homolog of SERT, NET, and DAT, in complex with leucine and the antidepressant desipramine. Desipramine binds at the inner end of the extracellular cavity of the transporter and is held in place by a hairpin loop and by a salt bridge. This binding site is separated from the leucine-binding site by the extracellular gate of the transporter. By directly locking the gate, desipramine prevents conformational changes and blocks substrate transport. Mutagenesis experiments on human SERT and DAT indicate that both the desipramine-binding site and its inhibition mechanism are probably conserved in the human neurotransmitter transporters.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3711652/" 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/PMC3711652/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhou, Zheng -- Zhen, Juan -- Karpowich, Nathan K -- Goetz, Regina M -- Law, Christopher J -- Reith, Maarten E A -- Wang, Da-Neng -- DA013261/DA/NIDA NIH HHS/ -- DA019676/DA/NIDA NIH HHS/ -- GM075026/GM/NIGMS NIH HHS/ -- GM075936/GM/NIGMS NIH HHS/ -- R01 DA013261/DA/NIDA NIH HHS/ -- R01 DA019676/DA/NIDA NIH HHS/ -- R01 DK053973/DK/NIDDK NIH HHS/ -- R21 DK060841/DK/NIDDK NIH HHS/ -- R21 GM075936/GM/NIGMS NIH HHS/ -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54 GM095315/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1390-3. Epub 2007 Aug 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17690258" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antidepressive Agents, Tricyclic/chemistry/*metabolism ; Bacterial Proteins/chemistry/*metabolism ; Binding Sites ; Caenorhabditis elegans Proteins/chemistry/metabolism ; Cell Line ; Conserved Sequence ; Crystallography, X-Ray ; Desipramine/chemistry/*metabolism ; Dopamine/chemistry/metabolism ; Dopamine Uptake Inhibitors/chemistry/metabolism ; Drosophila Proteins/chemistry/metabolism ; Humans ; Leucine/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Neurotransmitter Uptake Inhibitors/chemistry/*metabolism ; Norepinephrine/chemistry/metabolism ; Norepinephrine Plasma Membrane Transport Proteins/antagonists & ; inhibitors/chemistry/metabolism ; Plasma Membrane Neurotransmitter Transport Proteins/chemistry/*metabolism ; Protein Binding ; Protein Conformation ; Sequence Homology, Amino Acid ; Serotonin/chemistry/metabolism ; Serotonin Uptake Inhibitors/chemistry/metabolism
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    Stabilizing isopeptide bonds revealed in gram-positive bacterial pilus structure (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-12-08
    Description: Many bacterial pathogens have long, slender pili through which they adhere to host cells. The crystal structure of the major pilin subunit from the Gram-positive human pathogen Streptococcus pyogenes at 2.2 angstroms resolution reveals an extended structure comprising two all-beta domains. The molecules associate in columns through the crystal, with each carboxyl terminus adjacent to a conserved lysine of the next molecule. This lysine forms the isopeptide bonds that link the subunits in native pili, validating the relevance of the crystal assembly. Each subunit contains two lysine-asparagine isopeptide bonds generated by an intramolecular reaction, and we find evidence for similar isopeptide bonds in other cell surface proteins of Gram-positive bacteria. The present structure explains the strength and stability of such Gram-positive pili and could facilitate vaccine development.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kang, Hae Joo -- Coulibaly, Fasseli -- Clow, Fiona -- Proft, Thomas -- Baker, Edward N -- New York, N.Y. -- Science. 2007 Dec 7;318(5856):1625-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland 1010, New Zealand.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18063798" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Asparagine/chemistry ; Chemistry, Physical ; Crystallography, X-Ray ; Fimbriae Proteins/*chemistry ; Fimbriae, Bacterial/*chemistry/ultrastructure ; Hydrogen Bonding ; Lysine/chemistry ; Models, Molecular ; Molecular Sequence Data ; Peptides/chemistry ; Physicochemical Phenomena ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry ; Streptococcus pyogenes/*chemistry/metabolism/*ultrastructure
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    A membrane receptor for retinol binding protein mediates cellular uptake of vitamin A (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-01-27
    Description: Vitamin A has diverse biological functions. It is transported in the blood as a complex with retinol binding protein (RBP), but the molecular mechanism by which vitamin A is absorbed by cells from the vitamin A-RBP complex is not clearly understood. We identified in bovine retinal pigment epithelium cells STRA6, a multitransmembrane domain protein, as a specific membrane receptor for RBP. STRA6 binds to RBP with high affinity and has robust vitamin A uptake activity from the vitamin A-RBP complex. It is widely expressed in embryonic development and in adult organ systems. The RBP receptor represents a major physiological mediator of cellular vitamin A uptake.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kawaguchi, Riki -- Yu, Jiamei -- Honda, Jane -- Hu, Jane -- Whitelegge, Julian -- Ping, Peipei -- Wiita, Patrick -- Bok, Dean -- Sun, Hui -- 5T32EY07026/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2007 Feb 9;315(5813):820-5. Epub 2007 Jan 25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology, David Geffen School of Medicine at UCLA, 650 Charles E. Young Drive South, Los Angeles, CA 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17255476" target="_blank"〉PubMed〈/a〉
    Keywords: Acyltransferases/metabolism ; Amino Acid Sequence ; Animals ; Blood-Retinal Barrier ; COS Cells ; Cattle ; Cell Line ; Cell Line, Tumor ; Cell Membrane/metabolism ; Cercopithecus aethiops ; Embryonic Development ; Endocytosis ; Humans ; Molecular Sequence Data ; Mutation, Missense ; Pigment Epithelium of Eye/*metabolism ; Placenta/metabolism ; Receptors, Cell Surface/*metabolism ; Retinal Vessels/metabolism ; Retinol-Binding Proteins/*metabolism ; Spleen/metabolism ; Transfection ; Vitamin A/*metabolism
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    A bacterial effector acts as a plant transcription factor and induces a cell size regulator (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-10-27
    Description: Pathogenicity of many Gram-negative bacteria relies on the injection of effector proteins by type III secretion into eukaryotic cells, where they modulate host signaling pathways to the pathogen's benefit. One such effector protein injected by Xanthomonas into plants is AvrBs3, which localizes to the plant cell nucleus and causes hypertrophy of plant mesophyll cells. We show that AvrBs3 induces the expression of a master regulator of cell size, upa20, which encodes a transcription factor containing a basic helix-loop-helix domain. AvrBs3 binds to a conserved element in the upa20 promoter via its central repeat region and induces gene expression through its activation domain. Thus, AvrBs3 and likely other members of this family provoke developmental reprogramming of host cells by mimicking eukaryotic transcription factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kay, Sabine -- Hahn, Simone -- Marois, Eric -- Hause, Gerd -- Bonas, Ulla -- New York, N.Y. -- Science. 2007 Oct 26;318(5850):648-51.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Biology, Department of Genetics, Martin-Luther-University Halle-Wittenberg, Weinbergweg 10, D-06120 Halle (Saale), Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17962565" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/chemistry/genetics/*physiology ; Basic Helix-Loop-Helix Transcription Factors/chemistry/genetics/*physiology ; Capsicum/cytology/*genetics/*microbiology ; Cell Enlargement ; Cell Size ; Chromatin Immunoprecipitation ; Gene Expression Regulation, Plant ; Gene Silencing ; Molecular Sequence Data ; Plant Leaves/cytology/genetics/metabolism ; Plant Proteins/chemistry/genetics/metabolism/*physiology ; Promoter Regions, Genetic ; Tobacco/genetics ; Transcription, Genetic ; Xanthomonas campestris/genetics/*metabolism/pathogenicity
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Structural basis for substrate delivery by acyl carrier protein in the yeast fatty acid synthase (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-04-14
    Description: In the multifunctional fungal fatty acid synthase (FAS), the acyl carrier protein (ACP) domain shuttles reaction intermediates covalently attached to its prosthetic phosphopantetheine group between the different enzymatic centers of the reaction cycle. Here, we report the structure of the Saccharomyces cerevisiae FAS determined at 3.1 angstrom resolution with its ACP stalled at the active site of ketoacyl synthase. The ACP contacts the base of the reaction chamber through conserved, charge-complementary surfaces, which optimally position the ACP toward the catalytic cleft of ketoacyl synthase. The conformation of the prosthetic group suggests a switchblade mechanism for acyl chain delivery to the active site of the enzyme.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Leibundgut, Marc -- Jenni, Simon -- Frick, Christian -- Ban, Nenad -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):288-90.〈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/17431182" target="_blank"〉PubMed〈/a〉
    Keywords: Acyl Carrier Protein/*chemistry/metabolism ; Acyltransferases/metabolism ; Amino Acid Sequence ; Catalytic Domain ; Crystallography, X-Ray ; Fatty Acid Synthases/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Binding ; Protein Conformation ; Protein Structure, Tertiary ; Saccharomyces cerevisiae Proteins/*chemistry/metabolism
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  • 47
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    Conformational switching in the fungal light sensor Vivid (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-05-19
    Description: The Neurospora crassa photoreceptor Vivid tunes blue-light responses and modulates gating of the circadian clock. Crystal structures of dark-state and light-state Vivid reveal a light, oxygen, or voltage Per-Arnt-Sim domain with an unusual N-terminal cap region and a loop insertion that accommodates the flavin cofactor. Photoinduced formation of a cystein-flavin adduct drives flavin protonation to induce an N-terminal conformational change. A cysteine-to-serine substitution remote from the flavin adenine dinucleotide binding site decouples conformational switching from the flavin photocycle and prevents Vivid from sending signals in Neurospora. Key elements of this activation mechanism are conserved by other photosensors such as White Collar-1, ZEITLUPE, ENVOY, and flavin-binding, kelch repeat, F-BOX 1 (FKF1).〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3682417/" 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/PMC3682417/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zoltowski, Brian D -- Schwerdtfeger, Carsten -- Widom, Joanne -- Loros, Jennifer J -- Bilwes, Alexandrine M -- Dunlap, Jay C -- Crane, Brian R -- GM079879-01/GM/NIGMS NIH HHS/ -- MH44651/MH/NIMH NIH HHS/ -- P01 GM068087/GM/NIGMS NIH HHS/ -- R01 GM034985/GM/NIGMS NIH HHS/ -- R01 GM034985-24/GM/NIGMS NIH HHS/ -- R37GM34985/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 May 18;316(5827):1054-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17510367" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Amino Acid Sequence ; Amino Acid Substitution ; Binding Sites ; Crystallography, X-Ray ; Darkness ; Dimerization ; Flavin-Adenine Dinucleotide/chemistry ; Fungal Proteins/*chemistry/genetics/metabolism ; Light ; Molecular Sequence Data ; Mutagenesis ; Neurospora crassa/*chemistry ; Protein Conformation ; Protein Structure, Tertiary
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    DUBA: a deubiquitinase that regulates type I interferon production (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-10
    Description: Production of type I interferon (IFN-I) is a critical host defense triggered by pattern-recognition receptors (PRRs) of the innate immune system. Deubiquitinating enzyme A (DUBA), an ovarian tumor domain-containing deubiquitinating enzyme, was discovered in a small interfering RNA-based screen as a regulator of IFN-I production. Reduction of DUBA augmented the PRR-induced IFN-I response, whereas ectopic expression of DUBA had the converse effect. DUBA bound tumor necrosis factor receptor-associated factor 3 (TRAF3), an adaptor protein essential for the IFN-I response. TRAF3 is an E3 ubiquitin ligase that preferentially assembled lysine-63-linked polyubiquitin chains. DUBA selectively cleaved the lysine-63-linked polyubiquitin chains on TRAF3, resulting in its dissociation from the downstream signaling complex containing TANK-binding kinase 1. A discrete ubiquitin interaction motif within DUBA was required for efficient deubiquitination of TRAF3 and optimal suppression of IFN-I. Our data identify DUBA as a negative regulator of innate immune responses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kayagaki, Nobuhiko -- Phung, Qui -- Chan, Salina -- Chaudhari, Ruchir -- Quan, Casey -- O'Rourke, Karen M -- Eby, Michael -- Pietras, Eric -- Cheng, Genhong -- Bazan, J Fernando -- Zhang, Zemin -- Arnott, David -- Dixit, Vishva M -- New York, N.Y. -- Science. 2007 Dec 7;318(5856):1628-32. Epub 2007 Nov 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiological Chemistry, Genentech, South San Francisco, CA 94080, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991829" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cell Line ; Endopeptidases/*metabolism ; Humans ; Interferon Type I/*biosynthesis/genetics ; Interferon-alpha/genetics ; Molecular Sequence Data ; NF-kappa B/metabolism ; Protein Structure, Tertiary ; RNA, Small Interfering ; Signal Transduction ; TNF Receptor-Associated Factor 3/metabolism ; Toll-Like Receptor 3/metabolism ; Ubiquitin/metabolism ; Ubiquitination
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    The after-hours mutant reveals a role for Fbxl3 in determining mammalian circadian period (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-04-28
    Description: By screening N-ethyl-N-nitrosourea-mutagenized animals for alterations in rhythms of wheel-running activity, we identified a mouse mutation, after hours (Afh). The mutation, a Cys(358)Ser substitution in Fbxl3, an F-box protein with leucine-rich repeats, results in long free-running rhythms of about 27 hours in homozygotes. Circadian transcriptional and translational oscillations are attenuated in Afh mice. The Afh allele significantly affected Per2 expression and delayed the rate of Cry protein degradation in Per2::Luciferase tissue slices. Our in vivo and in vitro studies reveal a central role for Fbxl3 in mammalian circadian timekeeping.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Godinho, Sofia I H -- Maywood, Elizabeth S -- Shaw, Linda -- Tucci, Valter -- Barnard, Alun R -- Busino, Luca -- Pagano, Michele -- Kendall, Rachel -- Quwailid, Mohamed M -- Romero, M Rosario -- O'neill, John -- Chesham, Johanna E -- Brooker, Debra -- Lalanne, Zuzanna -- Hastings, Michael H -- Nolan, Patrick M -- MC_U105170643/Medical Research Council/United Kingdom -- MC_U142684172/Medical Research Council/United Kingdom -- MC_U142684173/Medical Research Council/United Kingdom -- MC_U142684175/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2007 May 11;316(5826):897-900. Epub 2007 Apr 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Medical Research Council (MRC) Mammalian Genetics Unit, Harwell, Oxfordshire OX11 0RD, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17463252" target="_blank"〉PubMed〈/a〉
    Keywords: ARNTL Transcription Factors ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Basic Helix-Loop-Helix Transcription Factors/genetics/metabolism ; CLOCK Proteins ; COS Cells ; Cell Cycle Proteins/genetics/metabolism ; Cercopithecus aethiops ; *Circadian Rhythm/genetics ; Crosses, Genetic ; Cryptochromes ; F-Box Proteins/*genetics/*physiology ; Female ; Flavoproteins/genetics/metabolism ; Gene Expression Regulation ; Liver/metabolism ; Lung/metabolism ; Male ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C3H ; Molecular Sequence Data ; Nuclear Proteins/genetics/metabolism ; Period Circadian Proteins ; *Point Mutation ; Suprachiasmatic Nucleus/metabolism ; Trans-Activators/genetics/metabolism ; Transcription Factors/genetics/metabolism ; Transcription, Genetic
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    Structural insight into the transglycosylation step of bacterial cell-wall biosynthesis (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-03-10
    Description: Peptidoglycan glycosyltransferases (GTs) catalyze the polymerization step of cell-wall biosynthesis, are membrane-bound, and are highly conserved across all bacteria. Long considered the "holy grail" of antibiotic research, they represent an essential and easily accessible drug target for antibiotic-resistant bacteria, including methicillin-resistant Staphylococcus aureus. We have determined the 2.8 angstrom structure of a bifunctional cell-wall cross-linking enzyme, including its transpeptidase and GT domains, both unliganded and complexed with the substrate analog moenomycin. The peptidoglycan GTs adopt a fold distinct from those of other GT classes. The structures give insight into critical features of the catalytic mechanism and key interactions required for enzyme inhibition.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lovering, Andrew L -- de Castro, Liza H -- Lim, Daniel -- Strynadka, Natalie C J -- New York, N.Y. -- Science. 2007 Mar 9;315(5817):1402-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, and Center for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Vancouver, Canada.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17347437" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Aminoacyltransferases/*chemistry/metabolism ; Anti-Bacterial Agents/chemistry/metabolism ; Apoenzymes/chemistry ; Binding Sites ; Carbohydrate Conformation ; Carbohydrate Sequence ; Catalytic Domain ; Cell Wall/*metabolism ; Crystallography, X-Ray ; Enzyme Inhibitors/chemistry/metabolism/pharmacology ; Glycosylation ; Models, Molecular ; Molecular Sequence Data ; Multienzyme Complexes/chemistry/metabolism ; Oligosaccharides/chemistry/metabolism/pharmacology ; Penicillin-Binding Proteins/*chemistry/metabolism ; Peptidoglycan/*biosynthesis ; Peptidoglycan Glycosyltransferase/*chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Tertiary ; Staphylococcus aureus/*enzymology/metabolism
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    Rtt109 acetylates histone H3 lysine 56 and functions in DNA replication (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-03
    Description: Acetylation of histone H3 lysine 56 (H3-K56) occurs in S phase, and cells lacking H3-K56 acetylation are sensitive to DNA-damaging agents. However, the histone acetyltransferase (HAT) that catalyzes global H3-K56 acetylation has not been found. Here we show that regulation of Ty1 transposition gene product 109 (Rtt109) is an H3-K56 HAT. Cells lacking Rtt109 or expressing rtt109 mutants with alterations at a conserved aspartate residue lose H3-K56 acetylation and exhibit increased sensitivity toward genotoxic agents, as well as elevated levels of spontaneous chromosome breaks. Thus, Rtt109, which shares no sequence homology with any other known HATs, is a unique HAT that acetylates H3-K56.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Han, Junhong -- Zhou, Hui -- Horazdovsky, Bruce -- Zhang, Kangling -- Xu, Rui-Ming -- Zhang, Zhiguo -- New York, N.Y. -- Science. 2007 Feb 2;315(5812):653-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First Street SW, Rochester, MN 55905, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17272723" target="_blank"〉PubMed〈/a〉
    Keywords: Acetylation ; Amino Acid Sequence ; Camptothecin/pharmacology ; Catalytic Domain ; Chromosome Breakage ; DNA Damage ; *DNA Replication ; Histone Acetyltransferases/chemistry/genetics/*metabolism ; Histones/*metabolism ; Hydroxyurea/pharmacology ; Lysine/*metabolism ; Methyl Methanesulfonate/pharmacology ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Mutagens/pharmacology ; Mutation ; Recombinant Proteins/metabolism ; S Phase ; Saccharomyces cerevisiae/genetics/*metabolism ; Saccharomyces cerevisiae Proteins/chemistry/genetics/*metabolism ; Sequence Homology, Amino Acid
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    Structure of the zinc transporter YiiP (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-08-25
    Description: YiiP is a membrane transporter that catalyzes Zn2+/H+ exchange across the inner membrane of Escherichia coli. Mammalian homologs of YiiP play critical roles in zinc homeostasis and cell signaling. Here, we report the x-ray structure of YiiP in complex with zinc at 3.8 angstrom resolution. YiiP is a homodimer held together in a parallel orientation through four Zn2+ ions at the interface of the cytoplasmic domains, whereas the two transmembrane domains swing out to yield a Y-shaped structure. In each protomer, the cytoplasmic domain adopts a metallochaperone-like protein fold; the transmembrane domain features a bundle of six transmembrane helices and a tetrahedral Zn2+ binding site located in a cavity that is open to both the membrane outer leaflet and the periplasm.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lu, Min -- Fu, Dax -- R01 GM065137/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 21;317(5845):1746-8. Epub 2007 Aug 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, Brookhaven National Laboratory, Upton, NY 11973, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17717154" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Crystallography, X-Ray ; Escherichia coli/chemistry/metabolism ; Escherichia coli Proteins/*chemistry/metabolism ; Membrane Transport Proteins/*chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Sequence Alignment ; Zinc/*chemistry/metabolism
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    Structure of C8alpha-MACPF reveals mechanism of membrane attack in complement immune defense (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-09-18
    Description: Membrane attack is important for mammalian immune defense against invading microorganisms and infected host cells. Proteins of the complement membrane attack complex (MAC) and the protein perforin share a common MACPF domain that is responsible for membrane insertion and pore formation. We determined the crystal structure of the MACPF domain of complement component C8alpha at 2.5 angstrom resolution and show that it is structurally homologous to the bacterial, pore-forming, cholesterol-dependent cytolysins. The structure displays two regions that (in the bacterial cytolysins) refold into transmembrane beta hairpins, forming the lining of a barrel pore. Local hydrophobicity explains why C8alpha is the first complement protein to insert into the membrane. The size of the MACPF domain is consistent with known C9 pore sizes. These data imply that these mammalian and bacterial cytolytic proteins share a common mechanism of membrane insertion.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hadders, Michael A -- Beringer, Dennis X -- Gros, Piet -- New York, N.Y. -- Science. 2007 Sep 14;317(5844):1552-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17872444" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cell Membrane/immunology/metabolism ; Complement C8/*chemistry/immunology/*metabolism ; Complement Membrane Attack Complex/*chemistry/immunology/*metabolism ; Crystallography, X-Ray ; Cytotoxins/chemistry/metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Membrane Glycoproteins/chemistry/metabolism ; Models, Molecular ; Molecular Sequence Data ; Perforin ; Pore Forming Cytotoxic Proteins/chemistry/metabolism ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; *Protein Structure, Tertiary
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    Chimeras of two isoprenoid synthases catalyze all four coupling reactions in isoprenoid biosynthesis (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-04-07
    Description: The carbon skeletons of over 55,000 naturally occurring isoprenoid compounds are constructed from four fundamental coupling reactions: chain elongation, cyclopropanation, branching, and cyclobutanation. Enzymes that catalyze chain elongation and cyclopropanation are well studied, whereas those that catalyze branching and cyclobutanation are unknown. We have catalyzed the four reactions with chimeric proteins generated by replacing segments of a chain-elongation enzyme with corresponding sequences from a cyclopropanation enzyme. Stereochemical and mechanistic considerations suggest that the four coupling enzymes could have evolved from a common ancestor through relatively small changes in the catalytic site.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thulasiram, Hirekodathakallu V -- Erickson, Hans K -- Poulter, C Dale -- GM 21328/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Apr 6;316(5821):73-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, UT 84112, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17412950" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Artemisia/enzymology ; Catalysis ; Catalytic Domain ; Chrysanthemum cinerariifolium/enzymology ; Cyclopropanes/chemistry ; Evolution, Molecular ; Geranyltranstransferase/chemistry/genetics/*metabolism ; Kinetics ; Molecular Conformation ; Molecular Sequence Data ; Molecular Structure ; Mutagenesis, Site-Directed ; Recombinant Fusion Proteins/chemistry/metabolism ; Stereoisomerism ; Terpenes/chemistry/*metabolism
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    Structure of a tyrosine phosphatase adhesive interaction reveals a spacer-clamp mechanism (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-09-01
    Description: Cell-cell contacts are fundamental to multicellular organisms and are subject to exquisite levels of control. Human RPTPmu is a type IIB receptor protein tyrosine phosphatase that both forms an adhesive contact itself and is involved in regulating adhesion by dephosphorylating components of cadherin-catenin complexes. Here we describe a 3.1 angstrom crystal structure of the RPTPmu ectodomain that forms a homophilic trans (antiparallel) dimer with an extended and rigid architecture, matching the dimensions of adherens junctions. Cell surface expression of deletion constructs induces intercellular spacings that correlate with the ectodomain length. These data suggest that the RPTPmu ectodomain acts as a distance gauge and plays a key regulatory function, locking the phosphatase to its appropriate functional location.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Aricescu, A Radu -- Siebold, Christian -- Choudhuri, Kaushik -- Chang, Veronica T -- Lu, Weixian -- Davis, Simon J -- van der Merwe, P Anton -- Jones, E Yvonne -- 081894/Wellcome Trust/United Kingdom -- G9722488/Medical Research Council/United Kingdom -- G9900061/Medical Research Council/United Kingdom -- New York, N.Y. -- Science. 2007 Aug 31;317(5842):1217-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Cancer Research UK Receptor Structure Research Group, University of Oxford, Henry Wellcome Building of Genomic Medicine, Division of Structural Biology, Roosevelt Drive, Oxford OX3 7BN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17761881" target="_blank"〉PubMed〈/a〉
    Keywords: Adherens Junctions/chemistry/*physiology/ultrastructure ; Amino Acid Sequence ; Cell Adhesion ; Cell Adhesion Molecules/*chemistry/metabolism ; Cell Membrane/chemistry/enzymology ; Conserved Sequence ; Dimerization ; Fibronectins/chemistry ; Humans ; Hydrogen Bonding ; Hydrogen-Ion Concentration ; Hydrophobic and Hydrophilic Interactions ; Immunoglobulins/chemistry ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; Protein Structure, Tertiary ; Protein Tyrosine Phosphatases/*chemistry/genetics/*metabolism ; Receptor-Like Protein Tyrosine Phosphatases, Class 2
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    JMJD6 is a histone arginine demethylase (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-10-20
    Description: Arginine methylation occurs on a number of proteins involved in a variety of cellular functions. Histone tails are known to be mono- and dimethylated on multiple arginine residues where they influence chromatin remodeling and gene expression. To date, no enzyme has been shown to reverse these regulatory modifications. We demonstrate that the Jumonji domain-containing 6 protein (JMJD6) is a JmjC-containing iron- and 2-oxoglutarate-dependent dioxygenase that demethylates histone H3 at arginine 2 (H3R2) and histone H4 at arginine 3 (H4R3) in both biochemical and cell-based assays. These findings may help explain the many developmental defects observed in the JMJD6(-/-) knockout mice.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Bingsheng -- Chen, Yue -- Zhao, Yingming -- Bruick, Richard K -- C06-RR15437-01/RR/NCRR NIH HHS/ -- CA107943/CA/NCI NIH HHS/ -- CA115962/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2007 Oct 19;318(5849):444-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17947579" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arginine/*metabolism ; HeLa Cells ; Histones/*metabolism ; Humans ; Jumonji Domain-Containing Histone Demethylases ; Methylation ; Molecular Sequence Data ; Oxidation-Reduction ; Protein Processing, Post-Translational ; Receptors, Cell Surface/chemistry/genetics/*metabolism ; Recombinant Proteins/metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
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    Ubiquitin-binding protein RAP80 mediates BRCA1-dependent DNA damage response (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-05-26
    Description: Mutations in the breast cancer susceptibility gene 1 (BRCA1) are associated with an increased risk of breast and ovarian cancers. BRCA1 participates in the cellular DNA damage response. We report the identification of receptor-associated protein 80 (RAP80) as a BRCA1-interacting protein in humans. RAP80 contains a tandem ubiquitin-interacting motif domain, which is required for its binding with ubiquitin in vitro and its damage-induced foci formation in vivo. Moreover, RAP80 specifically recruits BRCA1 to DNA damage sites and functions with BRCA1 in G2/M checkpoint control. Together, these results suggest the existence of a ubiquitination-dependent signaling pathway involved in the DNA damage response.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Hongtae -- Chen, Junjie -- Yu, Xiaochun -- R01CA089239/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2007 May 25;316(5828):1202-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Therapeutic Radiology, Yale University School of Medicine, Post Office Box 208040, New Haven, CT 06520, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17525342" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; BRCA1 Protein/*metabolism ; Carrier Proteins/*metabolism ; Cell Cycle ; Cell Line, Tumor ; DNA/*metabolism/radiation effects ; *DNA Damage ; DNA Repair/*physiology ; HeLa Cells ; Humans ; Molecular Sequence Data ; Nuclear Proteins/*metabolism ; Protein Binding ; Protein Structure, Tertiary ; RNA, Small Interfering ; Radiation, Ionizing ; Ubiquitin/*metabolism
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    Structural and regulatory genes required to make the gas dimethyl sulfide in bacteria (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-02-03
    Description: Dimethyl sulfide (DMS) is a key compound in global sulfur and carbon cycles. DMS oxidation products cause cloud nucleation and may affect weather and climate. DMS is generated largely by bacterial catabolism of dimethylsulfoniopropionate (DMSP), a secondary metabolite made by marine algae. We demonstrate that the bacterial gene dddD is required for this process and that its transcription is induced by the DMSP substrate. Cloned dddD from the marine bacterium Marinomonas and from two bacterial strains that associate with higher plants, the N(2)-fixing symbiont Rhizobium NGR234 and the root-colonizing Burkholderia cepacia AMMD, conferred to Escherichia coli the ability to make DMS from DMSP. The inferred enzymatic mechanism for DMS liberation involves an initial step in which DMSP is modified by addition of acyl coenzyme A, rather than the immediate release of DMS by a DMSP lyase, the previously suggested mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Todd, Jonathan D -- Rogers, Rachel -- Li, You Guo -- Wexler, Margaret -- Bond, Philip L -- Sun, Lei -- Curson, Andrew R J -- Malin, Gill -- Steinke, Michael -- Johnston, Andrew W B -- New York, N.Y. -- Science. 2007 Feb 2;315(5812):666-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17272727" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Proteins/genetics/*metabolism ; Burkholderia cepacia/genetics/growth & development/metabolism ; Cloning, Molecular ; Coenzyme A-Transferases/genetics/*metabolism ; DNA Transposable Elements ; Escherichia coli/genetics/metabolism ; *Genes, Bacterial ; *Genes, Regulator ; Marinomonas/*genetics/growth & development/*metabolism ; Molecular Sequence Data ; Operon ; Oxidation-Reduction ; Phenotype ; Poaceae/microbiology ; Promoter Regions, Genetic ; Rhizobium/genetics/growth & development/metabolism ; Sulfides/*metabolism ; Sulfonium Compounds/metabolism ; Transformation, Bacterial
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    HIV-1 proviral DNA excision using an evolved recombinase (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-06-30
    Description: HIV-1 integrates into the host chromosome and persists as a provirus flanked by long terminal repeats (LTRs). To date, treatment regimens primarily target the virus enzymes or virus-cell fusion, but not the integrated provirus. We report here the substrate-linked protein evolution of a tailored recombinase that recognizes an asymmetric sequence within an HIV-1 LTR. This evolved recombinase efficiently excised integrated HIV proviral DNA from the genome of infected cells. Although a long way from use in the clinic, we speculate that this type of technology might be adapted in future antiretroviral therapies, among other possible uses.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sarkar, Indrani -- Hauber, Ilona -- Hauber, Joachim -- Buchholz, Frank -- New York, N.Y. -- Science. 2007 Jun 29;316(5833):1912-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, D-01307 Dresden, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17600219" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Base Sequence ; DNA Shuffling ; DNA, Viral/*metabolism ; *Directed Molecular Evolution ; Escherichia coli/genetics ; Gene Library ; Genome, Human ; *HIV Long Terminal Repeat ; HIV-1/*metabolism ; HeLa Cells ; Humans ; Integrases/*genetics/*metabolism ; Molecular Sequence Data ; Mutation ; Proviruses/metabolism ; Recombination, Genetic ; *Virus Integration
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    Interpreting sequences from mastodon and T. rex (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-08
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Asara, John M -- Garavelli, John S -- Slatter, David A -- Schweitzer, Mary H -- Freimark, Lisa M -- Phillips, Matthew -- Cantley, Lewis C -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1324-5.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17823333" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bone and Bones/chemistry ; Collagen/*chemistry ; *Dinosaurs ; *Elephants ; *Fossils ; Glycine/chemistry ; Mass Spectrometry ; Molecular Sequence Data ; Proline/chemistry ; Tandem Mass Spectrometry
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    Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-04-14
    Description: Fossilized bones from extinct taxa harbor the potential for obtaining protein or DNA sequences that could reveal evolutionary links to extant species. We used mass spectrometry to obtain protein sequences from bones of a 160,000- to 600,000-year-old extinct mastodon (Mammut americanum) and a 68-million-year-old dinosaur (Tyrannosaurus rex). The presence of T. rex sequences indicates that their peptide bonds were remarkably stable. Mass spectrometry can thus be used to determine unique sequences from ancient organisms from peptide fragmentation patterns, a valuable tool to study the evolution and adaptation of ancient taxa from which genomic sequences are unlikely to be obtained.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Asara, John M -- Schweitzer, Mary H -- Freimark, Lisa M -- Phillips, Matthew -- Cantley, Lewis C -- New York, N.Y. -- Science. 2007 Apr 13;316(5822):280-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Division of Signal Transduction, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA. jasara@bidmc.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17431180" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bone and Bones/*chemistry ; Collagen/chemistry ; *Dinosaurs ; *Elephants ; Evolution, Molecular ; *Fossils ; Humans ; *Mass Spectrometry ; Molecular Sequence Data ; Proteins/analysis/*chemistry ; Reptilian Proteins/analysis/*chemistry ; Sequence Alignment ; Sequence Analysis, Protein ; Struthioniformes
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    Structure and function of an essential component of the outer membrane protein assembly machine (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-08-19
    Description: Integral beta-barrel proteins are found in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. The machine that assembles these proteins contains an integral membrane protein, called YaeT in Escherichia coli, which has one or more polypeptide transport-associated (POTRA) domains. The crystal structure of a periplasmic fragment of YaeT reveals the POTRA domain fold and suggests a model for how POTRA domains can bind different peptide sequences, as required for a machine that handles numerous beta-barrel protein precursors. Analysis of POTRA domain deletions shows which are essential and provides a view of the spatial organization of this assembly machine.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Seokhee -- Malinverni, Juliana C -- Sliz, Piotr -- Silhavy, Thomas J -- Harrison, Stephen C -- Kahne, Daniel -- GM34821/GM/NIGMS NIH HHS/ -- GM66174/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Aug 17;317(5840):961-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17702946" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Bacterial Outer Membrane Proteins/*chemistry/genetics/*metabolism ; Cell Membrane/metabolism ; Crystallography, X-Ray ; Dimerization ; Escherichia coli/*chemistry/*metabolism ; Escherichia coli Proteins/*chemistry/genetics/*metabolism ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Lipoproteins/chemistry/metabolism ; Models, Biological ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Protein Binding ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Protein Transport
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    Replication origin recognition and deformation by a heterodimeric archaeal Orc1 complex (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-09-01
    Description: The faithful duplication of genetic material depends on essential DNA replication initiation factors. Cellular initiators form higher-order assemblies on replication origins, using adenosine triphosphate (ATP) to locally remodel duplex DNA and facilitate proper loading of synthetic replisomal components. To better understand initiator function, we determined the 3.4 angstrom-resolution structure of an archaeal Cdc6/Orc1 heterodimer bound to origin DNA. The structure demonstrates that, in addition to conventional DNA binding elements, initiators use their AAA+ ATPase domains to recognize origin DNA. Together these interactions establish the polarity of initiator assembly on the origin and induce substantial distortions into origin DNA strands. Biochemical and comparative analyses indicate that AAA+/DNA contacts observed in the structure are dynamic and evolutionarily conserved, suggesting that the complex forms a core component of the basal initiation machinery.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dueber, Erin L Cunningham -- Corn, Jacob E -- Bell, Stephen D -- Berger, James M -- GM071747/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Aug 31;317(5842):1210-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Miller Institute for Basic Research in Science, 2536 Channing Way 5190, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17761879" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/chemistry ; Amino Acid Sequence ; Archaeal Proteins/*chemistry/metabolism ; Binding Sites ; Conserved Sequence ; Crystallography, X-Ray ; DNA, Archaeal/*chemistry/metabolism ; DNA, Single-Stranded/chemistry/metabolism ; Dimerization ; Helix-Turn-Helix Motifs ; Models, Molecular ; Nucleic Acid Conformation ; Origin Recognition Complex/*chemistry/metabolism ; Protein Structure, Secondary ; Protein Structure, Tertiary ; *Replication Origin ; Sulfolobus solfataricus/*chemistry/metabolism
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    Crystal structures of the adenylate sensor from fission yeast AMP-activated protein kinase (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-02-10
    Description: The 5'-AMP (adenosine monophosphate)-activated protein kinase (AMPK) coordinates metabolic function with energy availability by responding to changes in intracellular ATP (adenosine triphosphate) and AMP concentrations. Here, we report crystal structures at 2.9 and 2.6 A resolution for ATP- and AMP-bound forms of a core alphabetagamma adenylate-binding domain from the fission yeast AMPK homolog. ATP and AMP bind competitively to a single site in the gamma subunit, with their respective phosphate groups positioned near function-impairing mutants. Unexpectedly, ATP binds without counterions, amplifying its electrostatic effects on a critical regulatory region where all three subunits converge.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Townley, Robert -- Shapiro, Lawrence -- New York, N.Y. -- Science. 2007 Mar 23;315(5819):1726-9. Epub 2007 Feb 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17289942" target="_blank"〉PubMed〈/a〉
    Keywords: AMP-Activated Protein Kinases ; Adenosine Monophosphate/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; Binding, Competitive ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Multienzyme Complexes/*chemistry/metabolism ; Protein Kinases/*chemistry/metabolism ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Protein-Serine-Threonine Kinases/*chemistry/metabolism ; Schizosaccharomyces/*enzymology
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    Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007-10-06
    Description: Telomeres, the DNA-protein complexes located at the end of linear eukaryotic chromosomes, are essential for chromosome stability. Until now, telomeres have been considered to be transcriptionally silent. We demonstrate that mammalian telomeres are transcribed into telomeric repeat-containing RNA (TERRA). TERRA molecules are heterogeneous in length, are transcribed from several subtelomeric loci toward chromosome ends, and localize to telomeres. We also show that suppressors with morphogenetic defects in genitalia (SMG) proteins, which are effectors of nonsense-mediated messenger RNA decay, are enriched at telomeres in vivo, negatively regulate TERRA association with chromatin, and protect chromosome ends from telomere loss. Thus, telomeres are actively transcribed into TERRA, and SMG factors represent a molecular link between TERRA regulation and the maintenance of telomere integrity.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Azzalin, Claus M -- Reichenbach, Patrick -- Khoriauli, Lela -- Giulotto, Elena -- Lingner, Joachim -- New York, N.Y. -- Science. 2007 Nov 2;318(5851):798-801. Epub 2007 Oct 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Swiss Institute for Experimental Cancer Research (ISREC), CH-1066 Epalinges, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17916692" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Blotting, Northern ; Cells, Cultured ; Chromosomes, Human ; Chromosomes, Mammalian ; HeLa Cells ; Humans ; In Situ Hybridization, Fluorescence ; Mice ; Molecular Sequence Data ; Proteins/metabolism ; RNA/*genetics ; Repetitive Sequences, Nucleic Acid ; Telomerase/physiology ; Telomere/*genetics ; Transcription, Genetic ; Tumor Cells, Cultured
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    Genetic determinants of self identity and social recognition in bacteria (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    Tight regulation of unstructured proteins: from transcript synthesis to protein degradation (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Structural basis of toll-like receptor 3 signaling with double-stranded RNA (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    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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  • 70
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    Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry" (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    The premetazoan ancestry of cadherins (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    An agonist of toll-like receptor 5 has radioprotective activity in mouse and primate models (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    Beta-catenin defines head versus tail identity during planarian regeneration and homeostasis (2007)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2007
    Description: After amputation, freshwater planarians properly regenerate a head or tail from the resulting anterior or posterior wound. The mechanisms that differentiate anterior from posterior and direct the replacement of the appropriate missing body parts are unknown. We found that in the planarian Schmidtea mediterranea, RNA interference (RNAi) of beta-catenin or dishevelled causes the inappropriate regeneration of a head instead of a tail at posterior amputations. Conversely, RNAi of the beta-catenin antagonist adenomatous polyposis coli results in the regeneration of a tail at anterior wounds. In addition, the silencing of beta-catenin is sufficient to transform the tail of uncut adult animals into a head. We suggest that beta-catenin functions as a molecular switch to specify and maintain anteroposterior identity during regeneration and homeostasis in planarians.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2755502/" 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/PMC2755502/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gurley, Kyle A -- Rink, Jochen C -- Sanchez Alvarado, Alejandro -- F32GM082016/GM/NIGMS NIH HHS/ -- R0-1 GM57260/GM/NIGMS NIH HHS/ -- R01 GM057260/GM/NIGMS NIH HHS/ -- R01 GM057260-08/GM/NIGMS NIH HHS/ -- T32CA093247/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2008 Jan 18;319(5861):323-7. Epub 2007 Dec 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology and Anatomy, Howard Hughes Medical Institute, University of Utah School of Medicine, 401 MREB, 20N 1900E, Salt Lake City, UT 84132, USA. sanchez@neuro.utah.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18063757" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing/chemistry/genetics/physiology ; Adenomatous Polyposis Coli Protein/chemistry/physiology ; Amino Acid Sequence ; Animals ; Body Patterning ; Gene Expression Profiling ; Genes, APC ; Head ; Helminth Proteins/chemistry/genetics/physiology ; Homeostasis ; Molecular Sequence Data ; Phosphoproteins/chemistry/genetics/physiology ; Planarians/genetics/*physiology ; RNA Interference ; *Regeneration ; Signal Transduction ; Tail ; beta Catenin/chemistry/genetics/*physiology
    Print ISSN: 0036-8075
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    Structural evidence for common ancestry of the nuclear pore complex and vesicle coats (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    Regulatory genes control a key morphological and ecological trait transferred between species (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    Molecular architecture of the "stressosome," a signal integration and transduction hub (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    Structure and functional role of dynein's microtubule-binding domain (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    Virus population dynamics and acquired virus resistance in natural microbial communities (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Identification of SLEEPLESS, a sleep-promoting factor (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    TDP-43 mutations in familial and sporadic amyotrophic lateral sclerosis (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    Structural basis for specific substrate recognition by the chloroplast signal recognition particle protein cpSRP43 (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    The crystal structure of a sodium galactose transporter reveals mechanistic insights into Na+/sugar symport (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    Alignment uncertainty and genomic analysis (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    Leiomodin is an actin filament nucleator in muscle cells (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Coiled-coil irregularities and instabilities in group A Streptococcus M1 are required for virulence (2008)
    American Association for the Advancement of Science (AAAS)
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    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
    Print ISSN: 0036-8075
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    Four-jointed is a Golgi kinase that phosphorylates a subset of cadherin domains (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    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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    Human CHN1 mutations hyperactivate alpha2-chimaerin and cause Duane's retraction syndrome (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    Fission yeast Pot1-Tpp1 protects telomeres and regulates telomere length (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    Axle-less F1-ATPase rotates in the correct direction (2008)
    American Association for the Advancement of Science (AAAS)
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    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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  • 92
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    Divergence of quaternary structures among bacterial flagellar filaments (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    The high-affinity E. coli methionine ABC transporter: structure and allosteric regulation (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    A molecular clutch disables flagella in the Bacillus subtilis biofilm (2008)
    American Association for the Advancement of Science (AAAS)
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    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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    A conserved molecular framework for compound leaf development (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 96
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    Oncogenic CARD11 mutations in human diffuse large B cell lymphoma (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 97
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    The transcriptional repressor DEC2 regulates sleep length in mammals (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-08-15
    Description: Sleep deprivation can impair human health and performance. Habitual total sleep time and homeostatic sleep response to sleep deprivation are quantitative traits in humans. Genetic loci for these traits have been identified in model organisms, but none of these potential animal models have a corresponding human genotype and phenotype. We have identified a mutation in a transcriptional repressor (hDEC2-P385R) that is associated with a human short sleep phenotype. Activity profiles and sleep recordings of transgenic mice carrying this mutation showed increased vigilance time and less sleep time than control mice in a zeitgeber time- and sleep deprivation-dependent manner. These mice represent a model of human sleep homeostasis that provides an opportunity to probe the effect of sleep on human physical and mental health.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2884988/" 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/PMC2884988/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉He, Ying -- Jones, Christopher R -- Fujiki, Nobuhiro -- Xu, Ying -- Guo, Bin -- Holder, Jimmy L Jr -- Rossner, Moritz J -- Nishino, Seiji -- Fu, Ying-Hui -- HL059596/HL/NHLBI NIH HHS/ -- MH074924/MH/NIMH NIH HHS/ -- R01 HL059596/HL/NHLBI NIH HHS/ -- R01 HL059596-09/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2009 Aug 14;325(5942):866-70. doi: 10.1126/science.1174443.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurology, University of California at San Francisco, Mission Bay, 1550 Fourth Street, San Francisco, CA 94158, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19679812" target="_blank"〉PubMed〈/a〉
    Keywords: Activity Cycles/genetics ; Adolescent ; Adult ; Aged ; Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Animals, Genetically Modified ; Basic Helix-Loop-Helix Transcription Factors/chemistry/*genetics/physiology ; Child ; Circadian Rhythm/genetics ; Drosophila/genetics ; Electroencephalography ; Electromyography ; Female ; Homeostasis ; Humans ; Male ; Mice ; Mice, Knockout ; Mice, Transgenic ; Middle Aged ; Molecular Sequence Data ; Pedigree ; Point Mutation ; Sleep/*genetics/physiology ; Sleep Deprivation ; Sleep, REM/genetics/physiology ; Transcription Factors/chemistry/genetics/physiology ; Wakefulness
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 98
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    Haploid genetic screens in human cells identify host factors used by pathogens (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-12-08
    Description: Loss-of-function genetic screens in model organisms have elucidated numerous biological processes, but the diploid genome of mammalian cells has precluded large-scale gene disruption. We used insertional mutagenesis to develop a screening method to generate null alleles in a human cell line haploid for all chromosomes except chromosome 8. Using this approach, we identified host factors essential for infection with influenza and genes encoding important elements of the biosynthetic pathway of diphthamide, which are required for the cytotoxic effects of diphtheria toxin and exotoxin A. We also identified genes needed for the action of cytolethal distending toxin, including a cell-surface protein that interacts with the toxin. This approach has both conceptual and practical parallels with genetic approaches in haploid yeast.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carette, Jan E -- Guimaraes, Carla P -- Varadarajan, Malini -- Park, Annie S -- Wuethrich, Irene -- Godarova, Alzbeta -- Kotecki, Maciej -- Cochran, Brent H -- Spooner, Eric -- Ploegh, Hidde L -- Brummelkamp, Thijn R -- New York, N.Y. -- Science. 2009 Nov 27;326(5957):1231-5. doi: 10.1126/science.1178955.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965467" target="_blank"〉PubMed〈/a〉
    Keywords: ADP Ribose Transferases/metabolism/toxicity ; Adenosine Diphosphate Ribose/metabolism ; Amino Acid Sequence ; Antigens, Bacterial/metabolism/toxicity ; Bacterial Toxins/*metabolism/toxicity ; Biosynthetic Pathways ; Cell Line, Tumor ; Diphtheria Toxin/metabolism/toxicity ; Exotoxins/metabolism/toxicity ; Genes ; *Genetic Testing ; *Haploidy ; Histidine/analogs & derivatives/biosynthesis ; *Host-Pathogen Interactions ; Humans ; Influenza A Virus, H1N1 Subtype/*pathogenicity ; Molecular Sequence Data ; Monosaccharide Transport Proteins/genetics/metabolism ; Mutagenesis, Insertional ; N-Acylneuraminate Cytidylyltransferase/genetics/metabolism ; Peptide Elongation Factor 2/metabolism ; Proteins/chemistry/genetics/metabolism ; Virulence Factors/metabolism/toxicity
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 99
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    A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-12-08
    Description: Simocyclinones are bifunctional antibiotics that inhibit bacterial DNA gyrase by preventing DNA binding to the enzyme. We report the crystal structure of the complex formed between the N-terminal domain of the Escherichia coli gyrase A subunit and simocyclinone D8, revealing two binding pockets that separately accommodate the aminocoumarin and polyketide moieties of the antibiotic. These are close to, but distinct from, the quinolone-binding site, consistent with our observations that several mutations in this region confer resistance to both agents. Biochemical studies show that the individual moieties of simocyclinone D8 are comparatively weak inhibitors of gyrase relative to the parent compound, but their combination generates a more potent inhibitor. Our results should facilitate the design of drug molecules that target these unexploited binding pockets.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Edwards, Marcus J -- Flatman, Ruth H -- Mitchenall, Lesley A -- Stevenson, Clare E M -- Le, Tung B K -- Clarke, Thomas A -- McKay, Adam R -- Fiedler, Hans-Peter -- Buttner, Mark J -- Lawson, David M -- Maxwell, Anthony -- Biotechnology and Biological Sciences Research Council/United Kingdom -- New York, N.Y. -- Science. 2009 Dec 4;326(5958):1415-8. doi: 10.1126/science.1179123.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry, John Innes Centre, Colney, Norwich NR4 7UH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965760" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Anti-Bacterial Agents/chemistry/metabolism/pharmacology ; Binding Sites ; Coumarins/chemistry/metabolism/pharmacology ; Crystallography, X-Ray ; DNA Gyrase/*chemistry/genetics/*metabolism ; DNA, Bacterial/metabolism ; Drug Resistance, Bacterial ; Escherichia coli/drug effects/*enzymology/genetics ; Glycosides/chemistry/metabolism/pharmacology ; Ligands ; Models, Molecular ; Molecular Sequence Data ; Molecular Weight ; Mutagenesis, Site-Directed ; Mutation ; Protein Multimerization ; Protein Structure, Tertiary ; Topoisomerase II Inhibitors
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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    Structure and mechanism of a Na+-independent amino acid transporter (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-07-18
    Description: Amino acid, polyamine, and organocation (APC) transporters are secondary transporters that play essential roles in nutrient uptake, neurotransmitter recycling, ionic homeostasis, and regulation of cell volume. Here, we present the crystal structure of apo-ApcT, a proton-coupled broad-specificity amino acid transporter, at 2.35 angstrom resolution. The structure contains 12 transmembrane helices, with the first 10 consisting of an inverted structural repeat of 5 transmembrane helices like the leucine transporter LeuT. The ApcT structure reveals an inward-facing, apo state and an amine moiety of lysine-158 located in a position equivalent to the sodium ion site Na2 of LeuT. We propose that lysine-158 is central to proton-coupled transport and that the amine group serves the same functional role as the Na2 ion in LeuT, thus demonstrating common principles among proton- and sodium-coupled transporters.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851542/" 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/PMC2851542/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shaffer, Paul L -- Goehring, April -- Shankaranarayanan, Aruna -- Gouaux, Eric -- R01 MH070039/MH/NIMH NIH HHS/ -- R01 MH070039-05/MH/NIMH NIH HHS/ -- T32 GM008281/GM/NIGMS NIH HHS/ -- T32 GM008281-17/GM/NIGMS NIH HHS/ -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54 GM075026-040002/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2009 Aug 21;325(5943):1010-4. doi: 10.1126/science.1176088. Epub 2009 Jul 16.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vollum Institute, Oregon Health and Science University, 3181 Southwest Sam Jackson Park Road, Portland, OR 97239, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19608859" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Transport Systems/*chemistry/*metabolism ; Amino Acids/metabolism ; Antiporters/chemistry ; Apoproteins/chemistry/metabolism ; Archaeal Proteins/*chemistry/*metabolism ; Crystallization ; Crystallography, X-Ray ; Escherichia coli Proteins/chemistry ; Methanococcus/*chemistry ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Protons ; Sodium/metabolism ; Substrate Specificity
    Print ISSN: 0036-8075
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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