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  • 1
    Publication Date: 1994-06-24
    Description: Two ternary complexes of rat DNA polymerase beta (pol beta), a DNA template-primer, and dideoxycytidine triphosphate (ddCTP) have been determined at 2.9 A and 3.6 A resolution, respectively. ddCTP is the triphosphate of dideoxycytidine (ddC), a nucleoside analog that targets the reverse transcriptase of human immunodeficiency virus (HIV) and is at present used to treat AIDS. Although crystals of the two complexes belong to different space groups, the structures are similar, suggesting that the polymerase-DNA-ddCTP interactions are not affected by crystal packing forces. In the pol beta active site, the attacking 3'-OH of the elongating primer, the ddCTP phosphates, and two Mg2+ ions are all clustered around Asp190, Asp192, and Asp256. Two of these residues, Asp190 and Asp256, are present in the amino acid sequences of all polymerases so far studied and are also spatially similar in the four polymerases--the Klenow fragment of Escherichia coli DNA polymerase I, HIV-1 reverse transcriptase, T7 RNA polymerase, and rat DNA pol beta--whose crystal structures are now known. A two-metal ion mechanism is described for the nucleotidyl transfer reaction and may apply to all polymerases. In the ternary complex structures analyzed, pol beta binds to the DNA template-primer in a different manner from that recently proposed for other polymerase-DNA models.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pelletier, H -- Sawaya, M R -- Kumar, A -- Wilson, S H -- Kraut, J -- CA17374/CA/NCI NIH HHS/ -- ES06839/ES/NIEHS NIH HHS/ -- GM10928/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 1994 Jun 24;264(5167):1891-903.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, University of California, San Diego 92093-0317.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7516580" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Sequence ; Binding Sites ; Crystallization ; Crystallography, X-Ray ; DNA/chemistry/metabolism ; DNA Polymerase I/*chemistry/metabolism ; DNA Primers/*chemistry/metabolism ; DNA-Directed RNA Polymerases/chemistry/metabolism ; Deoxycytosine Nucleotides/*chemistry/metabolism ; Dideoxynucleotides ; HIV Reverse Transcriptase ; Humans ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; RNA-Directed DNA Polymerase/chemistry/metabolism ; Rats ; Recombinant Proteins ; Templates, Genetic ; Thymine Nucleotides/chemistry/metabolism ; Viral Proteins ; Zidovudine/analogs & derivatives/chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2009-06-23
    Description: Amyloids are highly organized cross-beta-sheet-rich protein or peptide aggregates that are associated with pathological conditions including Alzheimer's disease and type II diabetes. However, amyloids may also have a normal biological function, as demonstrated by fungal prions, which are involved in prion replication, and the amyloid protein Pmel17, which is involved in mammalian skin pigmentation. We found that peptide and protein hormones in secretory granules of the endocrine system are stored in an amyloid-like cross-beta-sheet-rich conformation. Thus, functional amyloids in the pituitary and other organs can contribute to normal cell and tissue physiology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2865899/" 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/PMC2865899/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Maji, Samir K -- Perrin, Marilyn H -- Sawaya, Michael R -- Jessberger, Sebastian -- Vadodaria, Krishna -- Rissman, Robert A -- Singru, Praful S -- Nilsson, K Peter R -- Simon, Rozalyn -- Schubert, David -- Eisenberg, David -- Rivier, Jean -- Sawchenko, Paul -- Vale, Wylie -- Riek, Roland -- P01 DK026741/DK/NIDDK NIH HHS/ -- P01 DK026741-29/DK/NIDDK NIH HHS/ -- P01 DK026741-30/DK/NIDDK NIH HHS/ -- New York, N.Y. -- Science. 2009 Jul 17;325(5938):328-32. doi: 10.1126/science.1173155. Epub 2009 Jun 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Physical Chemistry, Eidgenossische Technische Hochschule (ETH) Zurich, Wolfgang-Paulistrasse 10, CH-8093 Zurich, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19541956" target="_blank"〉PubMed〈/a〉
    Keywords: Adrenocorticotropic Hormone/chemistry/metabolism ; Amyloid/*chemistry/metabolism ; Animals ; Cell Survival ; Corticotropin-Releasing Hormone/chemistry/metabolism ; Heparin, Low-Molecular-Weight/chemistry ; Humans ; Hydrogen-Ion Concentration ; Mice ; Neurons/cytology/physiology ; Peptide Hormones/*chemistry/metabolism ; Pituitary Gland/*chemistry ; Pituitary Gland, Anterior/chemistry/metabolism ; Pituitary Gland, Posterior/chemistry/metabolism ; Pituitary Hormones/*chemistry/metabolism ; Protein Conformation ; Rats ; Secretory Vesicles/*chemistry/metabolism ; Sheep ; Urocortins/chemistry/metabolism ; beta-Endorphin/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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  • 3
    Publication Date: 2015-09-10
    Description: The protein alpha-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term NACore, appears to be responsible for amyloid formation and cytotoxicity of human alpha-synuclein. Here we describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure determination by synchrotron X-ray diffraction, we use micro-electron diffraction to determine the structure at atomic resolution. The 1.4 A resolution structure demonstrates that this method can determine previously unknown protein structures and here yields, to our knowledge, the highest resolution achieved by any cryo-electron microscopy method to date. The structure exhibits protofibrils built of pairs of face-to-face beta-sheets. X-ray fibre diffraction patterns show the similarity of NACore to toxic fibrils of full-length alpha-synuclein. The NACore structure, together with that of a second segment, inspires a model for most of the ordered portion of the toxic, full-length alpha-synuclein fibril, presenting opportunities for the design of inhibitors of alpha-synuclein fibrils.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rodriguez, Jose A -- Ivanova, Magdalena I -- Sawaya, Michael R -- Cascio, Duilio -- Reyes, Francis E -- Shi, Dan -- Sangwan, Smriti -- Guenther, Elizabeth L -- Johnson, Lisa M -- Zhang, Meng -- Jiang, Lin -- Arbing, Mark A -- Nannenga, Brent L -- Hattne, Johan -- Whitelegge, Julian -- Brewster, Aaron S -- Messerschmidt, Marc -- Boutet, Sebastien -- Sauter, Nicholas K -- Gonen, Tamir -- Eisenberg, David S -- 1R01-AG029430/AG/NIA NIH HHS/ -- AG016570/AG/NIA NIH HHS/ -- GM095887/GM/NIGMS NIH HHS/ -- GM102520/GM/NIGMS NIH HHS/ -- P41 GM103403/GM/NIGMS NIH HHS/ -- R01 GM095887/GM/NIGMS NIH HHS/ -- R01 GM102520/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Sep 24;525(7570):486-90. doi: 10.1038/nature15368. Epub 2015 Sep 9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry and Chemistry and Biochemistry, Box 951570, UCLA, Los Angeles, California 90095-1570, USA. ; Howard Hughes Medical Institute, Janelia Research Campus, 19700 Helix Drive, Ashburn, Virginia 20147, USA. ; Box 42, NPI-Semel Institute, 760 Westwood Plaza, UCLA, Los Angeles, California 90024, USA. ; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA. ; Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26352473" target="_blank"〉PubMed〈/a〉
    Keywords: Amyloid/chemistry ; Cryoelectron Microscopy ; Electrons ; Humans ; Lewy Bodies/chemistry ; Models, Molecular ; Nanoparticles/*chemistry/*toxicity ; Parkinson Disease ; Protein Structure, Tertiary ; Scattering, Radiation ; alpha-Synuclein/*chemistry/*toxicity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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