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  • Molecular Sequence Data  (18)
  • 2005-2009  (18)
  • 1
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    The genome of the simian and human malaria parasite Plasmodium knowlesi (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-10-10
    Description: Plasmodium knowlesi is an intracellular malaria parasite whose natural vertebrate host is Macaca fascicularis (the 'kra' monkey); however, it is now increasingly recognized as a significant cause of human malaria, particularly in southeast Asia. Plasmodium knowlesi was the first malaria parasite species in which antigenic variation was demonstrated, and it has a close phylogenetic relationship to Plasmodium vivax, the second most important species of human malaria parasite (reviewed in ref. 4). Despite their relatedness, there are important phenotypic differences between them, such as host blood cell preference, absence of a dormant liver stage or 'hypnozoite' in P. knowlesi, and length of the asexual cycle (reviewed in ref. 4). Here we present an analysis of the P. knowlesi (H strain, Pk1(A+) clone) nuclear genome sequence. This is the first monkey malaria parasite genome to be described, and it provides an opportunity for comparison with the recently completed P. vivax genome and other sequenced Plasmodium genomes. In contrast to other Plasmodium genomes, putative variant antigen families are dispersed throughout the genome and are associated with intrachromosomal telomere repeats. One of these families, the KIRs, contains sequences that collectively match over one-half of the host CD99 extracellular domain, which may represent an unusual form of molecular mimicry.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656934/" 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/PMC2656934/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pain, A -- Bohme, U -- Berry, A E -- Mungall, K -- Finn, R D -- Jackson, A P -- Mourier, T -- Mistry, J -- Pasini, E M -- Aslett, M A -- Balasubrammaniam, S -- Borgwardt, K -- Brooks, K -- Carret, C -- Carver, T J -- Cherevach, I -- Chillingworth, T -- Clark, T G -- Galinski, M R -- Hall, N -- Harper, D -- Harris, D -- Hauser, H -- Ivens, A -- Janssen, C S -- Keane, T -- Larke, N -- Lapp, S -- Marti, M -- Moule, S -- Meyer, I M -- Ormond, D -- Peters, N -- Sanders, M -- Sanders, S -- Sargeant, T J -- Simmonds, M -- Smith, F -- Squares, R -- Thurston, S -- Tivey, A R -- Walker, D -- White, B -- Zuiderwijk, E -- Churcher, C -- Quail, M A -- Cowman, A F -- Turner, C M R -- Rajandream, M A -- Kocken, C H M -- Thomas, A W -- Newbold, C I -- Barrell, B G -- Berriman, M -- 085775/Wellcome Trust/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2008 Oct 9;455(7214):799-803. doi: 10.1038/nature07306.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK. ap2@sanger.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18843368" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Antigens, CD/chemistry/genetics ; Chromosomes/genetics ; Conserved Sequence ; Genes, Protozoan/genetics ; Genome, Protozoan/*genetics ; *Genomics ; Humans ; Macaca mulatta/*parasitology ; Malaria/*parasitology ; Molecular Sequence Data ; Plasmodium knowlesi/classification/*genetics/physiology ; Protein Structure, Tertiary ; Protozoan Proteins/chemistry/genetics ; Sequence Analysis, DNA ; Telomere/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    An internal thermal sensor controlling temperature preference in Drosophila (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-06-13
    Description: Animals from flies to humans are able to distinguish subtle gradations in temperature and show strong temperature preferences. Animals move to environments of optimal temperature and some manipulate the temperature of their surroundings, as humans do using clothing and shelter. Despite the ubiquitous influence of environmental temperature on animal behaviour, the neural circuits and strategies through which animals select a preferred temperature remain largely unknown. Here we identify a small set of warmth-activated anterior cell (AC) neurons located in the Drosophila brain, the function of which is critical for preferred temperature selection. AC neuron activation occurs just above the fly's preferred temperature and depends on dTrpA1, an ion channel that functions as a molecular sensor of warmth. Flies that selectively express dTrpA1 in the AC neurons select normal temperatures, whereas flies in which dTrpA1 function is reduced or eliminated choose warmer temperatures. This internal warmth-sensing pathway promotes avoidance of slightly elevated temperatures and acts together with a distinct pathway for cold avoidance to set the fly's preferred temperature. Thus, flies select a preferred temperature by using a thermal sensing pathway tuned to trigger avoidance of temperatures that deviate even slightly from the preferred temperature. This provides a potentially general strategy for robustly selecting a narrow temperature range optimal for survival.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2730888/" 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/PMC2730888/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hamada, Fumika N -- Rosenzweig, Mark -- Kang, Kyeongjin -- Pulver, Stefan R -- Ghezzi, Alfredo -- Jegla, Timothy J -- Garrity, Paul A -- P01 NS044232/NS/NINDS NIH HHS/ -- P01 NS044232-060002/NS/NINDS NIH HHS/ -- P01 NS044232-070002/NS/NINDS NIH HHS/ -- P30 NS045713/NS/NINDS NIH HHS/ -- P30 NS045713-069006/NS/NINDS NIH HHS/ -- P30 NS045713S10/NS/NINDS NIH HHS/ -- R01 EY013874/EY/NEI NIH HHS/ -- R01 EY013874-06/EY/NEI NIH HHS/ -- R01 EY13874/EY/NEI NIH HHS/ -- R01 MH067284/MH/NIMH NIH HHS/ -- R01 MH067284-05/MH/NIMH NIH HHS/ -- RR16780/RR/NCRR NIH HHS/ -- England -- Nature. 2008 Jul 10;454(7201):217-20. doi: 10.1038/nature07001. Epub 2008 Jun 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Center for Behavioral Genomics, Volen Center for Complex Systems, Biology Department, Brandeis University MS-008, 415 South Street, Waltham, Massachusetts 02454, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18548007" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Avoidance Learning ; Body Temperature ; Choice Behavior/*physiology ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster/growth & development/*physiology ; Female ; Larva ; Molecular Sequence Data ; Neurons/metabolism ; Oocytes/metabolism ; TRPC Cation Channels/genetics/*metabolism ; *Temperature ; Xenopus laevis
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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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
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
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    Structure and function of an essential component of the outer membrane protein assembly machine (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    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
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    Alternative zippering as an on-off switch for SNARE-mediated fusion (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-01-24
    Description: Membrane fusion between vesicles and target membranes involves the zippering of a four-helix bundle generated by constituent helices derived from target- and vesicle-soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs). In neurons, the protein complexin clamps otherwise spontaneous fusion by SNARE proteins, allowing neurotransmitters and other mediators to be secreted when and where they are needed as this clamp is released. The membrane-proximal accessory helix of complexin is necessary for clamping, but its mechanism of action is unknown. Here, we present experiments using a reconstituted fusion system that suggest a simple model in which the complexin accessory helix forms an alternative four-helix bundle with the target-SNARE near the membrane, preventing the vesicle-SNARE from completing its zippering.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3736854/" 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/PMC3736854/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Giraudo, Claudio G -- Garcia-Diaz, Alejandro -- Eng, William S -- Chen, Yuhang -- Hendrickson, Wayne A -- Melia, Thomas J -- Rothman, James E -- R01 GM071458/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Jan 23;323(5913):512-6. doi: 10.1126/science.1166500.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Physiology and Cellular Biophysics, Columbia University, College of Physicians and Surgeons, 1150 Saint Nicholas Avenue, Russ Berrie Building, Room 520, New York, NY 10032, USA. claudio.giraudo@yale.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19164750" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Vesicular Transport ; Amino Acid Motifs ; Amino Acid Sequence ; HeLa Cells ; Humans ; Hydrophobic and Hydrophilic Interactions ; *Membrane Fusion ; Models, Molecular ; Molecular Sequence Data ; Mutant Proteins/chemistry/metabolism ; Mutation ; Nerve Tissue Proteins/*chemistry/genetics/*metabolism ; Protein Binding ; Protein Structure, Secondary ; Recombinant Fusion Proteins/chemistry/metabolism ; SNARE Proteins/*chemistry/*metabolism ; Vesicle-Associated Membrane Protein 2/*chemistry/*metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 6
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    The enigma of prokaryotic life in deep hypersaline anoxic basins (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-01-08
    Description: Deep hypersaline anoxic basins in the Mediterranean Sea are a legacy of dissolution of ancient subterranean salt deposits from the Miocene period. Our study revealed that these hypersaline basins are not biogeochemical dead ends, but support in situ sulfate reduction, methanogenesis, and heterotrophic activity. A wide diversity of prokaryotes was observed, including a new, abundant, deeply branching order within the Euryarchaeota. Furthermore, we demonstrated the presence of a unique, metabolically active microbial community in the Discovery basin, which is one of the most extreme terrestrial saline environments known, as it is almost saturated with MgCl2 (5 M).〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉van der Wielen, Paul W J J -- Bolhuis, Henk -- Borin, Sara -- Daffonchio, Daniele -- Corselli, Cesare -- Giuliano, Laura -- D'Auria, Giuseppe -- de Lange, Gert J -- Huebner, Andreas -- Varnavas, Sotirios P -- Thomson, John -- Tamburini, Christian -- Marty, Danielle -- McGenity, Terry J -- Timmis, Kenneth N -- BioDeep Scientific Party -- New York, N.Y. -- Science. 2005 Jan 7;307(5706):121-3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Microbial Ecology, University of Groningen, 9751 NN Haren, Netherlands. paul.van.der.wielen@kiwa.nl〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15637281" target="_blank"〉PubMed〈/a〉
    Keywords: Anaerobiosis ; Archaea/classification/isolation & purification/*physiology ; Bacteria/classification/isolation & purification ; *Bacterial Physiological Phenomena ; Biodiversity ; Cluster Analysis ; *Ecosystem ; Euryarchaeota/classification/isolation & purification/physiology ; Genes, Archaeal ; Genes, Bacterial ; Genes, rRNA ; Magnesium Chloride/analysis ; Mediterranean Sea ; Methane/metabolism ; Molecular Sequence Data ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seawater/chemistry/*microbiology ; *Sodium Chloride ; Sulfates/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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  • 7
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    The genome of the African trypanosome Trypanosoma brucei (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-07-16
    Description: African trypanosomes cause human sleeping sickness and livestock trypanosomiasis in sub-Saharan Africa. We present the sequence and analysis of the 11 megabase-sized chromosomes of Trypanosoma brucei. The 26-megabase genome contains 9068 predicted genes, including approximately 900 pseudogenes and approximately 1700 T. brucei-specific genes. Large subtelomeric arrays contain an archive of 806 variant surface glycoprotein (VSG) genes used by the parasite to evade the mammalian immune system. Most VSG genes are pseudogenes, which may be used to generate expressed mosaic genes by ectopic recombination. Comparisons of the cytoskeleton and endocytic trafficking systems with those of humans and other eukaryotic organisms reveal major differences. A comparison of metabolic pathways encoded by the genomes of T. brucei, T. cruzi, and Leishmania major reveals the least overall metabolic capability in T. brucei and the greatest in L. major. Horizontal transfer of genes of bacterial origin has contributed to some of the metabolic differences in these parasites, and a number of novel potential drug targets have been identified.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Berriman, Matthew -- Ghedin, Elodie -- Hertz-Fowler, Christiane -- Blandin, Gaelle -- Renauld, Hubert -- Bartholomeu, Daniella C -- Lennard, Nicola J -- Caler, Elisabet -- Hamlin, Nancy E -- Haas, Brian -- Bohme, Ulrike -- Hannick, Linda -- Aslett, Martin A -- Shallom, Joshua -- Marcello, Lucio -- Hou, Lihua -- Wickstead, Bill -- Alsmark, U Cecilia M -- Arrowsmith, Claire -- Atkin, Rebecca J -- Barron, Andrew J -- Bringaud, Frederic -- Brooks, Karen -- Carrington, Mark -- Cherevach, Inna -- Chillingworth, Tracey-Jane -- Churcher, Carol -- Clark, Louise N -- Corton, Craig H -- Cronin, Ann -- Davies, Rob M -- Doggett, Jonathon -- Djikeng, Appolinaire -- Feldblyum, Tamara -- Field, Mark C -- Fraser, Audrey -- Goodhead, Ian -- Hance, Zahra -- Harper, David -- Harris, Barbara R -- Hauser, Heidi -- Hostetler, Jessica -- Ivens, Al -- Jagels, Kay -- Johnson, David -- Johnson, Justin -- Jones, Kristine -- Kerhornou, Arnaud X -- Koo, Hean -- Larke, Natasha -- Landfear, Scott -- Larkin, Christopher -- Leech, Vanessa -- Line, Alexandra -- Lord, Angela -- Macleod, Annette -- Mooney, Paul J -- Moule, Sharon -- Martin, David M A -- Morgan, Gareth W -- Mungall, Karen -- Norbertczak, Halina -- Ormond, Doug -- Pai, Grace -- Peacock, Chris S -- Peterson, Jeremy -- Quail, Michael A -- Rabbinowitsch, Ester -- Rajandream, Marie-Adele -- Reitter, Chris -- Salzberg, Steven L -- Sanders, Mandy -- Schobel, Seth -- Sharp, Sarah -- Simmonds, Mark -- Simpson, Anjana J -- Tallon, Luke -- Turner, C Michael R -- Tait, Andrew -- Tivey, Adrian R -- Van Aken, Susan -- Walker, Danielle -- Wanless, David -- Wang, Shiliang -- White, Brian -- White, Owen -- Whitehead, Sally -- Woodward, John -- Wortman, Jennifer -- Adams, Mark D -- Embley, T Martin -- Gull, Keith -- Ullu, Elisabetta -- Barry, J David -- Fairlamb, Alan H -- Opperdoes, Fred -- Barrell, Barclay G -- Donelson, John E -- Hall, Neil -- Fraser, Claire M -- Melville, Sara E -- El-Sayed, Najib M -- AI43062/AI/NIAID NIH HHS/ -- R01 AI043062/AI/NIAID NIH HHS/ -- U01 AI043062/AI/NIAID NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2005 Jul 15;309(5733):416-22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK. mb4@sanger.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16020726" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acids/metabolism ; Animals ; Antigenic Variation ; Antigens, Protozoan/chemistry/genetics/immunology ; Carbohydrate Metabolism ; Chromosomes/genetics ; Cytoskeleton/chemistry/genetics/physiology ; Ergosterol/biosynthesis ; Genes, Protozoan ; *Genome, Protozoan ; Glutathione/*analogs & derivatives/metabolism ; Glycosylphosphatidylinositols/biosynthesis ; Humans ; Lipid Metabolism ; Molecular Sequence Data ; Protein Transport ; Protozoan Proteins/chemistry/*genetics/metabolism ; Pseudogenes ; Purines/metabolism ; Pyrimidines/biosynthesis ; Recombination, Genetic ; *Sequence Analysis, DNA ; Spermidine/*analogs & derivatives/metabolism ; Trypanosoma brucei brucei/chemistry/*genetics/immunology/metabolism ; Trypanosomiasis, African/parasitology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 8
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    PI(3,4,5)P3 and PI(4,5)P2 lipids target proteins with polybasic clusters to the plasma membrane (2006)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2006-11-11
    Description: Many signaling, cytoskeletal, and transport proteins have to be localized to the plasma membrane (PM) in order to carry out their function. We surveyed PM-targeting mechanisms by imaging the subcellular localization of 125 fluorescent protein-conjugated Ras, Rab, Arf, and Rho proteins. Out of 48 proteins that were PM-localized, 37 contained clusters of positively charged amino acids. To test whether these polybasic clusters bind negatively charged phosphatidylinositol 4,5-bisphosphate [PI(4,5)P2] lipids, we developed a chemical phosphatase activation method to deplete PM PI(4,5)P2. Unexpectedly, proteins with polybasic clusters dissociated from the PM only when both PI(4,5)P2 and phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P3] were depleted, arguing that both lipid second messengers jointly regulate PM targeting.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3579512/" 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/PMC3579512/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heo, Won Do -- Inoue, Takanari -- Park, Wei Sun -- Kim, Man Lyang -- Park, Byung Ouk -- Wandless, Thomas J -- Meyer, Tobias -- R01 GM030179/GM/NIGMS NIH HHS/ -- R01 GM030179-24A1/GM/NIGMS NIH HHS/ -- R01 GM030179-25/GM/NIGMS NIH HHS/ -- R01 GM063702/GM/NIGMS NIH HHS/ -- R01 MH064801/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 2006 Dec 1;314(5804):1458-61. Epub 2006 Nov 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Pharmacology, 318 Campus Drive, Clark Building, Stanford University Medical School, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17095657" target="_blank"〉PubMed〈/a〉
    Keywords: ADP-Ribosylation Factors/chemistry/metabolism ; Amino Acid Motifs ; Amino Acid Sequence ; Animals ; Cell Membrane/*metabolism ; GTP Phosphohydrolases/chemistry/*metabolism ; HeLa Cells ; Humans ; Hydrophobic and Hydrophilic Interactions ; Kinetics ; Mice ; Molecular Sequence Data ; NIH 3T3 Cells ; Phosphatidylinositol 4,5-Diphosphate/*metabolism ; Phosphatidylinositol Phosphates/*metabolism ; Second Messenger Systems ; Signal Transduction ; Static Electricity ; rab GTP-Binding Proteins/chemistry/metabolism ; ras Proteins/chemistry/metabolism ; rho GTP-Binding Proteins/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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  • 9
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    The Fusarium graminearum genome reveals a link between localized polymorphism and pathogen specialization (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-08
    Description: We sequenced and annotated the genome of the filamentous fungus Fusarium graminearum, a major pathogen of cultivated cereals. Very few repetitive sequences were detected, and the process of repeat-induced point mutation, in which duplicated sequences are subject to extensive mutation, may partially account for the reduced repeat content and apparent low number of paralogous (ancestrally duplicated) genes. A second strain of F. graminearum contained more than 10,000 single-nucleotide polymorphisms, which were frequently located near telomeres and within other discrete chromosomal segments. Many highly polymorphic regions contained sets of genes implicated in plant-fungus interactions and were unusually divergent, with higher rates of recombination. These regions of genome innovation may result from selection due to interactions of F. graminearum with its plant hosts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Cuomo, Christina A -- Guldener, Ulrich -- Xu, Jin-Rong -- Trail, Frances -- Turgeon, B Gillian -- Di Pietro, Antonio -- Walton, Jonathan D -- Ma, Li-Jun -- Baker, Scott E -- Rep, Martijn -- Adam, Gerhard -- Antoniw, John -- Baldwin, Thomas -- Calvo, Sarah -- Chang, Yueh-Long -- Decaprio, David -- Gale, Liane R -- Gnerre, Sante -- Goswami, Rubella S -- Hammond-Kosack, Kim -- Harris, Linda J -- Hilburn, Karen -- Kennell, John C -- Kroken, Scott -- Magnuson, Jon K -- Mannhaupt, Gertrud -- Mauceli, Evan -- Mewes, Hans-Werner -- Mitterbauer, Rudolf -- Muehlbauer, Gary -- Munsterkotter, Martin -- Nelson, David -- O'donnell, Kerry -- Ouellet, Therese -- Qi, Weihong -- Quesneville, Hadi -- Roncero, M Isabel G -- Seong, Kye-Yong -- Tetko, Igor V -- Urban, Martin -- Waalwijk, Cees -- Ward, Todd J -- Yao, Jiqiang -- Birren, Bruce W -- Kistler, H Corby -- U54 HG003067/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 7;317(5843):1400-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17823352" target="_blank"〉PubMed〈/a〉
    Keywords: DNA, Fungal ; Evolution, Molecular ; Fusarium/*genetics/physiology ; *Genome, Fungal ; Hordeum/microbiology ; Molecular Sequence Data ; Plant Diseases/microbiology ; Point Mutation ; *Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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    Solution structure of the integral human membrane protein VDAC-1 in detergent micelles (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-08-30
    Description: The voltage-dependent anion channel (VDAC) mediates trafficking of small molecules and ions across the eukaryotic outer mitochondrial membrane. VDAC also interacts with antiapoptotic proteins from the Bcl-2 family, and this interaction inhibits release of apoptogenic proteins from the mitochondrion. We present the nuclear magnetic resonance (NMR) solution structure of recombinant human VDAC-1 reconstituted in detergent micelles. It forms a 19-stranded beta barrel with the first and last strand parallel. The hydrophobic outside perimeter of the barrel is covered by detergent molecules in a beltlike fashion. In the presence of cholesterol, recombinant VDAC-1 can form voltage-gated channels in phospholipid bilayers similar to those of the native protein. NMR measurements revealed the binding sites of VDAC-1 for the Bcl-2 protein Bcl-x(L), for reduced beta-nicotinamide adenine dinucleotide, and for cholesterol. Bcl-x(L) interacts with the VDAC barrel laterally at strands 17 and 18.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2579273/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2579273/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hiller, Sebastian -- Garces, Robert G -- Malia, Thomas J -- Orekhov, Vladislav Y -- Colombini, Marco -- Wagner, Gerhard -- EB002026/EB/NIBIB NIH HHS/ -- GM066360/GM/NIGMS NIH HHS/ -- GM075879/GM/NIGMS NIH HHS/ -- GM47467/GM/NIGMS NIH HHS/ -- P01 GM047467/GM/NIGMS NIH HHS/ -- P01 GM047467-11/GM/NIGMS NIH HHS/ -- P01 GM047467-12/GM/NIGMS NIH HHS/ -- P01 GM047467-12S2/GM/NIGMS NIH HHS/ -- P01 GM047467-13/GM/NIGMS NIH HHS/ -- P01 GM047467-14/GM/NIGMS NIH HHS/ -- P01 GM047467-14S1/GM/NIGMS NIH HHS/ -- P01 GM047467-15/GM/NIGMS NIH HHS/ -- P01 GM047467-16/GM/NIGMS NIH HHS/ -- P01 GM047467-17/GM/NIGMS NIH HHS/ -- P41 EB002026/EB/NIBIB NIH HHS/ -- P41 EB002026-28/EB/NIBIB NIH HHS/ -- P41 EB002026-29/EB/NIBIB NIH HHS/ -- P41 EB002026-30/EB/NIBIB NIH HHS/ -- P41 EB002026-31/EB/NIBIB NIH HHS/ -- P41 EB002026-32/EB/NIBIB NIH HHS/ -- P41 EB002026-33/EB/NIBIB NIH HHS/ -- P41 GM066360/GM/NIGMS NIH HHS/ -- P41 GM066360-01/GM/NIGMS NIH HHS/ -- P41 GM066360-02/GM/NIGMS NIH HHS/ -- P41 GM066360-03/GM/NIGMS NIH HHS/ -- P41 GM066360-04/GM/NIGMS NIH HHS/ -- P41 GM066360-05/GM/NIGMS NIH HHS/ -- R01 GM075879/GM/NIGMS NIH HHS/ -- R01 GM075879-01/GM/NIGMS NIH HHS/ -- R01 GM075879-02/GM/NIGMS NIH HHS/ -- R01 GM075879-03/GM/NIGMS NIH HHS/ -- R01 GM075879-04/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2008 Aug 29;321(5893):1206-10. doi: 10.1126/science.1161302.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18755977" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Binding Sites ; Cholesterol/metabolism ; Detergents ; Dimethylamines ; Humans ; Hydrophobic and Hydrophilic Interactions ; Ion Channel Gating ; Lipid Bilayers ; Micelles ; Molecular Sequence Data ; NAD/metabolism ; Nuclear Magnetic Resonance, Biomolecular ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Recombinant Proteins/chemistry/metabolism ; Static Electricity ; Voltage-Dependent Anion Channel 1/*chemistry/*metabolism ; bcl-X Protein/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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