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  • Protein Structure, Tertiary  (222)
  • American Association for the Advancement of Science (AAAS)  (222)
  • American Meteorological Society
  • 2015-2019  (24)
  • 2010-2014  (77)
  • 2000-2004  (121)
  • 1955-1959
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  • 1
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    ACTIN-DIRECTED TOXIN. ACD toxin-produced actin oligomers poison formin-controlled actin polymerization (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-08-01
    Description: The actin cross-linking domain (ACD) is an actin-specific toxin produced by several pathogens, including life-threatening spp. of Vibrio cholerae, Vibrio vulnificus, and Aeromonas hydrophila. Actin cross-linking by ACD is thought to lead to slow cytoskeleton failure owing to a gradual sequestration of actin in the form of nonfunctional oligomers. Here, we found that ACD converted cytoplasmic actin into highly toxic oligomers that potently "poisoned" the ability of major actin assembly proteins, formins, to sustain actin polymerization. Thus, ACD can target the most abundant cellular protein by using actin oligomers as secondary toxins to efficiently subvert cellular functions of actin while functioning at very low doses.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4648357/" 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/PMC4648357/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heisler, David B -- Kudryashova, Elena -- Grinevich, Dmitry O -- Suarez, Cristian -- Winkelman, Jonathan D -- Birukov, Konstantin G -- Kotha, Sainath R -- Parinandi, Narasimham L -- Vavylonis, Dimitrios -- Kovar, David R -- Kudryashov, Dmitri S -- R01 GM079265/GM/NIGMS NIH HHS/ -- R01 GM098430/GM/NIGMS NIH HHS/ -- R01 GM114666/GM/NIGMS NIH HHS/ -- R01 HL076259/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2015 Jul 31;349(6247):535-9. doi: 10.1126/science.aab4090.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA. The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA. ; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA. kudryashov.1@osu.edu kudryashova.1@osu.edu. ; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA. ; Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA. ; Section of Pulmonary and Critical Care and Lung Injury Center, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA. ; Lipid Signaling and Lipidomics Laboratory, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Dorothy M. Davis Heart and Lung Research Institute, College of Medicine, The Ohio State University, Columbus, OH 43210, USA. ; Department of Physics, Lehigh University, Bethlehem, PA 18015, USA. ; Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, IL 60637, USA. Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA. ; Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA. The Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA. kudryashov.1@osu.edu kudryashova.1@osu.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26228148" target="_blank"〉PubMed〈/a〉
    Keywords: Actins/*metabolism ; Animals ; Antigens, Bacterial/*chemistry/genetics/*toxicity ; Bacterial Toxins/*chemistry/genetics/*toxicity ; Cell Line ; Fetal Proteins/*antagonists & inhibitors ; Intestinal Mucosa/drug effects/metabolism ; Microfilament Proteins/*antagonists & inhibitors ; Nuclear Proteins/*antagonists & inhibitors ; Polymerization/drug effects ; Protein Structure, Tertiary ; Rats
    Print ISSN: 0036-8075
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  • 2
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    Mutations in a human ROBO gene disrupt hindbrain axon pathway crossing and morphogenesis (2004)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2004-04-24
    Description: The mechanisms controlling axon guidance are of fundamental importance in understanding brain development. Growing corticospinal and somatosensory axons cross the midline in the medulla to reach their targets and thus form the basis of contralateral motor control and sensory input. The motor and sensory projections appeared uncrossed in patients with horizontal gaze palsy with progressive scoliosis (HGPPS). In patients affected with HGPPS, we identified mutations in the ROBO3 gene, which shares homology with roundabout genes important in axon guidance in developing Drosophila, zebrafish, and mouse. Like its murine homolog Rig1/Robo3, but unlike other Robo proteins, ROBO3 is required for hindbrain axon midline crossing.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618874/" 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/PMC1618874/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jen, Joanna C -- Chan, Wai-Man -- Bosley, Thomas M -- Wan, Jijun -- Carr, Janai R -- Rub, Udo -- Shattuck, David -- Salamon, Georges -- Kudo, Lili C -- Ou, Jing -- Lin, Doris D M -- Salih, Mustafa A M -- Kansu, Tulay -- Al Dhalaan, Hesham -- Al Zayed, Zayed -- MacDonald, David B -- Stigsby, Bent -- Plaitakis, Andreas -- Dretakis, Emmanuel K -- Gottlob, Irene -- Pieh, Christina -- Traboulsi, Elias I -- Wang, Qing -- Wang, Lejin -- Andrews, Caroline -- Yamada, Koki -- Demer, Joseph L -- Karim, Shaheen -- Alger, Jeffry R -- Geschwind, Daniel H -- Deller, Thomas -- Sicotte, Nancy L -- Nelson, Stanley F -- Baloh, Robert W -- Engle, Elizabeth C -- DC00162/DC/NIDCD NIH HHS/ -- DC05524/DC/NIDCD NIH HHS/ -- EY12498/EY/NEI NIH HHS/ -- EY13583/EY/NEI NIH HHS/ -- EY15298/EY/NEI NIH HHS/ -- EY15311/EY/NEI NIH HHS/ -- MH60233/MH/NIMH NIH HHS/ -- P30 HD 18655/HD/NICHD NIH HHS/ -- R01 EY008313/EY/NEI NIH HHS/ -- R01 EY008313-14/EY/NEI NIH HHS/ -- R01 HL066251/HL/NHLBI NIH HHS/ -- New York, N.Y. -- Science. 2004 Jun 4;304(5676):1509-13. Epub 2004 Apr 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurology, University of California, Los Angeles, CA 90095, USA. jjen@ucla.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15105459" target="_blank"〉PubMed〈/a〉
    Keywords: Adult ; Alternative Splicing ; Amino Acid Motifs ; Amino Acid Sequence ; Axons/*physiology ; Evoked Potentials, Motor ; Evoked Potentials, Somatosensory ; Female ; Functional Laterality ; Genetic Linkage ; Humans ; In Situ Hybridization ; Magnetic Resonance Imaging ; Male ; Medulla Oblongata/growth & development/pathology ; Microsatellite Repeats ; Molecular Sequence Data ; Morphogenesis ; Mutation ; Neural Pathways ; Ophthalmoplegia/*genetics/pathology/physiopathology ; Pedigree ; Protein Structure, Tertiary ; Receptors, Immunologic/chemistry/*genetics/*metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Rhombencephalon/*growth & development/pathology ; Scoliosis/*genetics/pathology/physiopathology ; Sequence Analysis, DNA ; Syndrome
    Print ISSN: 0036-8075
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  • 3
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    A natural product that lowers cholesterol as an antagonist ligand for FXR (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-05-04
    Description: Extracts of the resin of the guggul tree (Commiphora mukul) lower LDL (low-density lipoprotein) cholesterol levels in humans. The plant sterol guggulsterone [4,17(20)-pregnadiene-3,16-dione] is the active agent in this extract. We show that guggulsterone is a highly efficacious antagonist of the farnesoid X receptor (FXR), a nuclear hormone receptor that is activated by bile acids. Guggulsterone treatment decreases hepatic cholesterol in wild-type mice fed a high-cholesterol diet but is not effective in FXR-null mice. Thus, we propose that inhibition of FXR activation is the basis for the cholesterol-lowering activity of guggulsterone. Other natural products with specific biologic effects may modulate the activity of FXR or other relatively promiscuous nuclear hormone receptors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Urizar, Nancy L -- Liverman, Amy B -- Dodds, D'Nette T -- Silva, Frank Valentin -- Ordentlich, Peter -- Yan, Yingzhuo -- Gonzalez, Frank J -- Heyman, Richard A -- Mangelsdorf, David J -- Moore, David D -- New York, N.Y. -- Science. 2002 May 31;296(5573):1703-6. Epub 2002 May 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11988537" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Binding Sites ; Caco-2 Cells ; Carrier Proteins/genetics/metabolism ; Cells, Cultured ; Chenodeoxycholic Acid/pharmacology ; Cholesterol/*metabolism ; Cholesterol, Dietary/administration & dosage ; DNA/metabolism ; DNA-Binding Proteins/*antagonists & inhibitors/chemistry/genetics/*metabolism ; Hepatocytes/metabolism ; Histone Acetyltransferases ; Humans ; *Hydroxysteroid Dehydrogenases ; Hypolipidemic Agents/metabolism/*pharmacology ; Ligands ; Liver/metabolism ; *Membrane Glycoproteins ; Mice ; Nuclear Receptor Coactivator 1 ; Pregnenediones/metabolism/*pharmacology ; Promoter Regions, Genetic ; Protein Structure, Tertiary ; Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors/genetics/metabolism ; Receptors, Steroid/antagonists & inhibitors/metabolism ; Transcription Factors/*antagonists & inhibitors/chemistry/genetics/*metabolism ; Transcriptional Activation/drug effects ; Transfection ; Tumor Cells, Cultured
    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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    Rational HIV immunogen design to target specific germline B cell receptors (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-03-30
    Description: Vaccine development to induce broadly neutralizing antibodies (bNAbs) against HIV-1 is a global health priority. Potent VRC01-class bNAbs against the CD4 binding site of HIV gp120 have been isolated from HIV-1-infected individuals; however, such bNAbs have not been induced by vaccination. Wild-type gp120 proteins lack detectable affinity for predicted germline precursors of VRC01-class bNAbs, making them poor immunogens to prime a VRC01-class response. We employed computation-guided, in vitro screening to engineer a germline-targeting gp120 outer domain immunogen that binds to multiple VRC01-class bNAbs and germline precursors, and elucidated germline binding crystallographically. When multimerized on nanoparticles, this immunogen (eOD-GT6) activates germline and mature VRC01-class B cells. Thus, eOD-GT6 nanoparticles have promise as a vaccine prime. In principle, germline-targeting strategies could be applied to other epitopes and pathogens.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3689846/" 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/PMC3689846/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jardine, Joseph -- Julien, Jean-Philippe -- Menis, Sergey -- Ota, Takayuki -- Kalyuzhniy, Oleksandr -- McGuire, Andrew -- Sok, Devin -- Huang, Po-Ssu -- MacPherson, Skye -- Jones, Meaghan -- Nieusma, Travis -- Mathison, John -- Baker, David -- Ward, Andrew B -- Burton, Dennis R -- Stamatatos, Leonidas -- Nemazee, David -- Wilson, Ian A -- Schief, William R -- 5T32AI007606-10/AI/NIAID NIH HHS/ -- AI081625/AI/NIAID NIH HHS/ -- AI33292/AI/NIAID NIH HHS/ -- AI84817/AI/NIAID NIH HHS/ -- P01 AI094419/AI/NIAID NIH HHS/ -- P30 AI027767-24/AI/NIAID NIH HHS/ -- P41RR001209/RR/NCRR NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- R01 AI073148/AI/NIAID NIH HHS/ -- R01 AI081625/AI/NIAID NIH HHS/ -- R01 AI084817/AI/NIAID NIH HHS/ -- R37 AI033292/AI/NIAID NIH HHS/ -- T32 CA080416/CA/NCI NIH HHS/ -- T32CA080416/CA/NCI NIH HHS/ -- UM1 AI100663/AI/NIAID NIH HHS/ -- Y1-CO-1020/CO/NCI NIH HHS/ -- Y1-GM-1104/GM/NIGMS NIH HHS/ -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2013 May 10;340(6133):711-6. doi: 10.1126/science.1234150. Epub 2013 Mar 28.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23539181" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines/chemistry/genetics/*immunology ; Amino Acid Sequence ; Animals ; Antibodies, Neutralizing/immunology ; Antigens, CD4/immunology ; B-Lymphocytes/immunology ; Crystallography, X-Ray ; DNA Mutational Analysis ; Germ Cells/*immunology ; HIV Envelope Protein gp120/chemistry/genetics/*immunology ; HIV Infections/*prevention & control ; HIV-1/*immunology ; Humans ; Macaca ; Mice ; Models, Animal ; Molecular Sequence Data ; Nanoparticles ; Protein Engineering ; Protein Structure, Tertiary ; Receptors, Antigen, B-Cell/*immunology
    Print ISSN: 0036-8075
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  • 5
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    SIGNAL TRANSDUCTION. Structural basis for nucleotide exchange in heterotrimeric G proteins (2015)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2015-06-20
    Description: G protein-coupled receptors (GPCRs) relay diverse extracellular signals into cells by catalyzing nucleotide release from heterotrimeric G proteins, but the mechanism underlying this quintessential molecular signaling event has remained unclear. Here we use atomic-level simulations to elucidate the nucleotide-release mechanism. We find that the G protein alpha subunit Ras and helical domains-previously observed to separate widely upon receptor binding to expose the nucleotide-binding site-separate spontaneously and frequently even in the absence of a receptor. Domain separation is necessary but not sufficient for rapid nucleotide release. Rather, receptors catalyze nucleotide release by favoring an internal structural rearrangement of the Ras domain that weakens its nucleotide affinity. We use double electron-electron resonance spectroscopy and protein engineering to confirm predictions of our computationally determined mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dror, Ron O -- Mildorf, Thomas J -- Hilger, Daniel -- Manglik, Aashish -- Borhani, David W -- Arlow, Daniel H -- Philippsen, Ansgar -- Villanueva, Nicolas -- Yang, Zhongyu -- Lerch, Michael T -- Hubbell, Wayne L -- Kobilka, Brian K -- Sunahara, Roger K -- Shaw, David E -- P30EY00331/EY/NEI NIH HHS/ -- R01EY05216/EY/NEI NIH HHS/ -- R01GM083118/GM/NIGMS NIH HHS/ -- T32 GM008294/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2015 Jun 19;348(6241):1361-5. doi: 10.1126/science.aaa5264.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉D. E. Shaw Research, New York, NY 10036, USA. ron.dror@deshawresearch.com david.shaw@deshawresearch.com. ; D. E. Shaw Research, New York, NY 10036, USA. ; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA. ; Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI 48109, USA. ; Jules Stein Eye Institute and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA. ; D. E. Shaw Research, New York, NY 10036, USA. Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA. ron.dror@deshawresearch.com david.shaw@deshawresearch.com.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26089515" target="_blank"〉PubMed〈/a〉
    Keywords: GTP-Binding Protein alpha Subunits, Gi-Go/*chemistry ; GTP-Binding Protein alpha Subunits, Gs/*chemistry ; Guanine Nucleotide Exchange Factors/*chemistry ; Humans ; Models, Chemical ; Molecular Dynamics Simulation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Receptors, G-Protein-Coupled/*chemistry ; Signal Transduction
    Print ISSN: 0036-8075
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  • 6
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    Drug resistance. K13-propeller mutations confer artemisinin resistance in Plasmodium falciparum clinical isolates (2014)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2014-12-17
    Description: The emergence of artemisinin resistance in Southeast Asia imperils efforts to reduce the global malaria burden. We genetically modified the Plasmodium falciparum K13 locus using zinc-finger nucleases and measured ring-stage survival rates after drug exposure in vitro; these rates correlate with parasite clearance half-lives in artemisinin-treated patients. With isolates from Cambodia, where resistance first emerged, survival rates decreased from 13 to 49% to 0.3 to 2.4% after the removal of K13 mutations. Conversely, survival rates in wild-type parasites increased from 〈/=0.6% to 2 to 29% after the insertion of K13 mutations. These mutations conferred elevated resistance to recent Cambodian isolates compared with that of reference lines, suggesting a contemporary contribution of additional genetic factors. Our data provide a conclusive rationale for worldwide K13-propeller sequencing to identify and eliminate artemisinin-resistant parasites.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4349400/" 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/PMC4349400/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Straimer, Judith -- Gnadig, Nina F -- Witkowski, Benoit -- Amaratunga, Chanaki -- Duru, Valentine -- Ramadani, Arba Pramundita -- Dacheux, Melanie -- Khim, Nimol -- Zhang, Lei -- Lam, Stephen -- Gregory, Philip D -- Urnov, Fyodor D -- Mercereau-Puijalon, Odile -- Benoit-Vical, Francoise -- Fairhurst, Rick M -- Menard, Didier -- Fidock, David A -- R01 AI109023/AI/NIAID NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2015 Jan 23;347(6220):428-31. doi: 10.1126/science.1260867. Epub 2014 Dec 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY, USA. ; Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Cambodia. ; Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. ; Centre National de la Recherche Scientifique (CNRS), Laboratoire de Chimie de Coordination UPR8241, Toulouse, France. Universite de Toulouse, UPS, Institut National Polytechnique de Toulouse, Toulouse, France. ; Sangamo BioSciences, Richmond, CA, USA. ; Institut Pasteur, Parasite Molecular Immunology Unit, Paris, France. ; Department of Microbiology and Immunology, Columbia University College of Physicians and Surgeons, New York, NY, USA. Division of Infectious Diseases, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA. df2260@columbia.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25502314" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antimalarials/*pharmacology ; Artemisinins/*pharmacology ; Cambodia ; Drug Resistance/*genetics ; Genetic Loci ; Humans ; Malaria, Falciparum/drug therapy/parasitology ; Molecular Sequence Data ; Mutation ; Plasmodium falciparum/*drug effects/*genetics ; Protein Structure, Tertiary ; Protozoan Proteins/chemistry/*genetics
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  • 7
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    Two-state allosteric behavior in a single-domain signaling protein (2001)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2001-03-27
    Description: Protein actions are usually discussed in terms of static structures, but function requires motion. We find a strong correlation between phosphorylation-driven activation of the signaling protein NtrC and microsecond time-scale backbone dynamics. Using nuclear magnetic resonance relaxation, we characterized the motions of NtrC in three functional states: unphosphorylated (inactive), phosphorylated (active), and a partially active mutant. These dynamics are indicative of exchange between inactive and active conformations. Both states are populated in unphosphorylated NtrC, and phosphorylation shifts the equilibrium toward the active species. These results support a dynamic population shift between two preexisting conformations as the underlying mechanism of activation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Volkman, B F -- Lipson, D -- Wemmer, D E -- Kern, D -- GM62117/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2001 Mar 23;291(5512):2429-33.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉National Magnetic Resonance Facility at Madison (NMRFAM), Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11264542" target="_blank"〉PubMed〈/a〉
    Keywords: Allosteric Regulation ; *Bacterial Proteins ; Binding Sites ; DNA-Binding Proteins/*chemistry/genetics/*metabolism ; Models, Molecular ; Motion ; Mutation ; Nuclear Magnetic Resonance, Biomolecular ; PII Nitrogen Regulatory Proteins ; Phosphorylation ; *Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Signal Transduction ; Time ; *Trans-Activators ; *Transcription Factors
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  • 8
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    Asparagine hydroxylation of the HIF transactivation domain a hypoxic switch (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-02-02
    Description: The hypoxia-inducible factors (HIFs) 1alpha and 2alpha are key mammalian transcription factors that exhibit dramatic increases in both protein stability and intrinsic transcriptional potency during low-oxygen stress. This increased stability is due to the absence of proline hydroxylation, which in normoxia promotes binding of HIF to the von Hippel-Lindau (VHL tumor suppressor) ubiquitin ligase. We now show that hypoxic induction of the COOH-terminal transactivation domain (CAD) of HIF occurs through abrogation of hydroxylation of a conserved asparagine in the CAD. Inhibitors of Fe(II)- and 2-oxoglutarate-dependent dioxygenases prevented hydroxylation of the Asn, thus allowing the CAD to interact with the p300 transcription coactivator. Replacement of the conserved Asn by Ala resulted in constitutive p300 interaction and strong transcriptional activity. Full induction of HIF-1alpha and -2alpha, therefore, relies on the abrogation of both Pro and Asn hydroxylation, which during normoxia occur at the degradation and COOH-terminal transactivation domains, respectively.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lando, David -- Peet, Daniel J -- Whelan, Dean A -- Gorman, Jeffrey J -- Whitelaw, Murray L -- New York, N.Y. -- Science. 2002 Feb 1;295(5556):858-61.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular Biosciences (Biochemistry), Adelaide University, SA 5005, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11823643" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Amino Acid Substitution ; Animals ; Asparagine/*metabolism ; Basic Helix-Loop-Helix Transcription Factors ; Cell Hypoxia/*physiology ; Cell Line ; Humans ; Hydroxylation ; Hypoxia-Inducible Factor 1, alpha Subunit ; Mass Spectrometry ; Mice ; Mixed Function Oxygenases/metabolism ; Molecular Sequence Data ; Mutation ; Oxygen/*physiology ; Proline/metabolism ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/metabolism ; Trans-Activators/chemistry/genetics/*metabolism ; Transcription Factors/chemistry/genetics/*metabolism ; *Transcriptional Activation
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  • 9
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    Comparative genomics of the eukaryotes (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-03-24
    Description: A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae-and the proteins they are predicted to encode-was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2754258/" 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/PMC2754258/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rubin, G M -- Yandell, M D -- Wortman, J R -- Gabor Miklos, G L -- Nelson, C R -- Hariharan, I K -- Fortini, M E -- Li, P W -- Apweiler, R -- Fleischmann, W -- Cherry, J M -- Henikoff, S -- Skupski, M P -- Misra, S -- Ashburner, M -- Birney, E -- Boguski, M S -- Brody, T -- Brokstein, P -- Celniker, S E -- Chervitz, S A -- Coates, D -- Cravchik, A -- Gabrielian, A -- Galle, R F -- Gelbart, W M -- George, R A -- Goldstein, L S -- Gong, F -- Guan, P -- Harris, N L -- Hay, B A -- Hoskins, R A -- Li, J -- Li, Z -- Hynes, R O -- Jones, S J -- Kuehl, P M -- Lemaitre, B -- Littleton, J T -- Morrison, D K -- Mungall, C -- O'Farrell, P H -- Pickeral, O K -- Shue, C -- Vosshall, L B -- Zhang, J -- Zhao, Q -- Zheng, X H -- Lewis, S -- P4IHG00739/HG/NHGRI NIH HHS/ -- P50HG00750/HG/NHGRI NIH HHS/ -- R01 GM037193/GM/NIGMS NIH HHS/ -- R01 GM037193-14/GM/NIGMS NIH HHS/ -- R01 GM037193-15/GM/NIGMS NIH HHS/ -- R01 GM060988/GM/NIGMS NIH HHS/ -- R01 GM060988-01/GM/NIGMS NIH HHS/ -- R01 NS040296/NS/NINDS NIH HHS/ -- R01 NS040296-01/NS/NINDS NIH HHS/ -- New York, N.Y. -- Science. 2000 Mar 24;287(5461):2204-15.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Department of Molecular and Cell Biology, Berkeley Drosophila Genome Project, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10731134" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Apoptosis/genetics ; Biological Evolution ; Caenorhabditis elegans/chemistry/*genetics/physiology ; Cell Adhesion/genetics ; Cell Cycle/genetics ; Drosophila melanogaster/chemistry/*genetics/physiology ; Fungal Proteins/chemistry/genetics ; Genes, Duplicate ; Genetic Diseases, Inborn/genetics ; Genetics, Medical ; *Genome ; Helminth Proteins/chemistry/genetics ; Humans ; Immunity/genetics ; Insect Proteins/chemistry/genetics ; Multigene Family ; Neoplasms/genetics ; Protein Structure, Tertiary ; *Proteome ; Saccharomyces cerevisiae/chemistry/*genetics/physiology ; Signal Transduction/genetics
    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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  • 10
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    Unknown
    Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-10-05
    Description: Comparison of the genomes and proteomes of the two diptera Anopheles gambiae and Drosophila melanogaster, which diverged about 250 million years ago, reveals considerable similarities. However, numerous differences are also observed; some of these must reflect the selection and subsequent adaptation associated with different ecologies and life strategies. Almost half of the genes in both genomes are interpreted as orthologs and show an average sequence identity of about 56%, which is slightly lower than that observed between the orthologs of the pufferfish and human (diverged about 450 million years ago). This indicates that these two insects diverged considerably faster than vertebrates. Aligned sequences reveal that orthologous genes have retained only half of their intron/exon structure, indicating that intron gains or losses have occurred at a rate of about one per gene per 125 million years. Chromosomal arms exhibit significant remnants of homology between the two species, although only 34% of the genes colocalize in small "microsyntenic" clusters, and major interarm transfers as well as intra-arm shuffling of gene order are detected.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zdobnov, Evgeny M -- von Mering, Christian -- Letunic, Ivica -- Torrents, David -- Suyama, Mikita -- Copley, Richard R -- Christophides, George K -- Thomasova, Dana -- Holt, Robert A -- Subramanian, G Mani -- Mueller, Hans-Michael -- Dimopoulos, George -- Law, John H -- Wells, Michael A -- Birney, Ewan -- Charlab, Rosane -- Halpern, Aaron L -- Kokoza, Elena -- Kraft, Cheryl L -- Lai, Zhongwu -- Lewis, Suzanna -- Louis, Christos -- Barillas-Mury, Carolina -- Nusskern, Deborah -- Rubin, Gerald M -- Salzberg, Steven L -- Sutton, Granger G -- Topalis, Pantelis -- Wides, Ron -- Wincker, Patrick -- Yandell, Mark -- Collins, Frank H -- Ribeiro, Jose -- Gelbart, William M -- Kafatos, Fotis C -- Bork, Peer -- New York, N.Y. -- Science. 2002 Oct 4;298(5591):149-59.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12364792" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anopheles/chemistry/*genetics/physiology ; Biological Evolution ; Chromosome Inversion ; Chromosomes/genetics ; Cluster Analysis ; Dosage Compensation, Genetic ; Drosophila Proteins/chemistry/genetics/physiology ; Drosophila melanogaster/chemistry/*genetics/physiology ; Exons ; Gene Order ; Genes, Insect ; *Genome ; Insect Proteins/chemistry/genetics/physiology ; Introns ; Physical Chromosome Mapping ; Protein Structure, Tertiary ; *Proteome ; Pseudogenes ; Sequence Homology, Nucleic Acid ; Species Specificity ; Synteny
    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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